feat: updated version of pretext workflow developed by Delphine that takes HiFi and HiC as input. by Smeds · Pull Request #584 · galaxyproject/iwc

Smeds · 2024-10-28T14:02:10Z

updated version of pretext workflow developed by Delphine that takes HiFi and HiC as input.

…takes HiFi and HiC as input.

mvdbeek · 2024-10-30T15:18:04Z

Nice! Can you take a look at https://github.com/galaxyproject/iwc/blob/main/workflows/README.md#adding-workflows ?

Smeds · 2024-10-30T15:31:02Z

Nice! Can you take a look at https://github.com/galaxyproject/iwc/blob/main/workflows/README.md#adding-workflows ?

Thanks! I will read through the readme and update the workflow.

... and modify the replacement expressions so that users don't have to add the &. to the suffixes

… go around the fasta implicit conversion problem

Delphine-L · 2024-11-14T19:02:09Z

Need to solve galaxyproject/galaxy#19143 as soon as possible to settle on a way to deal with compressed haplotypes inputs

Delphine-L · 2024-11-26T03:38:00Z

I am not sure why the tests are not running. Could someone take a look ?

workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga

mvdbeek · 2024-11-26T08:52:55Z

I assume that's the reason ?

workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation-tests.yml

workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga

workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation-tests.yml

workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga

workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml

github-actions · 2024-12-16T20:50:38Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	0
Passed	0
Error	0
Failure	0
Skipped	0

…r testing

github-actions · 2025-02-14T02:51:09Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ hi-c-map-for-assembly-manual-curation.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '49' (Haplotype 2) is not optional and no input provided.","err_code":0}

Delphine-L · 2025-02-14T15:38:05Z

@Smeds @mvdbeek I'd be grateful for feedback on the latest version of the workflow.

I modified the workflow to :

use bwameme2 on paired collection instead of the filter and merge tool
take either 1 or 2 haplotypes
generate pretext maps with coverage and gaps even if telomeres track is empty (with all 3 tracks if not). I am not sure how often it could happen that no telomeres are detected, but it's there just in case.

Tests are :

one haplotype with telomeres found
one haplotype without telomeres found

I am not testing for 2 haplotypes right now because it takes too much memory for the CI to run, I am working on using smaller scaffolds to test it.

...ly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga

…-curation/hi-c-map-for-assembly-manual-curation.ga Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

github-actions · 2025-03-27T16:57:37Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	2
Passed	2
Error	0
Failure	0
Skipped	0

Passed Tests

✅ hi-c-map-for-assembly-manual-curation.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Haplotype 1:
- step_state: scheduled
Step 2: Will you use a second haplotype?:
- step_state: scheduled

Step 11: Hap2 not provided:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 3, "input_param": false, "mappings": [{"__index__": 0, "from": false, "to": "true"}, {"__index__": 1, "from": true, "to": "false"}], "type": "boolean"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "false", "on_unmapped": "default"}`

Step 12: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Hap1:
- step_state: scheduled
Step 2: Hap2:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa90b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 10, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 2, "src": "hda"}]}}]}}`

Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa90b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 12, "src": "hda"}]}}]`

Step 3: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 4: Hap1 suffix:
- step_state: scheduled
Step 5: Hap2 suffix:
- step_state: scheduled

Step 6: Expression for hap1 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa90b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 7: Expression for hap2 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa90b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H2", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 8: add hap1 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa90b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null}]`

Step 9: add hap2 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa90b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null}]`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa90b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 9, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 1, "src": "hda"}]}}]}}`

Step 13: concatenate HiFi:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpjw6cynca/files/f/a/3/dataset_fa361fb2-928f-4ed7-b3ce-3e94e0a2fc19.dat' >> '/tmp/tmpjw6cynca/job_working_directory/000/14/outputs/dataset_55626df1-c303-448c-a660-03c17d08c884.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[]`

Step 14: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Hap1:
- step_state: scheduled
Step 2: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 3: Hap1 suffix:
- step_state: scheduled

Step 4: Expression for hap1 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfaa0b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 5: add hap1 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed -r --sandbox -e 's/>.+$/&.H1/g' '/tmp/tmpjw6cynca/files/b/b/d/dataset_bbd8ca79-5158-4561-9ce2-b97edd1d5ee9.dat' > '/tmp/tmpjw6cynca/job_working_directory/000/16/outputs/dataset_45ad0f19-a975-4dd9-8a9c-399b876a7110.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfaa0b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": "&.H1"}]`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfaa0b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 16, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 1, "src": "hda"}]}}]}}`

Step 15: Pick Assembly:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 13, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 17, "src": "hda"}]}}]}}`

Step 16: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Reference:
- step_state: scheduled
Step 2: Hi-C reads:
- step_state: scheduled
Step 3: Do you want to trim the Hi-C data?:
- step_state: scheduled

Step 4: Trim Hi-C reads 2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpjw6cynca/files/3/a/a/dataset_3aab135c-81d0-452a-9b2c-d51e82ff9523.dat' 'Hi-C reads_1.fq.gz' && ln -f -s '/tmp/tmpjw6cynca/files/4/b/3/dataset_4b3834d9-9d1e-4668-92f7-8e961459e7ba.dat' 'Hi-C reads_2.fq.gz' &&  cutadapt  -j=${GALAXY_SLOTS:-4}     --error-rate=0.1 --times=1 --overlap=3    --action=trim   --cut=5 -U 5       --minimum-length=1      -o 'out1.fq.gz' -p 'out2.fq.gz'  'Hi-C reads_1.fq.gz' 'Hi-C reads_2.fq.gz'  > report.txt

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfab0b2811f0aeed000d3a3012a8"`
adapter_options	`{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"}`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}`
library	`{"__current_case__": 2, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired_collection"}`
other_trimming_options	`{"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}`
output_selector	`["report"]`
read_mod_options	`{"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfab0b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 7, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 2, "src": "dce"}]}}]}}`

Job 2:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfab0b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 8, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 3, "src": "dce"}]}}]}}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpjw6cynca/files/4/5/a/dataset_45ad0f19-a975-4dd9-8a9c-399b876a7110.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1   -k '19' -w '100' -d '100' -r '1.5' -y '20' -c '500' -D '0.5' -W '0' -m '50' -S -P    -T '20' -h '5' -a                      'localref.fa' '/tmp/tmpjw6cynca/files/9/9/8/dataset_9982f7a6-75ce-4729-a553-84eef307e54f.dat' '/tmp/tmpjw6cynca/files/3/0/8/dataset_308fc953-fa3c-4aa2-8158-585160c45907.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpjw6cynca/job_working_directory/000/22/outputs/dataset_201e0aaa-48a3-4dcb-9eec-6e19e90917f7.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.62 sec
* Entering FMI_search
init ticks = 10203051845
ref seq len = 279307354
binary seq ticks = 5180157794
build suffix-array ticks = 91861858347
pos: 34913420, ref_seq_len__: 34913419
build fm-index ticks = 21767177838
Total time taken: 53.4820
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 279307355
* sentinel-index: 13446364
* Count:
0,	1
1,	84204314
2,	139653678
3,	195103042
4,	279307355

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 279307354 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 139653677, n: 68494
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (1649, 4140, 6027)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 14783)
[0000][PE] mean and std.dev: (4063.15, 2569.67)
[0000][PE] low and high boundaries for proper pairs: (1, 19161)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (157, 248, 382)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 832)
[0000][PE] mean and std.dev: (254.60, 148.66)
[0000][PE] low and high boundaries for proper pairs: (1, 1057)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (2814, 4404, 5708)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 11496)
[0000][PE] mean and std.dev: (4321.60, 2279.57)
[0000][PE] low and high boundaries for proper pairs: (1, 14390)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (1378, 2846, 5532)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 13840)
[0000][PE] mean and std.dev: (3534.90, 2567.86)
[0000][PE] low and high boundaries for proper pairs: (1, 17994)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 68494 reads in 33.921 CPU sec, 34.042 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 139653677, n: 68494
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (1352, 2928, 5414)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 13538)
[0000][PE] mean and std.dev: (3677.61, 2704.12)
[0000][PE] low and high boundaries for proper pairs: (1, 17600)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (155, 240, 368)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 794)
[0000][PE] mean and std.dev: (241.09, 138.59)
[0000][PE] low and high boundaries for proper pairs: (1, 1007)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (2050, 3954, 6826)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 16378)
[0000][PE] mean and std.dev: (4268.57, 2763.35)
[0000][PE] low and high boundaries for proper pairs: (1, 21154)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (1927, 3814, 7217)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 17797)
[0000][PE] mean and std.dev: (4449.25, 2980.39)
[0000][PE] low and high boundaries for proper pairs: (1, 23087)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 68494 reads in 32.958 CPU sec, 33.871 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 139653677, n: 68494
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (1701, 3918, 5911)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 14331)
[0000][PE] mean and std.dev: (4026.81, 2594.52)
[0000][PE] low and high boundaries for proper pairs: (1, 18541)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (154, 239, 432)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 988)
[0000][PE] mean and std.dev: (258.53, 170.79)
[0000][PE] low and high boundaries for proper pairs: (1, 1266)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (1694, 2863, 6136)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 15020)
[0000][PE] mean and std.dev: (3923.51, 2842.81)
[0000][PE] low and high boundaries for proper pairs: (1, 19462)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (2159, 4591, 5807)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 13103)
[0000][PE] mean and std.dev: (4308.35, 2518.58)
[0000][PE] low and high boundaries for proper pairs: (1, 16751)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 68494 reads in 32.799 CPU sec, 33.724 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] 2. Calling kt_for - worker_aln
[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] Inferring insert size distribution of PE reads from data, l_pac: 139653677, n: 68494
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (1288, 3079, 5247)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 13165)
[0000][PE] mean and std.dev: (3554.44, 2757.92)
[0000][PE] low and high boundaries for proper pairs: (1, 17124)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (164, 272, 454)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 1034)
[0000][PE] mean and std.dev: (283.81, 181.48)
[0000][PE] low and high boundaries for proper pairs: (1, 1324)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (1107, 3976, 6440)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 17106)
[0000][PE] mean and std.dev: (3918.84, 2949.26)
[0000][PE] low and high boundaries for proper pairs: (1, 22439)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (1780, 4065, 6647)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 16381)
[0000][PE] mean and std.dev: (4110.26, 2635.19)
[0000][PE] low and high boundaries for proper pairs: (1, 21248)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 68494 reads in 32.706 CPU sec, 40.735 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3899368, nseq: 26708
	[0000][ M::kt_pipeline] read 26708 sequences (3899368 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 139653677, n: 68494
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (1322, 3322, 5913)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 15095)
[0000][PE] mean and std.dev: (3738.54, 2615.93)
[0000][PE] low and high boundaries for proper pairs: (1, 19686)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (159, 244, 399)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 879)
[0000][PE] mean and std.dev: (247.93, 143.14)
[0000][PE] low and high boundaries for proper pairs: (1, 1119)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (1392, 2569, 5634)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 14118)
[0000][PE] mean and std.dev: (3364.92, 2668.75)
[0000][PE] low and high boundaries for proper pairs: (1, 18360)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (1915, 3629, 5977)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 14101)
[0000][PE] mean and std.dev: (4139.37, 2620.32)
[0000][PE] low and high boundaries for proper pairs: (1, 18163)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 68494 reads in 29.939 CPU sec, 30.803 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 139653677, n: 26708
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (1905, 3648, 6371)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 15303)
[0000][PE] mean and std.dev: (3698.70, 2635.91)
[0000][PE] low and high boundaries for proper pairs: (1, 19769)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (154, 254, 370)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 802)
[0000][PE] mean and std.dev: (249.25, 145.76)
[0000][PE] low and high boundaries for proper pairs: (1, 1018)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (1977, 3673, 6050)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 14196)
[0000][PE] mean and std.dev: (4176.14, 2655.14)
[0000][PE] low and high boundaries for proper pairs: (1, 18269)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (1826, 3080, 5221)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 12011)
[0000][PE] mean and std.dev: (3522.50, 2457.06)
[0000][PE] low and high boundaries for proper pairs: (1, 15406)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 26708 reads in 11.809 CPU sec, 12.556 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.580347 MHz
Runtime profile:

	Time taken for main_mem function: 186.54 sec

	IO times (sec) :
	Reading IO time (reads) avg: 1.58, (1.58, 1.58)
	Writing IO time (SAM) avg: 25.10, (25.10, 25.10)
	Reading IO time (Reference Genome) avg: 0.05, (0.05, 0.05)
	Index read time avg: 0.25, (0.25, 0.25)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 186.24
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 185.72, (185.72, 185.72)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 94.55, (94.55, 94.55)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 91.14, (91.14, 91.14)
		SMEM compute avg: 36.54, (36.54, 36.54)
		SAL compute avg: 8.36, (8.36, 8.36)
				MEM_SA avg: 4.24, (4.24, 4.24)

		BSW time, avg: 36.81, (36.81, 36.81)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64
[bam_sort_core] merging from 1 files and 1 in-memory blocks...

Standard Output:

ref_seq_len = 279307354
count = 0, 84204313, 139653677, 195103041, 279307354
BWT[13446364] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 4364177

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfab0b2811f0aeed000d3a3012a8"`
analysis_type	{"__current_case__": 4, "algorithmic_options": {"D": "0.5", "P": true, "S": true, "W": "0", "__current_case__": 0, "algorithmic_options_selector": "set", "c": "500", "d": "100", "e": false, "k": "19", "m": "50", "r": "1.5", "w": "100", "y": "20"}, "analysis_type_selector": "full", "io_options": {"C": false, "K": null, "M": false, "T": "20", "V": false, "Y": false, "__current_case__": 0, "a": true, "five": false, "h": "5", "io_options_selector": "set", "q": false}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 9, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": null}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 18, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

_JAVA_OPTIONS=${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=${TMPDIR:-${_GALAXY_JOB_TMPDIR}}"} && export _JAVA_OPTIONS &&  picard MergeSamFiles  --INPUT '/tmp/tmpjw6cynca/files/2/0/1/dataset_201e0aaa-48a3-4dcb-9eec-6e19e90917f7.dat'  --OUTPUT '/tmp/tmpjw6cynca/job_working_directory/000/23/outputs/dataset_f7147647-0ee9-4451-9b72-f48958de3a2d.dat' --MERGE_SEQUENCE_DICTIONARIES 'false'  --ASSUME_SORTED 'true'  --USE_THREADING true --SORT_ORDER coordinate --VALIDATION_STRINGENCY 'LENIENT' --QUIET true --VERBOSITY ERROR

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m -Djava.io.tmpdir=/tmp/tmpjw6cynca/tmp
Mar 27, 2025 4:36:45 PM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfab0b2811f0aeed000d3a3012a8"`
assume_sorted	`true`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
merge_sequence_dictionaries	`false`
validation_stringency	`"LENIENT"`

Step 17: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpjw6cynca/files/4/5/a/dataset_45ad0f19-a975-4dd9-8a9c-399b876a7110.dat' --out-coord g   --tabular > '/tmp/tmpjw6cynca/job_working_directory/000/24/outputs/dataset_3e729f81-0bc8-412f-9c25-eb5a0a70eaef.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 1, "out_coord": "g", "selector": "coordinates"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

seqtk telo -m 'CCCTAA' -p '1' -d '2000' -s '300'  '/tmp/tmpjw6cynca/files/4/5/a/dataset_45ad0f19-a975-4dd9-8a9c-399b876a7110.dat' > '/tmp/tmpjw6cynca/job_working_directory/000/25/outputs/dataset_af1611cf-13ed-421f-aae1-dc003e14c3a8.dat'

Exit Code:

```
0
```

Standard Error:

```
11012	139653677
```

Traceback:

Job Parameters:

Job parameter	Parameter value
P	`false`
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
d	`"2000"`
dbkey	`"?"`
m	`"CCCTAA"`
p	`"1"`
s	`"300"`

Step 19: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpjw6cynca/files/4/5/a/dataset_45ad0f19-a975-4dd9-8a9c-399b876a7110.dat' reference.fa && minimap2 -x map-hifi    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpjw6cynca/files/5/5/6/dataset_55626df1-c303-448c-a660-03c17d08c884.dat' -a | samtools view --no-PG -hT reference.fa | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O BAM -o '/tmp/tmpjw6cynca/job_working_directory/000/26/outputs/dataset_c224f6b3-3caf-4c02-ae03-47a2efbb6173.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::4.467*0.78] collected minimizers
[M::mm_idx_gen::5.764*0.81] sorted minimizers
[M::main::5.764*0.81] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::5.894*0.81] mid_occ = 131
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 1
[M::mm_idx_stat::5.992*0.82] distinct minimizers: 11315845 (97.08% are singletons); average occurrences: 1.241; average spacing: 9.941; total length: 139653677
[M::worker_pipeline::148.131*0.98] mapped 5426 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x map-hifi --q-occ-frac 0.01 -t 1 -a reference.fa /tmp/tmpjw6cynca/files/5/5/6/dataset_55626df1-c303-448c-a660-03c17d08c884.dat
[M::main] Real time: 148.153 sec; CPU: 144.794 sec; Peak RSS: 1.376 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
alignment_options	`{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "map-hifi", "fastq_input1": {"values": [{"id": 14, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "BAM"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 18, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

samtools view -h '/tmp/tmpjw6cynca/files/f/7/1/dataset_f7147647-0ee9-4451-9b72-f48958de3a2d.dat' | PretextMap --sortby length --sortorder descend --mapq 0 -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextMap status] :: Mapping to 1 sequences, sorted by length, descending. Filtering by minimum mapping quality 0

                                                                                
[PretextMap status] :: 10.0 k reads processed, 3  read-pairs mapped
                                                                                
[PretextMap status] :: 20.0 k reads processed, 206  read-pairs mapped
                                                                                
[PretextMap status] :: 30.0 k reads processed, 337  read-pairs mapped
                                                                                
[PretextMap status] :: 40.0 k reads processed, 455  read-pairs mapped
                                                                                
[PretextMap status] :: 50.0 k reads processed, 537  read-pairs mapped
                                                                                
[PretextMap status] :: 60.0 k reads processed, 605  read-pairs mapped
                                                                                
[PretextMap status] :: 70.0 k reads processed, 681  read-pairs mapped
                                                                                
[PretextMap status] :: 80.0 k reads processed, 747  read-pairs mapped
                                                                                
[PretextMap status] :: 90.0 k reads processed, 815  read-pairs mapped
                                                                                
[PretextMap status] :: 100.0 k reads processed, 942  read-pairs mapped
                                                                                
[PretextMap status] :: 110.0 k reads processed, 1.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 120.0 k reads processed, 1.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 130.0 k reads processed, 1.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 140.0 k reads processed, 1.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 150.0 k reads processed, 1.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 160.0 k reads processed, 1.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 170.0 k reads processed, 1.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 180.0 k reads processed, 1.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 190.0 k reads processed, 2.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 200.0 k reads processed, 2.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 210.0 k reads processed, 2.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 220.0 k reads processed, 2.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 230.0 k reads processed, 2.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 240.0 k reads processed, 2.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 250.0 k reads processed, 2.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 260.0 k reads processed, 2.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 270.0 k reads processed, 3.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 280.0 k reads processed, 3.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 290.0 k reads processed, 3.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 300.0 k reads processed, 3.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 310.0 k reads processed, 3.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 320.0 k reads processed, 3.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 330.0 k reads processed, 3.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 340.0 k reads processed, 3.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 350.0 k reads processed, 3.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 360.0 k reads processed, 3.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 370.0 k reads processed, 4.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 380.0 k reads processed, 4.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 390.0 k reads processed, 4.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 400.0 k reads processed, 4.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 410.0 k reads processed, 4.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 420.0 k reads processed, 4.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 430.0 k reads processed, 4.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 440.0 k reads processed, 4.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 450.0 k reads processed, 4.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 460.0 k reads processed, 4.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 470.0 k reads processed, 5.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 480.0 k reads processed, 5.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 490.0 k reads processed, 5.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 500.0 k reads processed, 5.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 510.0 k reads processed, 5.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 520.0 k reads processed, 5.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 530.0 k reads processed, 5.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 540.0 k reads processed, 5.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 550.0 k reads processed, 5.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 560.0 k reads processed, 5.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 570.0 k reads processed, 5.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 580.0 k reads processed, 6.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 590.0 k reads processed, 6.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 600.0 k reads processed, 6.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 610.0 k reads processed, 6.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 620.0 k reads processed, 6.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 630.0 k reads processed, 6.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 640.0 k reads processed, 6.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 650.0 k reads processed, 6.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 660.0 k reads processed, 6.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 670.0 k reads processed, 7.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 680.0 k reads processed, 7.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 690.0 k reads processed, 7.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 700.0 k reads processed, 7.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 710.0 k reads processed, 7.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 720.0 k reads processed, 7.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 730.0 k reads processed, 7.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 740.0 k reads processed, 7.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 750.0 k reads processed, 7.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 760.0 k reads processed, 8.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 770.0 k reads processed, 8.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 780.0 k reads processed, 8.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 790.0 k reads processed, 8.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 800.0 k reads processed, 8.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 810.0 k reads processed, 8.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 820.0 k reads processed, 8.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 830.0 k reads processed, 8.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 840.0 k reads processed, 8.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 850.0 k reads processed, 8.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 860.0 k reads processed, 9.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 870.0 k reads processed, 9.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 880.0 k reads processed, 9.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 890.0 k reads processed, 9.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 900.0 k reads processed, 9.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 910.0 k reads processed, 9.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 920.0 k reads processed, 9.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 930.0 k reads processed, 9.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 940.0 k reads processed, 10.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 950.0 k reads processed, 10.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 960.0 k reads processed, 10.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 970.0 k reads processed, 10.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 980.0 k reads processed, 10.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 990.0 k reads processed, 10.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 1.0 M reads processed, 10.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 1.0 M reads processed, 10.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 1.0 M reads processed, 10.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 1.0 M reads processed, 10.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 1.0 M reads processed, 11.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 1.1 M reads processed, 11.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 1.1 M reads processed, 11.3 k read-pairs mapped
                                                                     
..
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[PretextMap status] :: 528/528 (100.00%) texture blocks written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`"0"`
sorting	`{"__current_case__": 1, "sortby": "length", "sortorder": "descend"}`

Step 3: Haplotype 2:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int  --file '/tmp/tmpjw6cynca/job_working_directory/000/28/configs/tmpzrpb6lx_' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpjw6cynca/files/3/e/7/dataset_3e729f81-0bc8-412f-9c25-eb5a0a70eaef.dat' '/tmp/tmpjw6cynca/job_working_directory/000/28/outputs/dataset_f00fd1b1-1133-4406-8967-88aa20e646f6.dat'

Exit Code:

```
0
```

Standard Output:

abs(int(c3)-int(c2))
Computing 1 new columns with instructions ['abs(int(c3)-int(c2));;']
Computed new column values for 100.00% of 4 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "abs(int(c3)-int(c2))"}], "header_lines_select": "no"}`

Step 22: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpjw6cynca/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpjw6cynca/files/a/f/1/dataset_af1611cf-13ed-421f-aae1-dc003e14c3a8.dat' 'c1,c2,c3' T '/tmp/tmpjw6cynca/job_working_directory/000/29/outputs/dataset_21c2db6c-ac4d-47c2-bb57-5add1aef8676.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1,c2,c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpjw6cynca/files/c/2/2/dataset_c224f6b3-3caf-4c02-ae03-47a2efbb6173.dat' one.bam && ln -s '/tmp/tmpjw6cynca/files/_metadata_files/0/b/c/metadata_0bcfa329-5226-4934-901c-ccca1b539490.dat' one.bam.bai &&  bamCoverage --numberOfProcessors "${GALAXY_SLOTS:-4}"  --bam one.bam --outFileName '/tmp/tmpjw6cynca/job_working_directory/000/30/outputs/dataset_78dcf67b-5870-4d0f-a2b7-1f069f4ffac2.dat' --outFileFormat 'bigwig'  --binSize 100

Exit Code:

```
0
```

Standard Error:

bamFilesList: ['one.bam']
binLength: 100
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 100
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
advancedOpt	`{"__current_case__": 0, "showAdvancedOpt": "no"}`
binSize	`"100"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exactScaling	`false`
outFileFormat	`"bigwig"`
region	`""`
scaling	`{"__current_case__": 3, "type": "no"}`

Step 24: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int  --file '/tmp/tmpjw6cynca/job_working_directory/000/31/configs/tmpgm6v07de' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpjw6cynca/files/2/1/c/dataset_21c2db6c-ac4d-47c2-bb57-5add1aef8676.dat' '/tmp/tmpjw6cynca/job_working_directory/000/31/outputs/dataset_a5724c45-94fc-4349-8fd5-b721397772b7.dat'

Exit Code:

```
0
```

Standard Output:

abs(int(c3)-int(c2))
Computing 1 new columns with instructions ['abs(int(c3)-int(c2));;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "abs(int(c3)-int(c2))"}], "header_lines_select": "no"}`

Step 25: Add Coverage Track:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmpjw6cynca/files/a/3/4/dataset_a3452744-f28b-4c9d-8269-4d586b345456.dat' input.pretext && ln -s '/tmp/tmpjw6cynca/files/7/8/d/dataset_78dcf67b-5870-4d0f-a2b7-1f069f4ffac2.dat' input.bigwig && bigWigToBedGraph input.bigwig /dev/stdout | PretextGraph -i input.pretext -n 'coverage' -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextGraph status] :: Release mode, number of thread: 4

[PretextGraph status] :: Pretext file: input.pretext
[PretextGraph status] :: Graph name: 'coverage'
[PretextGraph status] :: The extension of the graph name is default, set the data_type into 0 (default).
[PretextGraph status] :: Pretext file: output.pretext
[PretextGraph status] :: Reading file...
[PretextGraph status] :: File read

                                                                                
[PretextGraph status] :: 16.4 k bedgraph lines read
[PretextGraph status] :: Transfer f32 to s32...
[PretextGraph status] :: Saving graph...
[PretextGraph status] :: Done

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
name	`"coverage"`

Step 26: Test if telomere track is empty:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bedgraph"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 27: False if telomere track is empty:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "scaffold_10.H1\t0\t11012\t11012", "mappings": [{"__index__": 0, "from": "", "to": "false"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "true", "on_unmapped": "default"}`

Step 28: Add telomere track:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmpjw6cynca/files/b/9/2/dataset_b92d64c6-4413-4ff4-b384-2cbc6ccfa3f5.dat' input.pretext && cat '/tmp/tmpjw6cynca/files/a/5/7/dataset_a5724c45-94fc-4349-8fd5-b721397772b7.dat' | PretextGraph -i input.pretext -n 'telomeres_gap_format' -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextGraph status] :: Release mode, number of thread: 4

[PretextGraph status] :: Pretext file: input.pretext
[PretextGraph status] :: Graph name: 'telomeres_gap_format'
[PretextGraph status] :: The extension of the graph name is gap, set the data_type to 2 (gap).
[PretextGraph status] :: Pretext file: output.pretext
[PretextGraph status] :: Reading file...
[PretextGraph status] :: File read

[PretextGraph status] :: Transfer f32 to s32...
[PretextGraph status] :: Saving graph...
[PretextGraph status] :: Done

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
name	`"telomeres_gap_format"`

Step 29: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 37, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 34, "src": "hda"}]}}]}}`

Step 30: Add gaps track:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmpjw6cynca/files/5/a/9/dataset_5a9fa82f-ee8a-4417-9649-074eb90ae3ac.dat' input.pretext && cat '/tmp/tmpjw6cynca/files/f/0/0/dataset_f00fd1b1-1133-4406-8967-88aa20e646f6.dat' | PretextGraph -i input.pretext -n 'gaps' -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextGraph status] :: Release mode, number of thread: 4

[PretextGraph status] :: Pretext file: input.pretext
[PretextGraph status] :: Graph name: 'gaps'
[PretextGraph status] :: The extension of the graph name is gap, set the data_type to 2 (gap).
[PretextGraph status] :: Pretext file: output.pretext
[PretextGraph status] :: Reading file...
[PretextGraph status] :: File read

[PretextGraph status] :: Transfer f32 to s32...
[PretextGraph status] :: Saving graph...
[PretextGraph status] :: Done

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
name	`"gaps"`

Step 4: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

PretextSnapshot -m /tmp/tmpjw6cynca/files/a/3/0/dataset_a30298b0-a876-49c9-a1a3-27625a6707d9.dat -f png -r 2000 -c 5 --sequences '=full' --minTexels 64 --gridSize 1 --gridColour black '' -o output --prefix pretext_snapshot

Exit Code:

```
0
```

Standard Output:

[PretextSnapshot status] :: Input map: '/tmp/tmpjw6cynca/files/a/3/0/dataset_a30298b0-a876-49c9-a1a3-27625a6707d9.dat'
[PretextSnapshot status] :: Output format: png
[PretextSnapshot status] :: Output resolution: 2000 pixels
[PretextSnapshot status] :: Colour map: Three Wave Blue-Green-Yellow
[PretextSnapshot status] :: Minimum texels per image: 64
[PretextSnapshot status] :: Grid size: 1 pixel
[PretextSnapshot status] :: Grid colour: 000000ff
[PretextSnapshot status] :: Output path: 'output/pretext_snapshot'
[PretextSnapshot status] :: Indexing file...
[PretextSnapshot status] :: File indexed
[PretextSnapshot status] :: 'output/pretext_snapshotFullMap.png' written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 0, "gridcolor": "black", "gridsize": "1", "showGrid": "yes"}`
mintexels	`"64"`
resolution	`"2000"`
sequencenames	`false`
sequences	`"=full"`

Step 32: __EXTRACT_DATASET__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"aafebfa80b2811f0aeed000d3a3012a8"`
input	`{"values": [{"id": 7, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 5: First Haplotype suffix:
- step_state: scheduled
Step 6: Second Haplotype suffix:
- step_state: scheduled
Step 7: Hi-C reads:
- step_state: scheduled
Step 8: Do you want to trim the Hi-C data?:
- step_state: scheduled
Step 9: Telomere repeat to suit species:
- step_state: scheduled
Step 10: PacBio reads:
- step_state: scheduled

Other invocation details
- history_id
  - a807273f93b894f8
- history_state
  - ok
- invocation_id
  - a807273f93b894f8
- invocation_state
  - scheduled
- workflow_id
  - 6939a158f632cb4b

✅ hi-c-map-for-assembly-manual-curation.ga_1

Workflow invocation details

Invocation Messages

Steps

Step 1: Haplotype 1:
- step_state: scheduled
Step 2: Will you use a second haplotype?:
- step_state: scheduled

Step 11: Hap2 not provided:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 3, "input_param": false, "mappings": [{"__index__": 0, "from": false, "to": "true"}, {"__index__": 1, "from": true, "to": "false"}], "type": "boolean"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "false", "on_unmapped": "default"}`

Step 12: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Hap1:
- step_state: scheduled
Step 2: Hap2:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dd0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 51, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 43, "src": "hda"}]}}]}}`

Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dd0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 53, "src": "hda"}]}}]`

Step 3: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 4: Hap1 suffix:
- step_state: scheduled
Step 5: Hap2 suffix:
- step_state: scheduled

Step 6: Expression for hap1 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dd0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 7: Expression for hap2 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dd0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H2", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 8: add hap1 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dd0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null}]`

Step 9: add hap2 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dd0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null}]`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dd0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 50, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 42, "src": "hda"}]}}]}}`

Step 13: concatenate HiFi:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpjw6cynca/files/d/e/b/dataset_debe1cf0-9700-4541-88e7-cb4a46ecf254.dat' >> '/tmp/tmpjw6cynca/job_working_directory/000/53/outputs/dataset_56452c9a-629e-4d6e-9d61-6e2d04e5eebf.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[]`

Step 14: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Hap1:
- step_state: scheduled
Step 2: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 3: Hap1 suffix:
- step_state: scheduled

Step 4: Expression for hap1 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7de0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 5: add hap1 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed -r --sandbox -e 's/>.+$/&.H1/g' '/tmp/tmpjw6cynca/files/e/4/2/dataset_e42d62a1-2ebd-4547-ba8d-52e18bb7e813.dat' > '/tmp/tmpjw6cynca/job_working_directory/000/55/outputs/dataset_2a924c18-ec8a-47b0-a8de-8c8fa1d2c560.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7de0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": "&.H1"}]`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7de0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 57, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 42, "src": "hda"}]}}]}}`

Step 15: Pick Assembly:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 54, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 58, "src": "hda"}]}}]}}`

Step 16: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Reference:
- step_state: scheduled
Step 2: Hi-C reads:
- step_state: scheduled
Step 3: Do you want to trim the Hi-C data?:
- step_state: scheduled

Step 4: Trim Hi-C reads 2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpjw6cynca/files/1/f/6/dataset_1f641452-af7e-4f5c-890f-680ef4e97b47.dat' 'Hi-C reads_1.fq.gz' && ln -f -s '/tmp/tmpjw6cynca/files/3/b/6/dataset_3b6ecedd-64d9-4f7c-a352-aa905ac939f6.dat' 'Hi-C reads_2.fq.gz' &&  cutadapt  -j=${GALAXY_SLOTS:-4}     --error-rate=0.1 --times=1 --overlap=3    --action=trim   --cut=5 -U 5       --minimum-length=1      -o 'out1.fq.gz' -p 'out2.fq.gz'  'Hi-C reads_1.fq.gz' 'Hi-C reads_2.fq.gz'  > report.txt

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7df0b2a11f0aeed000d3a3012a8"`
adapter_options	`{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"}`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}`
library	`{"__current_case__": 2, "input_1": {"values": [{"id": 14, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired_collection"}`
other_trimming_options	`{"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}`
output_selector	`["report"]`
read_mod_options	`{"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7df0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 20, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 15, "src": "dce"}]}}]}}`

Job 2:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7df0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 21, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 16, "src": "dce"}]}}]}}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpjw6cynca/files/2/a/9/dataset_2a924c18-ec8a-47b0-a8de-8c8fa1d2c560.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1   -k '19' -w '100' -d '100' -r '1.5' -y '20' -c '500' -D '0.5' -W '0' -m '50' -S -P    -T '20' -h '5' -a                      'localref.fa' '/tmp/tmpjw6cynca/files/6/2/4/dataset_6249012f-cde2-4f53-b1c2-b1ea20099ae1.dat' '/tmp/tmpjw6cynca/files/7/5/a/dataset_75a8b988-ca3d-4f9d-bfed-0602f6bcb871.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpjw6cynca/job_working_directory/000/61/outputs/dataset_0935e66b-9f1f-45a7-bf8d-64ff6cba22f7.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.69 sec
* Entering FMI_search
init ticks = 12243835893
ref seq len = 275747614
binary seq ticks = 5904747156
build suffix-array ticks = 102461454974
pos: 34468452, ref_seq_len__: 34468451
build fm-index ticks = 22400054162
Total time taken: 59.5645
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 275747615
* sentinel-index: 224703773
* Count:
0,	1
1,	80527259
2,	137873808
3,	195220357
4,	275747615

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 275747614 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 137873807, n: 68494
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (2021, 3042, 5240)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 11678)
[0000][PE] mean and std.dev: (3782.74, 2698.62)
[0000][PE] low and high boundaries for proper pairs: (1, 14897)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (151, 230, 368)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 802)
[0000][PE] mean and std.dev: (244.21, 150.93)
[0000][PE] low and high boundaries for proper pairs: (1, 1019)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (2708, 3331, 6114)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 12926)
[0000][PE] mean and std.dev: (4077.29, 2787.30)
[0000][PE] low and high boundaries for proper pairs: (1, 16332)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (1608, 2936, 5772)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 14100)
[0000][PE] mean and std.dev: (3700.00, 2741.58)
[0000][PE] low and high boundaries for proper pairs: (1, 18264)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 68494 reads in 30.876 CPU sec, 31.117 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 137873807, n: 68494
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (1977, 3478, 6066)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 14244)
[0000][PE] mean and std.dev: (3961.96, 2537.86)
[0000][PE] low and high boundaries for proper pairs: (1, 18333)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (146, 241, 386)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 866)
[0000][PE] mean and std.dev: (246.95, 151.23)
[0000][PE] low and high boundaries for proper pairs: (1, 1106)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (1463, 3158, 6983)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 18023)
[0000][PE] mean and std.dev: (3938.16, 3007.49)
[0000][PE] low and high boundaries for proper pairs: (1, 23543)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (1764, 3269, 5104)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 11784)
[0000][PE] mean and std.dev: (3596.50, 2353.59)
[0000][PE] low and high boundaries for proper pairs: (1, 15124)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 68494 reads in 30.919 CPU sec, 31.775 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 137873807, n: 68494
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (1600, 3333, 5222)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 12466)
[0000][PE] mean and std.dev: (3541.11, 2405.55)
[0000][PE] low and high boundaries for proper pairs: (1, 16088)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (164, 263, 457)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 1043)
[0000][PE] mean and std.dev: (279.92, 172.80)
[0000][PE] low and high boundaries for proper pairs: (1, 1336)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (1761, 2418, 4426)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 9756)
[0000][PE] mean and std.dev: (3069.66, 2241.85)
[0000][PE] low and high boundaries for proper pairs: (1, 12421)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (2055, 4260, 7105)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 17205)
[0000][PE] mean and std.dev: (4350.33, 2963.76)
[0000][PE] low and high boundaries for proper pairs: (1, 22255)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 68494 reads in 29.930 CPU sec, 30.808 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] 2. Calling kt_for - worker_aln
[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] Inferring insert size distribution of PE reads from data, l_pac: 137873807, n: 68494
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (1364, 3003, 5283)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 13121)
[0000][PE] mean and std.dev: (3348.47, 2513.77)
[0000][PE] low and high boundaries for proper pairs: (1, 17040)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (164, 272, 463)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 1061)
[0000][PE] mean and std.dev: (271.60, 174.49)
[0000][PE] low and high boundaries for proper pairs: (1, 1360)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (2196, 3194, 6130)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 13998)
[0000][PE] mean and std.dev: (4047.59, 2612.96)
[0000][PE] low and high boundaries for proper pairs: (1, 17932)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (1777, 4213, 5514)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 12988)
[0000][PE] mean and std.dev: (4154.35, 2778.07)
[0000][PE] low and high boundaries for proper pairs: (1, 16725)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 68494 reads in 29.311 CPU sec, 36.966 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3899368, nseq: 26708
	[0000][ M::kt_pipeline] read 26708 sequences (3899368 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 137873807, n: 68494
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (1040, 2626, 5380)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 14060)
[0000][PE] mean and std.dev: (3261.88, 2607.72)
[0000][PE] low and high boundaries for proper pairs: (1, 18400)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (172, 281, 464)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 1048)
[0000][PE] mean and std.dev: (296.82, 192.41)
[0000][PE] low and high boundaries for proper pairs: (1, 1340)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (700, 2548, 5583)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 15349)
[0000][PE] mean and std.dev: (3176.85, 2680.05)
[0000][PE] low and high boundaries for proper pairs: (1, 20232)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (1957, 4138, 6358)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 15160)
[0000][PE] mean and std.dev: (4190.45, 2530.34)
[0000][PE] low and high boundaries for proper pairs: (1, 19561)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 68494 reads in 28.148 CPU sec, 28.882 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 137873807, n: 26708
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (1531, 3089, 5527)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 13519)
[0000][PE] mean and std.dev: (3502.83, 2580.78)
[0000][PE] low and high boundaries for proper pairs: (1, 17515)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (146, 223, 370)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 818)
[0000][PE] mean and std.dev: (233.56, 144.74)
[0000][PE] low and high boundaries for proper pairs: (1, 1042)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (1436, 3889, 6170)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 15638)
[0000][PE] mean and std.dev: (3972.06, 2638.61)
[0000][PE] low and high boundaries for proper pairs: (1, 20372)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (1130, 3715, 6897)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 18431)
[0000][PE] mean and std.dev: (4249.90, 3057.36)
[0000][PE] low and high boundaries for proper pairs: (1, 24198)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 26708 reads in 10.897 CPU sec, 11.550 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.568832 MHz
Runtime profile:

	Time taken for main_mem function: 171.97 sec

	IO times (sec) :
	Reading IO time (reads) avg: 1.57, (1.57, 1.57)
	Writing IO time (SAM) avg: 23.64, (23.64, 23.64)
	Reading IO time (Reference Genome) avg: 0.07, (0.07, 0.07)
	Index read time avg: 0.29, (0.29, 0.29)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 171.60
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 171.08, (171.08, 171.08)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 83.51, (83.51, 83.51)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 87.55, (87.55, 87.55)
		SMEM compute avg: 36.79, (36.79, 36.79)
		SAL compute avg: 8.05, (8.05, 8.05)
				MEM_SA avg: 3.84, (3.84, 3.84)

		BSW time, avg: 34.00, (34.00, 34.00)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64
[bam_sort_core] merging from 1 files and 1 in-memory blocks...

Standard Output:

ref_seq_len = 275747614
count = 0, 80527258, 137873807, 195220356, 275747614
BWT[224703773] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 4308556

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7df0b2a11f0aeed000d3a3012a8"`
analysis_type	{"__current_case__": 4, "algorithmic_options": {"D": "0.5", "P": true, "S": true, "W": "0", "__current_case__": 0, "algorithmic_options_selector": "set", "c": "500", "d": "100", "e": false, "k": "19", "m": "50", "r": "1.5", "w": "100", "y": "20"}, "analysis_type_selector": "full", "io_options": {"C": false, "K": null, "M": false, "T": "20", "V": false, "Y": false, "__current_case__": 0, "a": true, "five": false, "h": "5", "io_options_selector": "set", "q": false}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 22, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": null}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 59, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

_JAVA_OPTIONS=${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=${TMPDIR:-${_GALAXY_JOB_TMPDIR}}"} && export _JAVA_OPTIONS &&  picard MergeSamFiles  --INPUT '/tmp/tmpjw6cynca/files/0/9/3/dataset_0935e66b-9f1f-45a7-bf8d-64ff6cba22f7.dat'  --OUTPUT '/tmp/tmpjw6cynca/job_working_directory/000/62/outputs/dataset_703d773a-37db-4420-9d07-fd62b2cff94c.dat' --MERGE_SEQUENCE_DICTIONARIES 'false'  --ASSUME_SORTED 'true'  --USE_THREADING true --SORT_ORDER coordinate --VALIDATION_STRINGENCY 'LENIENT' --QUIET true --VERBOSITY ERROR

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m -Djava.io.tmpdir=/tmp/tmpjw6cynca/tmp
Mar 27, 2025 4:51:05 PM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7df0b2a11f0aeed000d3a3012a8"`
assume_sorted	`true`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
merge_sequence_dictionaries	`false`
validation_stringency	`"LENIENT"`

Step 17: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpjw6cynca/files/2/a/9/dataset_2a924c18-ec8a-47b0-a8de-8c8fa1d2c560.dat' --out-coord g   --tabular > '/tmp/tmpjw6cynca/job_working_directory/000/63/outputs/dataset_9a7f18e5-fbbe-4167-9f10-7dfb02c4c31a.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 1, "out_coord": "g", "selector": "coordinates"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

seqtk telo -m 'CCCTAA' -p '1' -d '2000' -s '300'  '/tmp/tmpjw6cynca/files/2/a/9/dataset_2a924c18-ec8a-47b0-a8de-8c8fa1d2c560.dat' > '/tmp/tmpjw6cynca/job_working_directory/000/64/outputs/dataset_3caa6820-5fb7-4260-acb4-ab5801408326.dat'

Exit Code:

```
0
```

Standard Error:

```
0	137873807
```

Traceback:

Job Parameters:

Job parameter	Parameter value
P	`false`
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
d	`"2000"`
dbkey	`"?"`
m	`"CCCTAA"`
p	`"1"`
s	`"300"`

Step 19: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpjw6cynca/files/2/a/9/dataset_2a924c18-ec8a-47b0-a8de-8c8fa1d2c560.dat' reference.fa && minimap2 -x map-hifi    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpjw6cynca/files/5/6/4/dataset_56452c9a-629e-4d6e-9d61-6e2d04e5eebf.dat' -a | samtools view --no-PG -hT reference.fa | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O BAM -o '/tmp/tmpjw6cynca/job_working_directory/000/65/outputs/dataset_4302f78e-444f-46b2-a31b-d8fd4444548b.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::4.964*0.75] collected minimizers
[M::mm_idx_gen::6.346*0.78] sorted minimizers
[M::main::6.346*0.78] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::6.516*0.78] mid_occ = 113
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 1
[M::mm_idx_stat::6.629*0.79] distinct minimizers: 11276538 (95.62% are singletons); average occurrences: 1.229; average spacing: 9.951; total length: 137873807
[M::worker_pipeline::146.365*0.98] mapped 5426 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x map-hifi --q-occ-frac 0.01 -t 1 -a reference.fa /tmp/tmpjw6cynca/files/5/6/4/dataset_56452c9a-629e-4d6e-9d61-6e2d04e5eebf.dat
[M::main] Real time: 146.444 sec; CPU: 142.957 sec; Peak RSS: 1.253 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
alignment_options	`{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "map-hifi", "fastq_input1": {"values": [{"id": 55, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "BAM"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 59, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

samtools view -h '/tmp/tmpjw6cynca/files/7/0/3/dataset_703d773a-37db-4420-9d07-fd62b2cff94c.dat' | PretextMap --sortby length --sortorder descend --mapq 0 -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextMap status] :: Mapping to 1 sequences, sorted by length, descending. Filtering by minimum mapping quality 0

                                                                                
[PretextMap status] :: 10.0 k reads processed, 147  read-pairs mapped
                                                                                
[PretextMap status] :: 20.0 k reads processed, 280  read-pairs mapped
                                                                                
[PretextMap status] :: 30.0 k reads processed, 389  read-pairs mapped
                                                                                
[PretextMap status] :: 40.0 k reads processed, 541  read-pairs mapped
                                                                                
[PretextMap status] :: 50.0 k reads processed, 654  read-pairs mapped
                                                                                
[PretextMap status] :: 60.0 k reads processed, 797  read-pairs mapped
                                                                                
[PretextMap status] :: 70.0 k reads processed, 890  read-pairs mapped
                                                                                
[PretextMap status] :: 80.0 k reads processed, 1 k read-pairs mapped
                                                                                
[PretextMap status] :: 90.0 k reads processed, 1.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 100.0 k reads processed, 1.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 110.0 k reads processed, 1.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 120.0 k reads processed, 1.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 130.0 k reads processed, 1.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 140.0 k reads processed, 1.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 150.0 k reads processed, 2.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 160.0 k reads processed, 2.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 170.0 k reads processed, 2.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 180.0 k reads processed, 2.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 190.0 k reads processed, 2.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 200.0 k reads processed, 2.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 210.0 k reads processed, 2.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 220.0 k reads processed, 2.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 230.0 k reads processed, 2.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 240.0 k reads processed, 3.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 250.0 k reads processed, 3.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 260.0 k reads processed, 3.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 270.0 k reads processed, 3.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 280.0 k reads processed, 3.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 290.0 k reads processed, 3.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 300.0 k reads processed, 3.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 310.0 k reads processed, 3.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 320.0 k reads processed, 3.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 330.0 k reads processed, 4.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 340.0 k reads processed, 4.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 350.0 k reads processed, 4.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 360.0 k reads processed, 4.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 370.0 k reads processed, 4.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 380.0 k reads processed, 4.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 390.0 k reads processed, 4.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 400.0 k reads processed, 4.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 410.0 k reads processed, 4.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 420.0 k reads processed, 4.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 430.0 k reads processed, 5.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 440.0 k reads processed, 5.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 450.0 k reads processed, 5.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 460.0 k reads processed, 5.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 470.0 k reads processed, 5.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 480.0 k reads processed, 5.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 490.0 k reads processed, 5.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 500.0 k reads processed, 5.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 510.0 k reads processed, 6.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 520.0 k reads processed, 6.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 530.0 k reads processed, 6.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 540.0 k reads processed, 6.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 550.0 k reads processed, 6.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 560.0 k reads processed, 6.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 570.0 k reads processed, 6.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 580.0 k reads processed, 6.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 590.0 k reads processed, 7.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 600.0 k reads processed, 7.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 610.0 k reads processed, 7.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 620.0 k reads processed, 7.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 630.0 k reads processed, 7.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 640.0 k reads processed, 7.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 650.0 k reads processed, 7.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 660.0 k reads processed, 7.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 670.0 k reads processed, 8.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 680.0 k reads processed, 8.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 690.0 k reads processed, 8.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 700.0 k reads processed, 8.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 710.0 k reads processed, 8.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 720.0 k reads processed, 8.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 730.0 k reads processed, 8.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 740.0 k reads processed, 8.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 750.0 k reads processed, 8.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 760.0 k reads processed, 9.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 770.0 k reads processed, 9.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 780.0 k reads processed, 9.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 790.0 k reads processed, 9.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 800.0 k reads processed, 9.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 810.0 k reads processed, 9.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 820.0 k reads processed, 9.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 830.0 k reads processed, 10.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 840.0 k reads processed, 10.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 850.0 k reads processed, 10.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 860.0 k reads processed, 10.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 870.0 k reads processed, 10.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 880.0 k reads processed, 10.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 890.0 k reads processed, 10.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 900.0 k reads processed, 10.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 910.0 k reads processed, 10.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 920.0 k reads processed, 11.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 930.0 k reads processed, 11.2 k read-pairs mapped
                                                                                
[PretextMap status] :: 940.0 k reads processed, 11.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 950.0 k reads processed, 11.3 k read-pairs mapped
                                                                                
[PretextMap status] :: 960.0 k reads processed, 11.4 k read-pairs mapped
                                                                                
[PretextMap status] :: 970.0 k reads processed, 11.5 k read-pairs mapped
                                                                                
[PretextMap status] :: 980.0 k reads processed, 11.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 990.0 k reads processed, 11.6 k read-pairs mapped
                                                                                
[PretextMap status] :: 1.0 M reads processed, 11.7 k read-pairs mapped
                                                                                
[PretextMap status] :: 1.0 M reads processed, 11.8 k read-pairs mapped
                                                                                
[PretextMap status] :: 1.0 M reads processed, 11.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 1.0 M reads processed, 11.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 1.0 M reads processed, 12.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 1.1 M reads processed, 12.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 1.1 M reads processed, 12.1 k read-pairs mapped
                                                       
..
:: 298/528 (56.44%) texture blocks written to disk
[PretextMap status] :: 299/528 (56.63%) texture blocks written to disk
[PretextMap status] :: 300/528 (56.82%) texture blocks written to disk
[PretextMap status] :: 301/528 (57.01%) texture blocks written to disk
[PretextMap status] :: 302/528 (57.20%) texture blocks written to disk
[PretextMap status] :: 303/528 (57.39%) texture blocks written to disk
[PretextMap status] :: 304/528 (57.58%) texture blocks written to disk
[PretextMap status] :: 305/528 (57.77%) texture blocks written to disk
[PretextMap status] :: 306/528 (57.95%) texture blocks written to disk
[PretextMap status] :: 307/528 (58.14%) texture blocks written to disk
[PretextMap status] :: 308/528 (58.33%) texture blocks written to disk
[PretextMap status] :: 309/528 (58.52%) texture blocks written to disk
[PretextMap status] :: 310/528 (58.71%) texture blocks written to disk
[PretextMap status] :: 311/528 (58.90%) texture blocks written to disk
[PretextMap status] :: 312/528 (59.09%) texture blocks written to disk
[PretextMap status] :: 313/528 (59.28%) texture blocks written to disk
[PretextMap status] :: 314/528 (59.47%) texture blocks written to disk
[PretextMap status] :: 315/528 (59.66%) texture blocks written to disk
[PretextMap status] :: 316/528 (59.85%) texture blocks written to disk
[PretextMap status] :: 317/528 (60.04%) texture blocks written to disk
[PretextMap status] :: 318/528 (60.23%) texture blocks written to disk
[PretextMap status] :: 319/528 (60.42%) texture blocks written to disk
[PretextMap status] :: 320/528 (60.61%) texture blocks written to disk
[PretextMap status] :: 321/528 (60.80%) texture blocks written to disk
[PretextMap status] :: 322/528 (60.98%) texture blocks written to disk
[PretextMap status] :: 323/528 (61.17%) texture blocks written to disk
[PretextMap status] :: 324/528 (61.36%) texture blocks written to disk
[PretextMap status] :: 325/528 (61.55%) texture blocks written to disk
[PretextMap status] :: 326/528 (61.74%) texture blocks written to disk
[PretextMap status] :: 327/528 (61.93%) texture blocks written to disk
[PretextMap status] :: 328/528 (62.12%) texture blocks written to disk
[PretextMap status] :: 329/528 (62.31%) texture blocks written to disk
[PretextMap status] :: 330/528 (62.50%) texture blocks written to disk
[PretextMap status] :: 331/528 (62.69%) texture blocks written to disk
[PretextMap status] :: 332/528 (62.88%) texture blocks written to disk
[PretextMap status] :: 333/528 (63.07%) texture blocks written to disk
[PretextMap status] :: 334/528 (63.26%) texture blocks written to disk
[PretextMap status] :: 335/528 (63.45%) texture blocks written to disk
[PretextMap status] :: 336/528 (63.64%) texture blocks written to disk
[PretextMap status] :: 337/528 (63.83%) texture blocks written to disk
[PretextMap status] :: 338/528 (64.02%) texture blocks written to disk
[PretextMap status] :: 339/528 (64.20%) texture blocks written to disk
[PretextMap status] :: 340/528 (64.39%) texture blocks written to disk
[PretextMap status] :: 341/528 (64.58%) texture blocks written to disk
[PretextMap status] :: 342/528 (64.77%) texture blocks written to disk
[PretextMap status] :: 343/528 (64.96%) texture blocks written to disk
[PretextMap status] :: 344/528 (65.15%) texture blocks written to disk
[PretextMap status] :: 345/528 (65.34%) texture blocks written to disk
[PretextMap status] :: 346/528 (65.53%) texture blocks written to disk
[PretextMap status] :: 347/528 (65.72%) texture blocks written to disk
[PretextMap status] :: 348/528 (65.91%) texture blocks written to disk
[PretextMap status] :: 349/528 (66.10%) texture blocks written to disk
[PretextMap status] :: 350/528 (66.29%) texture blocks written to disk
[PretextMap status] :: 351/528 (66.48%) texture blocks written to disk
[PretextMap status] :: 352/528 (66.67%) texture blocks written to disk
[PretextMap status] :: 353/528 (66.86%) texture blocks written to disk
[PretextMap status] :: 354/528 (67.05%) texture blocks written to disk
[PretextMap status] :: 355/528 (67.23%) texture blocks written to disk
[PretextMap status] :: 356/528 (67.42%) texture blocks written to disk
[PretextMap status] :: 357/528 (67.61%) texture blocks written to disk
[PretextMap status] :: 358/528 (67.80%) texture blocks written to disk
[PretextMap status] :: 359/528 (67.99%) texture blocks written to disk
[PretextMap status] :: 360/528 (68.18%) texture blocks written to disk
[PretextMap status] :: 361/528 (68.37%) texture blocks written to disk
[PretextMap status] :: 362/528 (68.56%) texture blocks written to disk
[PretextMap status] :: 363/528 (68.75%) texture blocks written to disk
[PretextMap status] :: 364/528 (68.94%) texture blocks written to disk
[PretextMap status] :: 365/528 (69.13%) texture blocks written to disk
[PretextMap status] :: 366/528 (69.32%) texture blocks written to disk
[PretextMap status] :: 367/528 (69.51%) texture blocks written to disk
[PretextMap status] :: 368/528 (69.70%) texture blocks written to disk
[PretextMap status] :: 369/528 (69.89%) texture blocks written to disk
[PretextMap status] :: 370/528 (70.08%) texture blocks written to disk
[PretextMap status] :: 371/528 (70.27%) texture blocks written to disk
[PretextMap status] :: 372/528 (70.45%) texture blocks written to disk
[PretextMap status] :: 373/528 (70.64%) texture blocks written to disk
[PretextMap status] :: 374/528 (70.83%) texture blocks written to disk
[PretextMap status] :: 375/528 (71.02%) texture blocks written to disk
[PretextMap status] :: 376/528 (71.21%) texture blocks written to disk
[PretextMap status] :: 377/528 (71.40%) texture blocks written to disk
[PretextMap status] :: 378/528 (71.59%) texture blocks written to disk
[PretextMap status] :: 379/528 (71.78%) texture blocks written to disk
[PretextMap status] :: 380/528 (71.97%) texture blocks written to disk
[PretextMap status] :: 381/528 (72.16%) texture blocks written to disk
[PretextMap status] :: 382/528 (72.35%) texture blocks written to disk
[PretextMap status] :: 383/528 (72.54%) texture blocks written to disk
[PretextMap status] :: 384/528 (72.73%) texture blocks written to disk
[PretextMap status] :: 385/528 (72.92%) texture blocks written to disk
[PretextMap status] :: 386/528 (73.11%) texture blocks written to disk
[PretextMap status] :: 387/528 (73.30%) texture blocks written to disk
[PretextMap status] :: 388/528 (73.48%) texture blocks written to disk
[PretextMap status] :: 389/528 (73.67%) texture blocks written to disk
[PretextMap status] :: 390/528 (73.86%) texture blocks written to disk
[PretextMap status] :: 391/528 (74.05%) texture blocks written to disk
[PretextMap status] :: 392/528 (74.24%) texture blocks written to disk
[PretextMap status] :: 393/528 (74.43%) texture blocks written to disk
[PretextMap status] :: 394/528 (74.62%) texture blocks written to disk
[PretextMap status] :: 395/528 (74.81%) texture blocks written to disk
[PretextMap status] :: 396/528 (75.00%) texture blocks written to disk
[PretextMap status] :: 397/528 (75.19%) texture blocks written to disk
[PretextMap status] :: 398/528 (75.38%) texture blocks written to disk
[PretextMap status] :: 399/528 (75.57%) texture blocks written to disk
[PretextMap status] :: 400/528 (75.76%) texture blocks written to disk
[PretextMap status] :: 401/528 (75.95%) texture blocks written to disk
[PretextMap status] :: 402/528 (76.14%) texture blocks written to disk
[PretextMap status] :: 403/528 (76.33%) texture blocks written to disk
[PretextMap status] :: 404/528 (76.52%) texture blocks written to disk
[PretextMap status] :: 405/528 (76.70%) texture blocks written to disk
[PretextMap status] :: 406/528 (76.89%) texture blocks written to disk
[PretextMap status] :: 407/528 (77.08%) texture blocks written to disk
[PretextMap status] :: 408/528 (77.27%) texture blocks written to disk
[PretextMap status] :: 409/528 (77.46%) texture blocks written to disk
[PretextMap status] :: 410/528 (77.65%) texture blocks written to disk
[PretextMap status] :: 411/528 (77.84%) texture blocks written to disk
[PretextMap status] :: 412/528 (78.03%) texture blocks written to disk
[PretextMap status] :: 413/528 (78.22%) texture blocks written to disk
[PretextMap status] :: 414/528 (78.41%) texture blocks written to disk
[PretextMap status] :: 415/528 (78.60%) texture blocks written to disk
[PretextMap status] :: 416/528 (78.79%) texture blocks written to disk
[PretextMap status] :: 417/528 (78.98%) texture blocks written to disk
[PretextMap status] :: 418/528 (79.17%) texture blocks written to disk
[PretextMap status] :: 419/528 (79.36%) texture blocks written to disk
[PretextMap status] :: 420/528 (79.55%) texture blocks written to disk
[PretextMap status] :: 421/528 (79.73%) texture blocks written to disk
[PretextMap status] :: 422/528 (79.92%) texture blocks written to disk
[PretextMap status] :: 423/528 (80.11%) texture blocks written to disk
[PretextMap status] :: 424/528 (80.30%) texture blocks written to disk
[PretextMap status] :: 425/528 (80.49%) texture blocks written to disk
[PretextMap status] :: 426/528 (80.68%) texture blocks written to disk
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[PretextMap status] :: 528/528 (100.00%) texture blocks written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`"0"`
sorting	`{"__current_case__": 1, "sortby": "length", "sortorder": "descend"}`

Step 3: Haplotype 2:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int  --file '/tmp/tmpjw6cynca/job_working_directory/000/67/configs/tmpeht25n09' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpjw6cynca/files/9/a/7/dataset_9a7f18e5-fbbe-4167-9f10-7dfb02c4c31a.dat' '/tmp/tmpjw6cynca/job_working_directory/000/67/outputs/dataset_12d228d7-477a-41a5-8b2f-4f4f219b1122.dat'

Exit Code:

```
0
```

Standard Output:

abs(int(c3)-int(c2))
Computing 1 new columns with instructions ['abs(int(c3)-int(c2));;']
Computed new column values for 100.00% of 8 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "abs(int(c3)-int(c2))"}], "header_lines_select": "no"}`

Step 22: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpjw6cynca/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpjw6cynca/files/3/c/a/dataset_3caa6820-5fb7-4260-acb4-ab5801408326.dat' 'c1,c2,c3' T '/tmp/tmpjw6cynca/job_working_directory/000/68/outputs/dataset_9ca98651-b162-459d-85bf-3f2f9e7f9314.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1,c2,c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpjw6cynca/files/4/3/0/dataset_4302f78e-444f-46b2-a31b-d8fd4444548b.dat' one.bam && ln -s '/tmp/tmpjw6cynca/files/_metadata_files/d/f/3/metadata_df3b600f-c351-4b09-bc60-12872e537c89.dat' one.bam.bai &&  bamCoverage --numberOfProcessors "${GALAXY_SLOTS:-4}"  --bam one.bam --outFileName '/tmp/tmpjw6cynca/job_working_directory/000/69/outputs/dataset_2451f336-5538-4514-b277-5dad48f1cbe0.dat' --outFileFormat 'bigwig'  --binSize 100

Exit Code:

```
0
```

Standard Error:

bamFilesList: ['one.bam']
binLength: 100
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 100
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
advancedOpt	`{"__current_case__": 0, "showAdvancedOpt": "no"}`
binSize	`"100"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exactScaling	`false`
outFileFormat	`"bigwig"`
region	`""`
scaling	`{"__current_case__": 3, "type": "no"}`

Step 24: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types  --file '/tmp/tmpjw6cynca/job_working_directory/000/70/configs/tmpdu5zb0oz' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpjw6cynca/files/9/c/a/dataset_9ca98651-b162-459d-85bf-3f2f9e7f9314.dat' '/tmp/tmpjw6cynca/job_working_directory/000/70/outputs/dataset_fcfc5b1f-d91e-4d9d-b975-4e8c04ca91bd.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "abs(int(c3)-int(c2))"}], "header_lines_select": "no"}`

Step 25: Add Coverage Track:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmpjw6cynca/files/3/f/c/dataset_3fc2587e-f204-4a6c-8818-cf4d45aa0b1e.dat' input.pretext && ln -s '/tmp/tmpjw6cynca/files/2/4/5/dataset_2451f336-5538-4514-b277-5dad48f1cbe0.dat' input.bigwig && bigWigToBedGraph input.bigwig /dev/stdout | PretextGraph -i input.pretext -n 'coverage' -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextGraph status] :: Release mode, number of thread: 4

[PretextGraph status] :: Pretext file: input.pretext
[PretextGraph status] :: Graph name: 'coverage'
[PretextGraph status] :: The extension of the graph name is default, set the data_type into 0 (default).
[PretextGraph status] :: Pretext file: output.pretext
[PretextGraph status] :: Reading file...
[PretextGraph status] :: File read

                                                                                
[PretextGraph status] :: 16.4 k bedgraph lines read
[PretextGraph status] :: Transfer f32 to s32...
[PretextGraph status] :: Saving graph...
[PretextGraph status] :: Done

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
name	`"coverage"`

Step 26: Test if telomere track is empty:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bedgraph"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 27: False if telomere track is empty:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "", "mappings": [{"__index__": 0, "from": "", "to": "false"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "true", "on_unmapped": "default"}`

Step 28: Add telomere track:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
name	`"telomeres_gap_format"`

Step 29: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 78, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 75, "src": "hda"}]}}]}}`

Step 30: Add gaps track:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmpjw6cynca/files/4/d/5/dataset_4d5fd6d7-b139-4137-83f6-2f0fec200e31.dat' input.pretext && cat '/tmp/tmpjw6cynca/files/1/2/d/dataset_12d228d7-477a-41a5-8b2f-4f4f219b1122.dat' | PretextGraph -i input.pretext -n 'gaps' -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextGraph status] :: Release mode, number of thread: 4

[PretextGraph status] :: Pretext file: input.pretext
[PretextGraph status] :: Graph name: 'gaps'
[PretextGraph status] :: The extension of the graph name is gap, set the data_type to 2 (gap).
[PretextGraph status] :: Pretext file: output.pretext
[PretextGraph status] :: Reading file...
[PretextGraph status] :: File read

[PretextGraph status] :: Transfer f32 to s32...
[PretextGraph status] :: Saving graph...
[PretextGraph status] :: Done

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
name	`"gaps"`

Step 4: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

PretextSnapshot -m /tmp/tmpjw6cynca/files/8/3/3/dataset_833d2fd3-488b-4be9-b131-68b875454ab7.dat -f png -r 2000 -c 5 --sequences '=full' --minTexels 64 --gridSize 1 --gridColour black '' -o output --prefix pretext_snapshot

Exit Code:

```
0
```

Standard Output:

[PretextSnapshot status] :: Input map: '/tmp/tmpjw6cynca/files/8/3/3/dataset_833d2fd3-488b-4be9-b131-68b875454ab7.dat'
[PretextSnapshot status] :: Output format: png
[PretextSnapshot status] :: Output resolution: 2000 pixels
[PretextSnapshot status] :: Colour map: Three Wave Blue-Green-Yellow
[PretextSnapshot status] :: Minimum texels per image: 64
[PretextSnapshot status] :: Grid size: 1 pixel
[PretextSnapshot status] :: Grid colour: 000000ff
[PretextSnapshot status] :: Output path: 'output/pretext_snapshot'
[PretextSnapshot status] :: Indexing file...
[PretextSnapshot status] :: File indexed
[PretextSnapshot status] :: 'output/pretext_snapshotFullMap.png' written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
chromInfo	`"/tmp/tmpjw6cynca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 0, "gridcolor": "black", "gridsize": "1", "showGrid": "yes"}`
mintexels	`"64"`
resolution	`"2000"`
sequencenames	`false`
sequences	`"=full"`

Step 32: __EXTRACT_DATASET__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"e2d2d7dc0b2a11f0aeed000d3a3012a8"`
input	`{"values": [{"id": 14, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 5: First Haplotype suffix:
- step_state: scheduled
Step 6: Second Haplotype suffix:
- step_state: scheduled
Step 7: Hi-C reads:
- step_state: scheduled
Step 8: Do you want to trim the Hi-C data?:
- step_state: scheduled
Step 9: Telomere repeat to suit species:
- step_state: scheduled
Step 10: PacBio reads:
- step_state: scheduled

Other invocation details
- history_id
  - 496fdcad65465798
- history_state
  - ok
- invocation_id
  - 74d2c40334dbdfb1
- invocation_state
  - scheduled
- workflow_id
  - 6939a158f632cb4b

github-actions · 2025-03-27T17:12:01Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	2
Passed	0
Error	2
Failure	0
Skipped	0

Errored Tests

❌ hi-c-map-for-assembly-manual-curation.ga_0

Execution Problem:

Final state of invocation 6b6f885a347c1737 is [failed]. Failed to run workflow, at least one job is in [paused] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 28 requires a dataset, but dataset entered a failed state.

Steps

Step 1: Haplotype 1:
- step_state: scheduled
Step 2: Will you use a second haplotype?:
- step_state: scheduled

Step 11: Hap2 not provided:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d60b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 3, "input_param": false, "mappings": [{"__index__": 0, "from": false, "to": "true"}, {"__index__": 1, "from": true, "to": "false"}], "type": "boolean"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "false", "on_unmapped": "default"}`

Step 12: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Hap1:
- step_state: scheduled
Step 2: Hap2:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d70b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 10, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 2, "src": "hda"}]}}]}}`

Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d70b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 12, "src": "hda"}]}}]`

Step 3: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 4: Hap1 suffix:
- step_state: scheduled
Step 5: Hap2 suffix:
- step_state: scheduled

Step 6: Expression for hap1 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d70b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 7: Expression for hap2 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d70b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H2", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 8: add hap1 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d70b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null}]`

Step 9: add hap2 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d70b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null}]`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d70b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 9, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 1, "src": "hda"}]}}]}}`

Step 13: concatenate HiFi:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp94ch8nif/files/b/5/5/dataset_b55e5453-0ab1-48ba-a8f4-42917ce4e1de.dat' >> '/tmp/tmp94ch8nif/job_working_directory/000/14/outputs/dataset_234accb8-bbf8-4f8d-a670-b9726f819999.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d60b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[]`

Step 14: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Hap1:
- step_state: scheduled
Step 2: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 3: Hap1 suffix:
- step_state: scheduled

Step 4: Expression for hap1 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d80b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 5: add hap1 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed -r --sandbox -e 's/>.+$/&.H1/g' '/tmp/tmp94ch8nif/files/0/7/c/dataset_07c18519-71f5-43c7-bee5-1f2ee6661491.dat' > '/tmp/tmp94ch8nif/job_working_directory/000/16/outputs/dataset_c1b44820-ed47-49a4-8ff0-bf5c6c919a85.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d80b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": "&.H1"}]`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d80b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 16, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 1, "src": "hda"}]}}]}}`

Step 15: Pick Assembly:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d60b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 13, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 17, "src": "hda"}]}}]}}`

Step 16: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Reference:
- step_state: scheduled
Step 2: Hi-C reads:
- step_state: scheduled
Step 3: Do you want to trim the Hi-C data?:
- step_state: scheduled

Step 4: Trim Hi-C reads 2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmp94ch8nif/files/2/b/6/dataset_2b67fe9a-77cf-4b89-8dc4-86c38b532bb2.dat' 'Hi-C reads_1.fq.gz' && ln -f -s '/tmp/tmp94ch8nif/files/9/7/a/dataset_97aabc98-c477-4b13-af10-b97e1777d9f4.dat' 'Hi-C reads_2.fq.gz' &&  cutadapt  -j=${GALAXY_SLOTS:-4}     --error-rate=0.1 --times=1 --overlap=3    --action=trim   --cut=5 -U 5       --minimum-length=1      -o 'out1.fq.gz' -p 'out2.fq.gz'  'Hi-C reads_1.fq.gz' 'Hi-C reads_2.fq.gz'  > report.txt

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d90b2c11f08a576045bd086594"`
adapter_options	`{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"}`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}`
library	`{"__current_case__": 2, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired_collection"}`
other_trimming_options	`{"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}`
output_selector	`["report"]`
read_mod_options	`{"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d90b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 7, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 2, "src": "dce"}]}}]}}`

Job 2:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d90b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 8, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 3, "src": "dce"}]}}]}}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmp94ch8nif/files/c/1/b/dataset_c1b44820-ed47-49a4-8ff0-bf5c6c919a85.dat' 'localref.fasta' && bwa-mem2 index 'localref.fasta' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1   -k '19' -w '100' -d '100' -r '1.5' -y '20' -c '500' -D '0.5' -W '0' -m '50' -S -P    -T '20' -h '5' -a                      'localref.fasta' '/tmp/tmp94ch8nif/files/b/7/6/dataset_b76235dd-eadb-427c-a44f-d09e8fca5fed.dat' '/tmp/tmp94ch8nif/files/4/6/2/dataset_46280c71-12da-4c80-8eb3-b2b92e47f9c2.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmp94ch8nif/job_working_directory/000/22/outputs/dataset_31837295-affd-4fae-a4b4-7e6de13fe606.dat'

Exit Code:

```
127
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.65 sec
* Entering FMI_search
init ticks = 13841455736
ref seq len = 279307354
binary seq ticks = 5258441738
build suffix-array ticks = 91854353683
pos: 34913420, ref_seq_len__: 34913419
build fm-index ticks = 22451527139
Total time taken: 55.2677
/tmp/tmp94ch8nif/job_working_directory/000/22/tool_script.sh: line 23: samtools: command not found
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fasta
* Entering FMI_search
* Index file found. Loading index from localref.fasta.bwt.2bit.64
* Reference seq len for bi-index = 279307355
* sentinel-index: 13446364
* Count:
0,	1
1,	84204314
2,	139653678
3,	195103042
4,	279307355

* Reading other elements of the index from files localref.fasta
* Index prefix: localref.fasta
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fasta.0123
* Reference genome size: 279307354 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 139653677, n: 68494
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (1649, 4140, 6027)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 14783)
[0000][PE] mean and std.dev: (4063.15, 2569.67)
[0000][PE] low and high boundaries for proper pairs: (1, 19161)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (157, 248, 382)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 832)
[0000][PE] mean and std.dev: (254.60, 148.66)
[0000][PE] low and high boundaries for proper pairs: (1, 1057)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (2814, 4404, 5708)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 11496)
[0000][PE] mean and std.dev: (4321.60, 2279.57)
[0000][PE] low and high boundaries for proper pairs: (1, 14390)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (1378, 2846, 5532)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 13840)
[0000][PE] mean and std.dev: (3534.90, 2567.86)
[0000][PE] low and high boundaries for proper pairs: (1, 17994)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 68494 reads in 92.671 CPU sec, 92.889 real sec

Standard Output:

ref_seq_len = 279307354
count = 0, 84204313, 139653677, 195103041, 279307354
BWT[13446364] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 4364177

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d90b2c11f08a576045bd086594"`
analysis_type	{"__current_case__": 4, "algorithmic_options": {"D": "0.5", "P": true, "S": true, "W": "0", "__current_case__": 0, "algorithmic_options_selector": "set", "c": "500", "d": "100", "e": false, "k": "19", "m": "50", "r": "1.5", "w": "100", "y": "20"}, "analysis_type_selector": "full", "io_options": {"C": false, "K": null, "M": false, "T": "20", "V": false, "Y": false, "__current_case__": 0, "a": true, "five": false, "h": "5", "io_options_selector": "set", "q": false}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 9, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": null}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 18, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d90b2c11f08a576045bd086594"`
bed_file	`None`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
headerbam	`None`
idpg	`false`
idrg	`false`
region	`None`
seed	`"1"`

Step 17: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp94ch8nif/files/c/1/b/dataset_c1b44820-ed47-49a4-8ff0-bf5c6c919a85.dat' --out-coord g   --tabular > '/tmp/tmp94ch8nif/job_working_directory/000/24/outputs/dataset_4e81dfd3-c328-45a5-90d7-00640ed80f7e.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d60b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 1, "out_coord": "g", "selector": "coordinates"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

seqtk telo -m 'CCCTAA' -p '1' -d '2000' -s '300'  '/tmp/tmp94ch8nif/files/c/1/b/dataset_c1b44820-ed47-49a4-8ff0-bf5c6c919a85.dat' > '/tmp/tmp94ch8nif/job_working_directory/000/25/outputs/dataset_0f6ad7af-63e8-4547-b519-1636b8eb7e8e.dat'

Exit Code:

```
0
```

Standard Error:

```
11012	139653677
```

Traceback:

Job Parameters:

Job parameter	Parameter value
P	`false`
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d60b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
d	`"2000"`
dbkey	`"?"`
m	`"CCCTAA"`
p	`"1"`
s	`"300"`

Step 19: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmp94ch8nif/files/c/1/b/dataset_c1b44820-ed47-49a4-8ff0-bf5c6c919a85.dat' reference.fa && minimap2 -x map-hifi    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmp94ch8nif/files/2/3/4/dataset_234accb8-bbf8-4f8d-a670-b9726f819999.dat' -a | samtools view --no-PG -hT reference.fa | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O BAM -o '/tmp/tmp94ch8nif/job_working_directory/000/26/outputs/dataset_19ccb6f0-c197-432d-b1f2-b41297632f06.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::4.322*0.80] collected minimizers
[M::mm_idx_gen::5.658*0.82] sorted minimizers
[M::main::5.659*0.82] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::5.784*0.83] mid_occ = 131
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 1
[M::mm_idx_stat::5.874*0.83] distinct minimizers: 11315845 (97.08% are singletons); average occurrences: 1.241; average spacing: 9.941; total length: 139653677
[M::worker_pipeline::146.117*0.98] mapped 5426 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x map-hifi --q-occ-frac 0.01 -t 1 -a reference.fa /tmp/tmp94ch8nif/files/2/3/4/dataset_234accb8-bbf8-4f8d-a670-b9726f819999.dat
[M::main] Real time: 146.132 sec; CPU: 143.204 sec; Peak RSS: 1.375 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d60b2c11f08a576045bd086594"`
alignment_options	`{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "map-hifi", "fastq_input1": {"values": [{"id": 14, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "BAM"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 18, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d60b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`"0"`
sorting	`{"__current_case__": 1, "sortby": "length", "sortorder": "descend"}`

Step 3: Haplotype 2:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int  --file '/tmp/tmp94ch8nif/job_working_directory/000/28/configs/tmpk2c9hj33' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp94ch8nif/files/4/e/8/dataset_4e81dfd3-c328-45a5-90d7-00640ed80f7e.dat' '/tmp/tmp94ch8nif/job_working_directory/000/28/outputs/dataset_60aa9889-5f0c-425d-b50f-fdd3fc603770.dat'

Exit Code:

```
0
```

Standard Output:

abs(int(c3)-int(c2))
Computing 1 new columns with instructions ['abs(int(c3)-int(c2));;']
Computed new column values for 100.00% of 4 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d60b2c11f08a576045bd086594"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "abs(int(c3)-int(c2))"}], "header_lines_select": "no"}`

Step 22: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp94ch8nif/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp94ch8nif/files/0/f/6/dataset_0f6ad7af-63e8-4547-b519-1636b8eb7e8e.dat' 'c1,c2,c3' T '/tmp/tmp94ch8nif/job_working_directory/000/29/outputs/dataset_b4c9e5ff-27b5-412f-b75c-a0b7342f46de.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"f6aba3d60b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1,c2,c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp94ch8nif/files/1/9/c/dataset_19ccb6f0-c197-432d-b1f2-b41297632f06.dat' one.bam && ln -s '/tmp/tmp94ch8nif/files/_metadata_files/1/4/e/metadata_14e632ef-42c3-4a1a-978d-859dd76c6650.dat' one.bam.bai &&  bamCoverage --numberOfProcessors "${GALAXY_SLOTS:-4}"  --bam one.bam --outFileName '/tmp/tmp94ch8nif/job_working_directory/000/30/outputs/dataset_1218cdec-ee4f-4a1b-95a1-2bd97063da48.dat' --outFileFormat 'bigwig'  --binSize 100

Exit Code:

```
0
```

Standard Error:

bamFilesList: ['one.bam']
binLength: 100
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 100
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d60b2c11f08a576045bd086594"`
advancedOpt	`{"__current_case__": 0, "showAdvancedOpt": "no"}`
binSize	`"100"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exactScaling	`false`
outFileFormat	`"bigwig"`
region	`""`
scaling	`{"__current_case__": 3, "type": "no"}`

Step 24: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int  --file '/tmp/tmp94ch8nif/job_working_directory/000/31/configs/tmp3i3b9rag' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp94ch8nif/files/b/4/c/dataset_b4c9e5ff-27b5-412f-b75c-a0b7342f46de.dat' '/tmp/tmp94ch8nif/job_working_directory/000/31/outputs/dataset_8a0dd52c-e3e8-4638-85c8-5b652c016ab3.dat'

Exit Code:

```
0
```

Standard Output:

abs(int(c3)-int(c2))
Computing 1 new columns with instructions ['abs(int(c3)-int(c2));;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d60b2c11f08a576045bd086594"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "abs(int(c3)-int(c2))"}], "header_lines_select": "no"}`

Step 25: Add Coverage Track:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d60b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
name	`"coverage"`

Step 26: Test if telomere track is empty:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bedgraph"`
__workflow_invocation_uuid__	`"f6aba3d60b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 27: False if telomere track is empty:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6aba3d60b2c11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "scaffold_10.H1\t0\t11012\t11012", "mappings": [{"__index__": 0, "from": "", "to": "false"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "true", "on_unmapped": "default"}`

Step 28: Add telomere track:
- step_state: new
Step 29: Unlabelled step:
- step_state: new
Step 30: Add gaps track:
- step_state: new
Step 4: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 31: Unlabelled step:
- step_state: new
Step 32: Unlabelled step:
- step_state: new
Step 5: First Haplotype suffix:
- step_state: scheduled
Step 6: Second Haplotype suffix:
- step_state: scheduled
Step 7: Hi-C reads:
- step_state: scheduled
Step 8: Do you want to trim the Hi-C data?:
- step_state: scheduled
Step 9: Telomere repeat to suit species:
- step_state: scheduled
Step 10: PacBio reads:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation 6b6f885a347c1737 is [failed]. Failed to run workflow, at least one job is in [paused] state.
- history_id
  - 6b6f885a347c1737
- history_state
  - paused
- invocation_id
  - 6b6f885a347c1737
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': None, 'hda_id': '00507017c18859da', 'reason': 'dataset_failed', 'workflow_step_id': 27}]
- workflow_id
  - 5c0594841f9dcc30

❌ hi-c-map-for-assembly-manual-curation.ga_1

Execution Problem:

Final state of invocation f44384aa1da712c8 is [failed]. Failed to run workflow, at least one job is in [paused] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 28 requires a dataset, but dataset entered a failed state.

Steps

Step 1: Haplotype 1:
- step_state: scheduled
Step 2: Will you use a second haplotype?:
- step_state: scheduled

Step 11: Hap2 not provided:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a60b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 3, "input_param": false, "mappings": [{"__index__": 0, "from": false, "to": "true"}, {"__index__": 1, "from": true, "to": "false"}], "type": "boolean"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "false", "on_unmapped": "default"}`

Step 12: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Hap1:
- step_state: scheduled
Step 2: Hap2:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a70b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 46, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 38, "src": "hda"}]}}]}}`

Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a70b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 48, "src": "hda"}]}}]`

Step 3: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 4: Hap1 suffix:
- step_state: scheduled
Step 5: Hap2 suffix:
- step_state: scheduled

Step 6: Expression for hap1 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a70b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 7: Expression for hap2 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a70b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H2", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 8: add hap1 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a70b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null}]`

Step 9: add hap2 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a70b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null}]`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a70b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 45, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 37, "src": "hda"}]}}]}}`

Step 13: concatenate HiFi:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp94ch8nif/files/9/5/b/dataset_95be8062-98b6-41d8-93b2-1e965b5ff5d8.dat' >> '/tmp/tmp94ch8nif/job_working_directory/000/48/outputs/dataset_1dcb7377-156e-420e-ad94-e73047a76ea8.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a60b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[]`

Step 14: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Hap1:
- step_state: scheduled
Step 2: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 3: Hap1 suffix:
- step_state: scheduled

Step 4: Expression for hap1 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a80b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 5: add hap1 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed -r --sandbox -e 's/>.+$/&.H1/g' '/tmp/tmp94ch8nif/files/8/f/a/dataset_8fa9524f-a180-4b7b-9914-7f85a4b7d35e.dat' > '/tmp/tmp94ch8nif/job_working_directory/000/50/outputs/dataset_ad381e9f-6e2a-49de-b7d3-e9e0e088c622.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a80b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": "&.H1"}]`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a80b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 52, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 37, "src": "hda"}]}}]}}`

Step 15: Pick Assembly:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a60b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 49, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 53, "src": "hda"}]}}]}}`

Step 16: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Reference:
- step_state: scheduled
Step 2: Hi-C reads:
- step_state: scheduled
Step 3: Do you want to trim the Hi-C data?:
- step_state: scheduled

Step 4: Trim Hi-C reads 2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmp94ch8nif/files/4/0/4/dataset_4047d1b7-efa4-4130-bd7c-d016b594ba7c.dat' 'Hi-C reads_1.fq.gz' && ln -f -s '/tmp/tmp94ch8nif/files/c/0/3/dataset_c034b934-a19f-4b55-8a84-0d609f9766fe.dat' 'Hi-C reads_2.fq.gz' &&  cutadapt  -j=${GALAXY_SLOTS:-4}     --error-rate=0.1 --times=1 --overlap=3    --action=trim   --cut=5 -U 5       --minimum-length=1      -o 'out1.fq.gz' -p 'out2.fq.gz'  'Hi-C reads_1.fq.gz' 'Hi-C reads_2.fq.gz'  > report.txt

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a90b2d11f08a576045bd086594"`
adapter_options	`{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"}`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}`
library	`{"__current_case__": 2, "input_1": {"values": [{"id": 13, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired_collection"}`
other_trimming_options	`{"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}`
output_selector	`["report"]`
read_mod_options	`{"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a90b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 19, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 14, "src": "dce"}]}}]}}`

Job 2:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a90b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 20, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 15, "src": "dce"}]}}]}}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmp94ch8nif/files/a/d/3/dataset_ad381e9f-6e2a-49de-b7d3-e9e0e088c622.dat' 'localref.fasta' && bwa-mem2 index 'localref.fasta' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1   -k '19' -w '100' -d '100' -r '1.5' -y '20' -c '500' -D '0.5' -W '0' -m '50' -S -P    -T '20' -h '5' -a                      'localref.fasta' '/tmp/tmp94ch8nif/files/1/a/4/dataset_1a44c31d-51c6-4d78-8d4a-e896a84303fb.dat' '/tmp/tmp94ch8nif/files/a/a/0/dataset_aa0b4fdc-e780-45e4-80fb-8662f0df9de3.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmp94ch8nif/job_working_directory/000/56/outputs/dataset_d9f62870-ba76-4a4d-884e-cfecab515c21.dat'

Exit Code:

```
127
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.65 sec
* Entering FMI_search
init ticks = 13114870874
ref seq len = 275747614
binary seq ticks = 5681283856
build suffix-array ticks = 100589467818
pos: 34468452, ref_seq_len__: 34468451
build fm-index ticks = 21257192819
Total time taken: 58.2091
/tmp/tmp94ch8nif/job_working_directory/000/56/tool_script.sh: line 23: samtools: command not found
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fasta
* Entering FMI_search
* Index file found. Loading index from localref.fasta.bwt.2bit.64
* Reference seq len for bi-index = 275747615
* sentinel-index: 224703773
* Count:
0,	1
1,	80527259
2,	137873808
3,	195220357
4,	275747615

* Reading other elements of the index from files localref.fasta
* Index prefix: localref.fasta
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fasta.0123
* Reference genome size: 275747614 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 137873807, n: 68494
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (2021, 3042, 5240)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 11678)
[0000][PE] mean and std.dev: (3782.74, 2698.62)
[0000][PE] low and high boundaries for proper pairs: (1, 14897)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (151, 230, 368)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 802)
[0000][PE] mean and std.dev: (244.21, 150.93)
[0000][PE] low and high boundaries for proper pairs: (1, 1019)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (2708, 3331, 6114)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 12926)
[0000][PE] mean and std.dev: (4077.29, 2787.30)
[0000][PE] low and high boundaries for proper pairs: (1, 16332)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (1608, 2936, 5772)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 14100)
[0000][PE] mean and std.dev: (3700.00, 2741.58)
[0000][PE] low and high boundaries for proper pairs: (1, 18264)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 68494 reads in 81.560 CPU sec, 81.608 real sec
[0000] Calling mem_process_seqs.., task: 1

Standard Output:

ref_seq_len = 275747614
count = 0, 80527258, 137873807, 195220356, 275747614
BWT[224703773] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 4308556

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a90b2d11f08a576045bd086594"`
analysis_type	{"__current_case__": 4, "algorithmic_options": {"D": "0.5", "P": true, "S": true, "W": "0", "__current_case__": 0, "algorithmic_options_selector": "set", "c": "500", "d": "100", "e": false, "k": "19", "m": "50", "r": "1.5", "w": "100", "y": "20"}, "analysis_type_selector": "full", "io_options": {"C": false, "K": null, "M": false, "T": "20", "V": false, "Y": false, "__current_case__": 0, "a": true, "five": false, "h": "5", "io_options_selector": "set", "q": false}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 21, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": null}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 54, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a90b2d11f08a576045bd086594"`
bed_file	`None`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
headerbam	`None`
idpg	`false`
idrg	`false`
region	`None`
seed	`"1"`

Step 17: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp94ch8nif/files/a/d/3/dataset_ad381e9f-6e2a-49de-b7d3-e9e0e088c622.dat' --out-coord g   --tabular > '/tmp/tmp94ch8nif/job_working_directory/000/58/outputs/dataset_31de9602-8f42-4bc4-aaf8-c5b537972b0f.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a60b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 1, "out_coord": "g", "selector": "coordinates"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

seqtk telo -m 'CCCTAA' -p '1' -d '2000' -s '300'  '/tmp/tmp94ch8nif/files/a/d/3/dataset_ad381e9f-6e2a-49de-b7d3-e9e0e088c622.dat' > '/tmp/tmp94ch8nif/job_working_directory/000/59/outputs/dataset_32b6643b-fdb7-4109-bec8-3ed3a7ecb4bf.dat'

Exit Code:

```
0
```

Standard Error:

```
0	137873807
```

Traceback:

Job Parameters:

Job parameter	Parameter value
P	`false`
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a60b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
d	`"2000"`
dbkey	`"?"`
m	`"CCCTAA"`
p	`"1"`
s	`"300"`

Step 19: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmp94ch8nif/files/a/d/3/dataset_ad381e9f-6e2a-49de-b7d3-e9e0e088c622.dat' reference.fa && minimap2 -x map-hifi    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmp94ch8nif/files/1/d/c/dataset_1dcb7377-156e-420e-ad94-e73047a76ea8.dat' -a | samtools view --no-PG -hT reference.fa | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O BAM -o '/tmp/tmp94ch8nif/job_working_directory/000/60/outputs/dataset_88399275-d760-4d15-acf5-3848322acef5.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::4.470*0.77] collected minimizers
[M::mm_idx_gen::5.825*0.81] sorted minimizers
[M::main::5.826*0.81] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::5.956*0.81] mid_occ = 113
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 1
[M::mm_idx_stat::6.056*0.82] distinct minimizers: 11276538 (95.62% are singletons); average occurrences: 1.229; average spacing: 9.951; total length: 137873807
[M::worker_pipeline::143.520*0.98] mapped 5426 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x map-hifi --q-occ-frac 0.01 -t 1 -a reference.fa /tmp/tmp94ch8nif/files/1/d/c/dataset_1dcb7377-156e-420e-ad94-e73047a76ea8.dat
[M::main] Real time: 143.535 sec; CPU: 140.513 sec; Peak RSS: 1.257 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a60b2d11f08a576045bd086594"`
alignment_options	`{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "map-hifi", "fastq_input1": {"values": [{"id": 50, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "BAM"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 54, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a60b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`"0"`
sorting	`{"__current_case__": 1, "sortby": "length", "sortorder": "descend"}`

Step 3: Haplotype 2:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int  --file '/tmp/tmp94ch8nif/job_working_directory/000/62/configs/tmpg6_hv1n3' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp94ch8nif/files/3/1/d/dataset_31de9602-8f42-4bc4-aaf8-c5b537972b0f.dat' '/tmp/tmp94ch8nif/job_working_directory/000/62/outputs/dataset_c9a4bd44-f832-4a87-8f68-5e861cf89113.dat'

Exit Code:

```
0
```

Standard Output:

abs(int(c3)-int(c2))
Computing 1 new columns with instructions ['abs(int(c3)-int(c2));;']
Computed new column values for 100.00% of 8 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a60b2d11f08a576045bd086594"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "abs(int(c3)-int(c2))"}], "header_lines_select": "no"}`

Step 22: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp94ch8nif/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp94ch8nif/files/3/2/b/dataset_32b6643b-fdb7-4109-bec8-3ed3a7ecb4bf.dat' 'c1,c2,c3' T '/tmp/tmp94ch8nif/job_working_directory/000/63/outputs/dataset_6f4d8408-c90c-4538-b820-220c36659c15.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"e2dc92a60b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1,c2,c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp94ch8nif/files/8/8/3/dataset_88399275-d760-4d15-acf5-3848322acef5.dat' one.bam && ln -s '/tmp/tmp94ch8nif/files/_metadata_files/1/b/4/metadata_1b4ae637-1394-4169-94fc-91813f3e1b04.dat' one.bam.bai &&  bamCoverage --numberOfProcessors "${GALAXY_SLOTS:-4}"  --bam one.bam --outFileName '/tmp/tmp94ch8nif/job_working_directory/000/64/outputs/dataset_c9f4f5ee-d298-40a3-8d96-673b8dc3a639.dat' --outFileFormat 'bigwig'  --binSize 100

Exit Code:

```
0
```

Standard Error:

bamFilesList: ['one.bam']
binLength: 100
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 100
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a60b2d11f08a576045bd086594"`
advancedOpt	`{"__current_case__": 0, "showAdvancedOpt": "no"}`
binSize	`"100"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exactScaling	`false`
outFileFormat	`"bigwig"`
region	`""`
scaling	`{"__current_case__": 3, "type": "no"}`

Step 24: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types  --file '/tmp/tmp94ch8nif/job_working_directory/000/65/configs/tmp6d21jbrj' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp94ch8nif/files/6/f/4/dataset_6f4d8408-c90c-4538-b820-220c36659c15.dat' '/tmp/tmp94ch8nif/job_working_directory/000/65/outputs/dataset_8dcd5910-6423-4b52-a222-379d87353d5c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a60b2d11f08a576045bd086594"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "abs(int(c3)-int(c2))"}], "header_lines_select": "no"}`

Step 25: Add Coverage Track:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a60b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
name	`"coverage"`

Step 26: Test if telomere track is empty:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bedgraph"`
__workflow_invocation_uuid__	`"e2dc92a60b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 27: False if telomere track is empty:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e2dc92a60b2d11f08a576045bd086594"`
chromInfo	`"/tmp/tmp94ch8nif/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "", "mappings": [{"__index__": 0, "from": "", "to": "false"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "true", "on_unmapped": "default"}`

Step 28: Add telomere track:
- step_state: new
Step 29: Unlabelled step:
- step_state: new
Step 30: Add gaps track:
- step_state: new
Step 4: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 31: Unlabelled step:
- step_state: new
Step 32: Unlabelled step:
- step_state: new
Step 5: First Haplotype suffix:
- step_state: scheduled
Step 6: Second Haplotype suffix:
- step_state: scheduled
Step 7: Hi-C reads:
- step_state: scheduled
Step 8: Do you want to trim the Hi-C data?:
- step_state: scheduled
Step 9: Telomere repeat to suit species:
- step_state: scheduled
Step 10: PacBio reads:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation f44384aa1da712c8 is [failed]. Failed to run workflow, at least one job is in [paused] state.
- history_id
  - ccf04a673afd229c
- history_state
  - paused
- invocation_id
  - f44384aa1da712c8
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': None, 'hda_id': '35e1bbbab2d37aa0', 'reason': 'dataset_failed', 'workflow_step_id': 27}]
- workflow_id
  - 5c0594841f9dcc30

github-actions · 2025-03-27T17:40:13Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	2
Passed	0
Error	2
Failure	0
Skipped	0

Errored Tests

❌ hi-c-map-for-assembly-manual-curation.ga_0

Execution Problem:

Final state of invocation 426c98cdc83d7e58 is [failed]. Failed to run workflow, at least one job is in [paused] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 28 requires a dataset, but dataset entered a failed state.

Steps

Step 1: Haplotype 1:
- step_state: scheduled
Step 2: Will you use a second haplotype?:
- step_state: scheduled

Step 11: Hap2 not provided:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53c0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 3, "input_param": false, "mappings": [{"__index__": 0, "from": false, "to": "true"}, {"__index__": 1, "from": true, "to": "false"}], "type": "boolean"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "false", "on_unmapped": "default"}`

Step 12: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Hap1:
- step_state: scheduled
Step 2: Hap2:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53d0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 10, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 2, "src": "hda"}]}}]}}`

Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53d0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 12, "src": "hda"}]}}]`

Step 3: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 4: Hap1 suffix:
- step_state: scheduled
Step 5: Hap2 suffix:
- step_state: scheduled

Step 6: Expression for hap1 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53d0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 7: Expression for hap2 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53d0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H2", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 8: add hap1 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53d0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null}]`

Step 9: add hap2 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53d0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null}]`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53d0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 9, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 1, "src": "hda"}]}}]}}`

Step 13: concatenate HiFi:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpkp3ixf17/files/9/3/d/dataset_93d2fae1-7f12-43c2-a620-8edc84a5e9aa.dat' >> '/tmp/tmpkp3ixf17/job_working_directory/000/14/outputs/dataset_5e607b56-db95-44e4-be2b-43b2b4653fe7.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53c0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[]`

Step 14: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Hap1:
- step_state: scheduled
Step 2: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 3: Hap1 suffix:
- step_state: scheduled

Step 4: Expression for hap1 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53e0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 5: add hap1 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed -r --sandbox -e 's/>.+$/&.H1/g' '/tmp/tmpkp3ixf17/files/4/3/1/dataset_4318a073-31ad-46b7-aa34-8d07b97ede11.dat' > '/tmp/tmpkp3ixf17/job_working_directory/000/16/outputs/dataset_1a673082-9227-49d5-9725-d3fd3b2aafa2.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53e0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": "&.H1"}]`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53e0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 16, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 1, "src": "hda"}]}}]}}`

Step 15: Pick Assembly:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53c0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 13, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 17, "src": "hda"}]}}]}}`

Step 16: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Reference:
- step_state: scheduled
Step 2: Hi-C reads:
- step_state: scheduled
Step 3: Do you want to trim the Hi-C data?:
- step_state: scheduled

Step 4: Trim Hi-C reads 2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpkp3ixf17/files/6/5/4/dataset_6545ecab-df9d-4a0c-abd7-1140a62d9f69.dat' 'Hi-C reads_1.fq.gz' && ln -f -s '/tmp/tmpkp3ixf17/files/f/0/1/dataset_f01beb80-c6e6-4f81-bd8d-768f5090963b.dat' 'Hi-C reads_2.fq.gz' &&  cutadapt  -j=${GALAXY_SLOTS:-4}     --error-rate=0.1 --times=1 --overlap=3    --action=trim   --cut=5 -U 5       --minimum-length=1      -o 'out1.fq.gz' -p 'out2.fq.gz'  'Hi-C reads_1.fq.gz' 'Hi-C reads_2.fq.gz'  > report.txt

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53f0b3011f08a576045bdd71c8b"`
adapter_options	`{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"}`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}`
library	`{"__current_case__": 2, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired_collection"}`
other_trimming_options	`{"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}`
output_selector	`["report"]`
read_mod_options	`{"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53f0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 7, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 2, "src": "dce"}]}}]}}`

Job 2:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53f0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 8, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 3, "src": "dce"}]}}]}}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpkp3ixf17/files/1/a/6/dataset_1a673082-9227-49d5-9725-d3fd3b2aafa2.dat' 'localref.fasta' && bwa-mem2 index 'localref.fasta' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1   -k '19' -w '100' -d '100' -r '1.5' -y '20' -c '500' -D '0.5' -W '0' -m '50' -S -P    -T '20' -h '5' -a                      'localref.fasta' '/tmp/tmpkp3ixf17/files/d/4/1/dataset_d41d1393-b065-4360-ae8b-5413875feca6.dat' '/tmp/tmpkp3ixf17/files/2/8/e/dataset_28e14152-ff7c-4d3a-82d6-9b138838fbc3.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpkp3ixf17/job_working_directory/000/22/outputs/dataset_9479d8dc-aee0-4d0b-a017-e49e82bd3104.dat'

Exit Code:

```
127
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.60 sec
* Entering FMI_search
init ticks = 13443405854
ref seq len = 279307354
binary seq ticks = 5386094896
build suffix-array ticks = 88242136442
pos: 34913420, ref_seq_len__: 34913419
build fm-index ticks = 20970795659
Total time taken: 53.0134
/tmp/tmpkp3ixf17/job_working_directory/000/22/tool_script.sh: line 23: samtools: command not found
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fasta
* Entering FMI_search
* Index file found. Loading index from localref.fasta.bwt.2bit.64
* Reference seq len for bi-index = 279307355
* sentinel-index: 13446364
* Count:
0,	1
1,	84204314
2,	139653678
3,	195103042
4,	279307355

* Reading other elements of the index from files localref.fasta
* Index prefix: localref.fasta
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fasta.0123
* Reference genome size: 279307354 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 139653677, n: 68494
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (1649, 4140, 6027)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 14783)
[0000][PE] mean and std.dev: (4063.15, 2569.67)
[0000][PE] low and high boundaries for proper pairs: (1, 19161)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (157, 248, 382)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 832)
[0000][PE] mean and std.dev: (254.60, 148.66)
[0000][PE] low and high boundaries for proper pairs: (1, 1057)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (2814, 4404, 5708)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 11496)
[0000][PE] mean and std.dev: (4321.60, 2279.57)
[0000][PE] low and high boundaries for proper pairs: (1, 14390)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (1378, 2846, 5532)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 13840)
[0000][PE] mean and std.dev: (3534.90, 2567.86)
[0000][PE] low and high boundaries for proper pairs: (1, 17994)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 68494 reads in 93.442 CPU sec, 93.703 real sec

Standard Output:

ref_seq_len = 279307354
count = 0, 84204313, 139653677, 195103041, 279307354
BWT[13446364] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 4364177

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53f0b3011f08a576045bdd71c8b"`
analysis_type	{"__current_case__": 4, "algorithmic_options": {"D": "0.5", "P": true, "S": true, "W": "0", "__current_case__": 0, "algorithmic_options_selector": "set", "c": "500", "d": "100", "e": false, "k": "19", "m": "50", "r": "1.5", "w": "100", "y": "20"}, "analysis_type_selector": "full", "io_options": {"C": false, "K": null, "M": false, "T": "20", "V": false, "Y": false, "__current_case__": 0, "a": true, "five": false, "h": "5", "io_options_selector": "set", "q": false}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 9, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": null}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 18, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53f0b3011f08a576045bdd71c8b"`
bed_file	`None`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
headerbam	`None`
idpg	`false`
idrg	`false`
region	`None`
seed	`"1"`

Step 17: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpkp3ixf17/files/1/a/6/dataset_1a673082-9227-49d5-9725-d3fd3b2aafa2.dat' --out-coord g   --tabular > '/tmp/tmpkp3ixf17/job_working_directory/000/24/outputs/dataset_b3ac5b46-e92f-4422-8a54-f26e223298ad.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53c0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 1, "out_coord": "g", "selector": "coordinates"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

seqtk telo -m 'CCCTAA' -p '1' -d '2000' -s '300'  '/tmp/tmpkp3ixf17/files/1/a/6/dataset_1a673082-9227-49d5-9725-d3fd3b2aafa2.dat' > '/tmp/tmpkp3ixf17/job_working_directory/000/25/outputs/dataset_006a287f-de60-486b-b08b-acf15c23b6b1.dat'

Exit Code:

```
0
```

Standard Error:

```
11012	139653677
```

Traceback:

Job Parameters:

Job parameter	Parameter value
P	`false`
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53c0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
d	`"2000"`
dbkey	`"?"`
m	`"CCCTAA"`
p	`"1"`
s	`"300"`

Step 19: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpkp3ixf17/files/1/a/6/dataset_1a673082-9227-49d5-9725-d3fd3b2aafa2.dat' reference.fa && minimap2 -x map-hifi    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpkp3ixf17/files/5/e/6/dataset_5e607b56-db95-44e4-be2b-43b2b4653fe7.dat' -a | samtools view --no-PG -hT reference.fa | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O BAM -o '/tmp/tmpkp3ixf17/job_working_directory/000/26/outputs/dataset_c7be03cd-7de3-4a54-8959-efb87252b58a.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::4.515*0.77] collected minimizers
[M::mm_idx_gen::5.954*0.80] sorted minimizers
[M::main::5.954*0.80] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::6.082*0.81] mid_occ = 131
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 1
[M::mm_idx_stat::6.183*0.81] distinct minimizers: 11315845 (97.08% are singletons); average occurrences: 1.241; average spacing: 9.941; total length: 139653677
[M::worker_pipeline::146.477*0.98] mapped 5426 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x map-hifi --q-occ-frac 0.01 -t 1 -a reference.fa /tmp/tmpkp3ixf17/files/5/e/6/dataset_5e607b56-db95-44e4-be2b-43b2b4653fe7.dat
[M::main] Real time: 146.492 sec; CPU: 143.732 sec; Peak RSS: 1.376 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53c0b3011f08a576045bdd71c8b"`
alignment_options	`{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "map-hifi", "fastq_input1": {"values": [{"id": 14, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "BAM"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 18, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53c0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`"0"`
sorting	`{"__current_case__": 1, "sortby": "length", "sortorder": "descend"}`

Step 3: Haplotype 2:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int  --file '/tmp/tmpkp3ixf17/job_working_directory/000/28/configs/tmpa9l0hkk5' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpkp3ixf17/files/b/3/a/dataset_b3ac5b46-e92f-4422-8a54-f26e223298ad.dat' '/tmp/tmpkp3ixf17/job_working_directory/000/28/outputs/dataset_9d66fc6f-055f-4132-ad25-de220e4080ba.dat'

Exit Code:

```
0
```

Standard Output:

abs(int(c3)-int(c2))
Computing 1 new columns with instructions ['abs(int(c3)-int(c2));;']
Computed new column values for 100.00% of 4 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53c0b3011f08a576045bdd71c8b"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "abs(int(c3)-int(c2))"}], "header_lines_select": "no"}`

Step 22: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpkp3ixf17/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpkp3ixf17/files/0/0/6/dataset_006a287f-de60-486b-b08b-acf15c23b6b1.dat' 'c1,c2,c3' T '/tmp/tmpkp3ixf17/job_working_directory/000/29/outputs/dataset_3c0b3f62-2684-4179-803b-fc0140bf1404.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"ef47f53c0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1,c2,c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpkp3ixf17/files/c/7/b/dataset_c7be03cd-7de3-4a54-8959-efb87252b58a.dat' one.bam && ln -s '/tmp/tmpkp3ixf17/files/_metadata_files/5/2/7/metadata_527aa75f-5481-4ef0-b410-72487b7b9009.dat' one.bam.bai &&  bamCoverage --numberOfProcessors "${GALAXY_SLOTS:-4}"  --bam one.bam --outFileName '/tmp/tmpkp3ixf17/job_working_directory/000/30/outputs/dataset_849824e7-db94-4400-aeff-c3b0e1af3c47.dat' --outFileFormat 'bigwig'  --binSize 100

Exit Code:

```
0
```

Standard Error:

bamFilesList: ['one.bam']
binLength: 100
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 100
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53c0b3011f08a576045bdd71c8b"`
advancedOpt	`{"__current_case__": 0, "showAdvancedOpt": "no"}`
binSize	`"100"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exactScaling	`false`
outFileFormat	`"bigwig"`
region	`""`
scaling	`{"__current_case__": 3, "type": "no"}`

Step 24: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int  --file '/tmp/tmpkp3ixf17/job_working_directory/000/31/configs/tmpna_v2lbp' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpkp3ixf17/files/3/c/0/dataset_3c0b3f62-2684-4179-803b-fc0140bf1404.dat' '/tmp/tmpkp3ixf17/job_working_directory/000/31/outputs/dataset_04753e13-318d-45f4-94fd-a08e72bb6f29.dat'

Exit Code:

```
0
```

Standard Output:

abs(int(c3)-int(c2))
Computing 1 new columns with instructions ['abs(int(c3)-int(c2));;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53c0b3011f08a576045bdd71c8b"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "abs(int(c3)-int(c2))"}], "header_lines_select": "no"}`

Step 25: Add Coverage Track:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53c0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
name	`"coverage"`

Step 26: Test if telomere track is empty:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bedgraph"`
__workflow_invocation_uuid__	`"ef47f53c0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 27: False if telomere track is empty:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef47f53c0b3011f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "scaffold_10.H1\t0\t11012\t11012", "mappings": [{"__index__": 0, "from": "", "to": "false"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "true", "on_unmapped": "default"}`

Step 28: Add telomere track:
- step_state: new
Step 29: Unlabelled step:
- step_state: new
Step 30: Add gaps track:
- step_state: new
Step 4: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 31: Unlabelled step:
- step_state: new
Step 32: Unlabelled step:
- step_state: new
Step 5: First Haplotype suffix:
- step_state: scheduled
Step 6: Second Haplotype suffix:
- step_state: scheduled
Step 7: Hi-C reads:
- step_state: scheduled
Step 8: Do you want to trim the Hi-C data?:
- step_state: scheduled
Step 9: Telomere repeat to suit species:
- step_state: scheduled
Step 10: PacBio reads:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation 426c98cdc83d7e58 is [failed]. Failed to run workflow, at least one job is in [paused] state.
- history_id
  - 426c98cdc83d7e58
- history_state
  - paused
- invocation_id
  - 426c98cdc83d7e58
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': None, 'hda_id': '27149de321e48428', 'reason': 'dataset_failed', 'workflow_step_id': 27}]
- workflow_id
  - a7fef001aff9b2a8

❌ hi-c-map-for-assembly-manual-curation.ga_1

Execution Problem:

Final state of invocation fb7f479106dc95b8 is [failed]. Failed to run workflow, at least one job is in [paused] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 28 requires a dataset, but dataset entered a failed state.

Steps

Step 1: Haplotype 1:
- step_state: scheduled
Step 2: Will you use a second haplotype?:
- step_state: scheduled

Step 11: Hap2 not provided:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d00b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 3, "input_param": false, "mappings": [{"__index__": 0, "from": false, "to": "true"}, {"__index__": 1, "from": true, "to": "false"}], "type": "boolean"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "false", "on_unmapped": "default"}`

Step 12: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Hap1:
- step_state: scheduled
Step 2: Hap2:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d10b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 46, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 38, "src": "hda"}]}}]}}`

Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d10b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 48, "src": "hda"}]}}]`

Step 3: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 4: Hap1 suffix:
- step_state: scheduled
Step 5: Hap2 suffix:
- step_state: scheduled

Step 6: Expression for hap1 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d10b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 7: Expression for hap2 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d10b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H2", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 8: add hap1 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d10b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null}]`

Step 9: add hap2 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d10b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null}]`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d10b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 45, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 37, "src": "hda"}]}}]}}`

Step 13: concatenate HiFi:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpkp3ixf17/files/8/9/c/dataset_89cb1f46-316a-4da1-af87-e7e37384ce6e.dat' >> '/tmp/tmpkp3ixf17/job_working_directory/000/48/outputs/dataset_2b0c450e-61ee-411c-ad19-acfd711002f5.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d00b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[]`

Step 14: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Hap1:
- step_state: scheduled
Step 2: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 3: Hap1 suffix:
- step_state: scheduled

Step 4: Expression for hap1 suffixing:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d20b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 5: add hap1 suffix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed -r --sandbox -e 's/>.+$/&.H1/g' '/tmp/tmpkp3ixf17/files/6/b/2/dataset_6b24f0a0-f773-463f-b1f7-3eb8a96cbed2.dat' > '/tmp/tmpkp3ixf17/job_working_directory/000/50/outputs/dataset_34cad202-e811-43a9-97f1-dd2a90a3fcd2.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d20b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": "&.H1"}]`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d20b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 52, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 37, "src": "hda"}]}}]}}`

Step 15: Pick Assembly:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d00b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 49, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 53, "src": "hda"}]}}]}}`

Step 16: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Reference:
- step_state: scheduled
Step 2: Hi-C reads:
- step_state: scheduled
Step 3: Do you want to trim the Hi-C data?:
- step_state: scheduled

Step 4: Trim Hi-C reads 2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpkp3ixf17/files/9/3/c/dataset_93caf481-bec4-4f0b-b4e5-7e9878ef7c9a.dat' 'Hi-C reads_1.fq.gz' && ln -f -s '/tmp/tmpkp3ixf17/files/0/a/9/dataset_0a9a4408-75bb-4f60-9a68-96c37ba70ddc.dat' 'Hi-C reads_2.fq.gz' &&  cutadapt  -j=${GALAXY_SLOTS:-4}     --error-rate=0.1 --times=1 --overlap=3    --action=trim   --cut=5 -U 5       --minimum-length=1      -o 'out1.fq.gz' -p 'out2.fq.gz'  'Hi-C reads_1.fq.gz' 'Hi-C reads_2.fq.gz'  > report.txt

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d30b3111f08a576045bdd71c8b"`
adapter_options	`{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"}`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}`
library	`{"__current_case__": 2, "input_1": {"values": [{"id": 13, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired_collection"}`
other_trimming_options	`{"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}`
output_selector	`["report"]`
read_mod_options	`{"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d30b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 19, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 14, "src": "dce"}]}}]}}`

Job 2:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d30b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 20, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 15, "src": "dce"}]}}]}}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpkp3ixf17/files/3/4/c/dataset_34cad202-e811-43a9-97f1-dd2a90a3fcd2.dat' 'localref.fasta' && bwa-mem2 index 'localref.fasta' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1   -k '19' -w '100' -d '100' -r '1.5' -y '20' -c '500' -D '0.5' -W '0' -m '50' -S -P    -T '20' -h '5' -a                      'localref.fasta' '/tmp/tmpkp3ixf17/files/8/a/9/dataset_8a9cfcc2-5f71-4269-bdfa-fddf0b5c2075.dat' '/tmp/tmpkp3ixf17/files/3/a/c/dataset_3ac6184b-1061-411a-9979-bddcaaaef6a0.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpkp3ixf17/job_working_directory/000/56/outputs/dataset_e4b427c0-2f03-440b-9ed9-474a56ad0e6b.dat'

Exit Code:

```
127
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.64 sec
* Entering FMI_search
init ticks = 13841978616
ref seq len = 275747614
binary seq ticks = 5425065674
build suffix-array ticks = 91645903764
pos: 34468452, ref_seq_len__: 34468451
build fm-index ticks = 22116170997
Total time taken: 55.1316
/tmp/tmpkp3ixf17/job_working_directory/000/56/tool_script.sh: line 23: samtools: command not found
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fasta
* Entering FMI_search
* Index file found. Loading index from localref.fasta.bwt.2bit.64
* Reference seq len for bi-index = 275747615
* sentinel-index: 224703773
* Count:
0,	1
1,	80527259
2,	137873808
3,	195220357
4,	275747615

* Reading other elements of the index from files localref.fasta
* Index prefix: localref.fasta
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fasta.0123
* Reference genome size: 275747614 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000124, nseq: 68494
	[0000][ M::kt_pipeline] read 68494 sequences (10000124 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 137873807, n: 68494
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (2021, 3042, 5240)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 11678)
[0000][PE] mean and std.dev: (3782.74, 2698.62)
[0000][PE] low and high boundaries for proper pairs: (1, 14897)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (151, 230, 368)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 802)
[0000][PE] mean and std.dev: (244.21, 150.93)
[0000][PE] low and high boundaries for proper pairs: (1, 1019)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (2708, 3331, 6114)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 12926)
[0000][PE] mean and std.dev: (4077.29, 2787.30)
[0000][PE] low and high boundaries for proper pairs: (1, 16332)
[0000][PE] analyzing insert size distribution for orientation RR...
[0000][PE] (25, 50, 75) percentile: (1608, 2936, 5772)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 14100)
[0000][PE] mean and std.dev: (3700.00, 2741.58)
[0000][PE] low and high boundaries for proper pairs: (1, 18264)
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 68494 reads in 82.758 CPU sec, 83.273 real sec

Standard Output:

ref_seq_len = 275747614
count = 0, 80527258, 137873807, 195220356, 275747614
BWT[224703773] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 4308556

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d30b3111f08a576045bdd71c8b"`
analysis_type	{"__current_case__": 4, "algorithmic_options": {"D": "0.5", "P": true, "S": true, "W": "0", "__current_case__": 0, "algorithmic_options_selector": "set", "c": "500", "d": "100", "e": false, "k": "19", "m": "50", "r": "1.5", "w": "100", "y": "20"}, "analysis_type_selector": "full", "io_options": {"C": false, "K": null, "M": false, "T": "20", "V": false, "Y": false, "__current_case__": 0, "a": true, "five": false, "h": "5", "io_options_selector": "set", "q": false}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 21, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": null}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 54, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d30b3111f08a576045bdd71c8b"`
bed_file	`None`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
headerbam	`None`
idpg	`false`
idrg	`false`
region	`None`
seed	`"1"`

Step 17: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpkp3ixf17/files/3/4/c/dataset_34cad202-e811-43a9-97f1-dd2a90a3fcd2.dat' --out-coord g   --tabular > '/tmp/tmpkp3ixf17/job_working_directory/000/58/outputs/dataset_aa60f11b-fb46-4cc2-8d6e-a73922745bff.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d00b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 1, "out_coord": "g", "selector": "coordinates"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

seqtk telo -m 'CCCTAA' -p '1' -d '2000' -s '300'  '/tmp/tmpkp3ixf17/files/3/4/c/dataset_34cad202-e811-43a9-97f1-dd2a90a3fcd2.dat' > '/tmp/tmpkp3ixf17/job_working_directory/000/59/outputs/dataset_b7b75e32-b416-4512-9b7e-4ec47b4eaad9.dat'

Exit Code:

```
0
```

Standard Error:

```
0	137873807
```

Traceback:

Job Parameters:

Job parameter	Parameter value
P	`false`
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d00b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
d	`"2000"`
dbkey	`"?"`
m	`"CCCTAA"`
p	`"1"`
s	`"300"`

Step 19: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpkp3ixf17/files/3/4/c/dataset_34cad202-e811-43a9-97f1-dd2a90a3fcd2.dat' reference.fa && minimap2 -x map-hifi    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpkp3ixf17/files/2/b/0/dataset_2b0c450e-61ee-411c-ad19-acfd711002f5.dat' -a | samtools view --no-PG -hT reference.fa | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O BAM -o '/tmp/tmpkp3ixf17/job_working_directory/000/60/outputs/dataset_87fd14b6-cd94-4287-88bd-0708e477e07f.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::4.540*0.77] collected minimizers
[M::mm_idx_gen::5.865*0.80] sorted minimizers
[M::main::5.865*0.80] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::5.997*0.81] mid_occ = 113
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 1
[M::mm_idx_stat::6.095*0.81] distinct minimizers: 11276538 (95.62% are singletons); average occurrences: 1.229; average spacing: 9.951; total length: 137873807
[M::worker_pipeline::144.110*0.98] mapped 5426 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x map-hifi --q-occ-frac 0.01 -t 1 -a reference.fa /tmp/tmpkp3ixf17/files/2/b/0/dataset_2b0c450e-61ee-411c-ad19-acfd711002f5.dat
[M::main] Real time: 144.186 sec; CPU: 141.192 sec; Peak RSS: 1.257 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d00b3111f08a576045bdd71c8b"`
alignment_options	`{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "map-hifi", "fastq_input1": {"values": [{"id": 50, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "BAM"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 54, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d00b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`"0"`
sorting	`{"__current_case__": 1, "sortby": "length", "sortorder": "descend"}`

Step 3: Haplotype 2:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int  --file '/tmp/tmpkp3ixf17/job_working_directory/000/62/configs/tmpsydjm92o' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpkp3ixf17/files/a/a/6/dataset_aa60f11b-fb46-4cc2-8d6e-a73922745bff.dat' '/tmp/tmpkp3ixf17/job_working_directory/000/62/outputs/dataset_d9eb1354-e3d2-4ba9-8e82-49879e1c0900.dat'

Exit Code:

```
0
```

Standard Output:

abs(int(c3)-int(c2))
Computing 1 new columns with instructions ['abs(int(c3)-int(c2));;']
Computed new column values for 100.00% of 8 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d00b3111f08a576045bdd71c8b"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "abs(int(c3)-int(c2))"}], "header_lines_select": "no"}`

Step 22: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpkp3ixf17/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpkp3ixf17/files/b/7/b/dataset_b7b75e32-b416-4512-9b7e-4ec47b4eaad9.dat' 'c1,c2,c3' T '/tmp/tmpkp3ixf17/job_working_directory/000/63/outputs/dataset_dbe7ecfd-e155-44f9-b183-7bbd58d9f890.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"d1e134d00b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1,c2,c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpkp3ixf17/files/8/7/f/dataset_87fd14b6-cd94-4287-88bd-0708e477e07f.dat' one.bam && ln -s '/tmp/tmpkp3ixf17/files/_metadata_files/b/0/f/metadata_b0fe352b-dbb4-423c-ae33-2def3e812c05.dat' one.bam.bai &&  bamCoverage --numberOfProcessors "${GALAXY_SLOTS:-4}"  --bam one.bam --outFileName '/tmp/tmpkp3ixf17/job_working_directory/000/64/outputs/dataset_de145cf4-f094-446e-8d7a-b18cf108f9d1.dat' --outFileFormat 'bigwig'  --binSize 100

Exit Code:

```
0
```

Standard Error:

bamFilesList: ['one.bam']
binLength: 100
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 100
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d00b3111f08a576045bdd71c8b"`
advancedOpt	`{"__current_case__": 0, "showAdvancedOpt": "no"}`
binSize	`"100"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exactScaling	`false`
outFileFormat	`"bigwig"`
region	`""`
scaling	`{"__current_case__": 3, "type": "no"}`

Step 24: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types  --file '/tmp/tmpkp3ixf17/job_working_directory/000/65/configs/tmp2s7jutw3' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpkp3ixf17/files/d/b/e/dataset_dbe7ecfd-e155-44f9-b183-7bbd58d9f890.dat' '/tmp/tmpkp3ixf17/job_working_directory/000/65/outputs/dataset_0ab8c90b-81c0-48de-adfe-dc4c553a8a39.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d00b3111f08a576045bdd71c8b"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "abs(int(c3)-int(c2))"}], "header_lines_select": "no"}`

Step 25: Add Coverage Track:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d00b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
name	`"coverage"`

Step 26: Test if telomere track is empty:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bedgraph"`
__workflow_invocation_uuid__	`"d1e134d00b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 27: False if telomere track is empty:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d1e134d00b3111f08a576045bdd71c8b"`
chromInfo	`"/tmp/tmpkp3ixf17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "", "mappings": [{"__index__": 0, "from": "", "to": "false"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "true", "on_unmapped": "default"}`

Step 28: Add telomere track:
- step_state: new
Step 29: Unlabelled step:
- step_state: new
Step 30: Add gaps track:
- step_state: new
Step 4: Do you want to add suffixes to the scaffold names?:
- step_state: scheduled
Step 31: Unlabelled step:
- step_state: new
Step 32: Unlabelled step:
- step_state: new
Step 5: First Haplotype suffix:
- step_state: scheduled
Step 6: Second Haplotype suffix:
- step_state: scheduled
Step 7: Hi-C reads:
- step_state: scheduled
Step 8: Do you want to trim the Hi-C data?:
- step_state: scheduled
Step 9: Telomere repeat to suit species:
- step_state: scheduled
Step 10: PacBio reads:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation fb7f479106dc95b8 is [failed]. Failed to run workflow, at least one job is in [paused] state.
- history_id
  - 938e59a159cb21e6
- history_state
  - paused
- invocation_id
  - fb7f479106dc95b8
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': None, 'hda_id': '14027bef5e10794d', 'reason': 'dataset_failed', 'workflow_step_id': 27}]
- workflow_id
  - a7fef001aff9b2a8

Smeds marked this pull request as draft October 28, 2024 14:03

Smeds force-pushed the update-pretext branch from a28b907 to 7d6c4b1 Compare October 28, 2024 14:40

Smeds changed the title ~~feat: updated version of pretext workflow developed by Delphine that …~~ feat: updated version of pretext workflow developed by Delphine that takes HiFi and HiC as input. Oct 28, 2024

Smeds mentioned this pull request Oct 28, 2024

A simplified Pretext workflow specs galaxyproject/VGPWorkflows#3

Open

feat: updated version of pretext workflow developed by Delphine that …

35d936d

…takes HiFi and HiC as input.

Smeds force-pushed the update-pretext branch from 7d6c4b1 to 35d936d Compare October 30, 2024 14:41

Delphine-L added 6 commits November 5, 2024 10:50

Fix connections between optional parameters and mandatory inputs,...

5ce525d

... and modify the replacement expressions so that users don't have to add the &. to the suffixes

add license, authors, and diverse labels and tags

4e20b69

change telomere track height to correspond to the size of the telomeres

b666689

Add README and CHANGELOG

42a7240

update pretextgraph to fix track display issue, and add parameters to…

e6c4591

… go around the fasta implicit conversion problem

add new parameter to the README

6cc5b23

Delphine-L added 4 commits November 20, 2024 11:29

Remove explicit data conversion, it got fixed in galaxy

851f762

Rename folder

0cf305a

add release number and remove parameter from the READMA

2a0c7bb

expose output to be used for Jbrowse2 workflow

4de0fbc

Delphine-L mentioned this pull request Nov 20, 2024

add pre-curation jbrowse generation workflow complementary to the PretextMap generation #612

Draft

Delphine-L added 2 commits November 25, 2024 21:33

add tests

3cf74ab

replace dockstore file after cleaning my local repository

95bd01c

Delphine-L marked this pull request as ready for review November 26, 2024 03:37

mvdbeek reviewed Nov 26, 2024

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mvdbeek reviewed Nov 26, 2024

View reviewed changes

Delphine-L added 3 commits November 26, 2024 08:55

add Marius comments

2779664

rename folder

d4ba83e

Make more clear that HiC reads need to be in collections

ce121eb

Delphine-L added 2 commits December 16, 2024 15:54

update dockstore file

3264afa

make hap2 optionnal, correct input names in test

e01dabe

Delphine-L added autoupdate 'artefact' Autoupdate generated a new version but does not worth releasing it and removed autoupdate 'artefact' Autoupdate generated a new version but does not worth releasing it labels Feb 4, 2025

Delphine-L added 3 commits February 12, 2025 13:38

replace filter and merge by bwamem2 sp option and use smaller data fo…

04217d4

…r testing

skip telomere track if no telomeres are found and smaller test data

c7b78b5

correct missing input in tests

62aaceb

add second test

9587f82

remove unnecessary name sorting

fff0f60

mvdbeek approved these changes Mar 19, 2025

View reviewed changes

Delphine-L added 2 commits March 27, 2025 11:51

Update README.md

c86520d

add Beta to the workflow name

2d6620b

Delphine-L enabled auto-merge March 27, 2025 15:55

mvdbeek reviewed Mar 27, 2025

View reviewed changes

...ly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga Outdated Show resolved Hide resolved

mvdbeek disabled auto-merge March 27, 2025 16:02

mvdbeek reviewed Mar 27, 2025

View reviewed changes

...ly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga Outdated Show resolved Hide resolved

mvdbeek reviewed Mar 27, 2025

View reviewed changes

...ly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga Outdated Show resolved Hide resolved

Delphine-L and others added 2 commits March 27, 2025 12:09

Update workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual…

7d241b4

…-curation/hi-c-map-for-assembly-manual-curation.ga Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

Update workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual…

9ecfd15

…-curation/hi-c-map-for-assembly-manual-curation.ga Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

mvdbeek enabled auto-merge March 27, 2025 16:11

Delphine-L added 2 commits March 27, 2025 12:28

Update CHANGELOG.md with beta version number

65de146

replace the tool for merging alignments with samtool merge

b7c176f

update bwa-mem2

7c5c96b

mvdbeek merged commit f7a004d into galaxyproject:main Mar 28, 2025
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