quantms with Mac

[eemiljohansson]

ERROR ~ Error executing process > 'NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv)'

Caused by:
Process NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv) terminated with an error exit status (1)

Command executed:

check_samplesheet.py "sdrf.tsv" true --CHECK_MS 2>&1 | tee input_check.log

cat <<-END_VERSIONS > versions.yml
"NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK":
sdrf-pipelines: $(parse_sdrf --version 2>&1 | awk -F ' ' '{print $2}')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
Unable to find image 'quay.io/biocontainers/sdrf-pipelines:0.0.24--pyhdfd78af_0' locally
2024/08/15 16:38:14 must use ASL logging (which requires CGO) if running as root
0.0.24--pyhdfd78af_0: Pulling from biocontainers/sdrf-pipelines
f03c707b3130: Pulling fs layer
5e3ed8cd934c: Pulling fs layer
c8581de4638a: Pulling fs layer
24cbf6bc5826: Pulling fs layer
bd9ddc54bea9: Pulling fs layer
3d4871c716e4: Pulling fs layer
bd9ddc54bea9: Waiting
24cbf6bc5826: Waiting
3d4871c716e4: Waiting
c8581de4638a: Verifying Checksum
c8581de4638a: Download complete
24cbf6bc5826: Download complete
bd9ddc54bea9: Download complete
f03c707b3130: Verifying Checksum
f03c707b3130: Download complete
5e3ed8cd934c: Verifying Checksum
5e3ed8cd934c: Download complete
f03c707b3130: Pull complete
5e3ed8cd934c: Pull complete
c8581de4638a: Pull complete
24cbf6bc5826: Pull complete
bd9ddc54bea9: Pull complete
3d4871c716e4: Verifying Checksum
3d4871c716e4: Download complete
3d4871c716e4: Pull complete
Digest: sha256:4338b0aa445b76b203567d6cb737971bcefc61829369344b8e91af09046e3ddc
Status: Downloaded newer image for quay.io/biocontainers/sdrf-pipelines:0.0.24--pyhdfd78af_0
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
touch: cannot touch '.command.trace': Permission denied

Work dir:
/Users/emiljohansson/CB2110/lab1/work/6f/92138a71361381a29ac2c9ff7ab0dc

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details

[eemiljohansson]

Tried out the same pipeline in VScode and got a similar error:

(R-cb2110) emiljohansson@emiljmbp lab1 % sudo nextflow run bigbio/quantms -r master --input 'sdrf.tsv' --outdir 'results' --database 'uniprotkb_Human_AND_reviewed_true_2024_08_15.fasta' -profile docker --root_folder ~/emiljohansson/R/CB2110/lab1 --local_input_type raw --add_decoys true --max_memory 8GB --max_cpus 4 --platform linux/amd64
Password:

N E X T F L O W ~ version 24.07.0-edge

Launching https://github.com/bigbio/quantms [crazy_tesla] DSL2 - revision: 3586089523 [master]

WARN: The following invalid input values have been detected:

• --platform: linux/amd64

---

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,'
nf-core/quantms v1.2.0-g3586089

Core Nextflow options
revision : master
runName : crazy_tesla
containerEngine : docker
launchDir : /Users/emiljohansson/R/CB2110/lab1
workDir : /Users/emiljohansson/R/CB2110/lab1/work
projectDir : /Users/emiljohansson/.nextflow/assets/bigbio/quantms
userName : root
profile : docker
configFiles :

Input/output options
input : sdrf.tsv
outdir : results
root_folder : /Users/emiljohansson/emiljohansson/R/CB2110/lab1
local_input_type : raw
acquisition_method : null

Protein database
database : uniprotkb_Human_AND_reviewed_true_2024_08_15.fasta
add_decoys : true

Database search
instrument : null

Modification localization
luciphor_debug : 0

PSM re-scoring (general)
run_fdr_cutoff : 0.10

PSM re-scoring (Percolator)
description_correct_features : 0

Consensus ID
consensusid_considered_top_hits: 0
min_consensus_support : 0

Isobaric analyzer
select_activation : HCD

Protein Quantification (LFQ)
feature_with_id_min_score : 0.10
feature_without_id_min_score : 0.75
lfq_intensity_threshold : 1000

DIA-NN
scan_window : 8

Statistical post-processing
contrasts : pairwise

Quality control
enable_pmultiqc : true
pmultiqc_idxml_skip : true

Max job request options
max_cpus : 4
max_memory : 8GB
max_time : 10d

!! Only displaying parameters that differ from the pipeline defaults !!

If you use nf-core/quantms for your analysis please cite:

• The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

• Software dependencies
  https://github.com/nf-core/quantms/blob/master/CITATIONS.md

executor > local (1)
[87/a4b657] NFC…QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv) | 0 of 1
[- ] NFC…QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRFPARSING -
executor > local (1)
[87/a4b657] NFC…QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv) | 0 of 1
[- ] NFC…QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRFPARSING -
[- ] NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:DECOMPRESS -
[- ] NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLINDEXING -
[- ] NFC…TMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER -
[- ] NFC…_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLSTATISTICS -
[- ] NFCORE_QUANTMS:QUANTMS:DECOYDATABASE -
[- ] NFC…S:TMT:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET -
[- ] NFC…S:QUANTMS:TMT:ID:PSMRESCORING:EXTRACTPSMFEATURES -
Plus 29 more processes waiting for tasks…
WARN: There's no process matching config selector: MULTIQC -- Did you mean: PMULTIQC?
WARN: Undocumented setting docker.userEmulation is not supported any more - please remove it from your config
ERROR ~ Error executing process > 'NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv)'

Caused by:
Process NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv) terminated with an error exit status (1)

Command executed:

check_samplesheet.py "sdrf.tsv" true --CHECK_MS 2>&1 | tee input_check.log

cat <<-END_VERSIONS > versions.yml
"NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK":
sdrf-pipelines: $(parse_sdrf --version 2>&1 | awk -F ' ' '{print $2}')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
executor > local (1)
[87/a4b657] NFC…QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv) | 1 of 1, failed: 1 ✘
[- ] NFC…QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRFPARSING -
[- ] NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:DECOMPRESS -
[- ] NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLINDEXING -
[- ] NFC…TMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER -
[- ] NFC…_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLSTATISTICS -
[- ] NFCORE_QUANTMS:QUANTMS:DECOYDATABASE -
[- ] NFC…S:TMT:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET -
[- ] NFC…S:QUANTMS:TMT:ID:PSMRESCORING:EXTRACTPSMFEATURES -
Plus 29 more processes waiting for tasks…
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/quantms] Pipeline completed with errors-
WARN: There's no process matching config selector: MULTIQC -- Did you mean: PMULTIQC?
WARN: Undocumented setting docker.userEmulation is not supported any more - please remove it from your config
ERROR ~ Error executing process > 'NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv)'

Caused by:
Process NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv) terminated with an error exit status (1)

Command executed:

check_samplesheet.py "sdrf.tsv" true --CHECK_MS 2>&1 | tee input_check.log

cat <<-END_VERSIONS > versions.yml
"NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK":
sdrf-pipelines: $(parse_sdrf --version 2>&1 | awk -F ' ' '{print $2}')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
executor > local (1)
[87/a4b657] NFC…QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv) | 1 of 1, failed: 1 ✘
[- ] NFC…QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRFPARSING -
[- ] NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:DECOMPRESS -
[- ] NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLINDEXING -
[- ] NFC…TMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER -
[- ] NFC…_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLSTATISTICS -
[- ] NFCORE_QUANTMS:QUANTMS:DECOYDATABASE -
[- ] NFC…S:TMT:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET -
[- ] NFC…S:QUANTMS:TMT:ID:PSMRESCORING:EXTRACTPSMFEATURES -
Plus 29 more processes waiting for tasks…
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/quantms] Pipeline completed with errors-
WARN: There's no process matching config selector: MULTIQC -- Did you mean: PMULTIQC?
WARN: Undocumented setting docker.userEmulation is not supported any more - please remove it from your config
ERROR ~ Error executing process > 'NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv)'

Caused by:
Process NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv) terminated with an error exit status (1)

Command executed:

check_samplesheet.py "sdrf.tsv" true --CHECK_MS 2>&1 | tee input_check.log

cat <<-END_VERSIONS > versions.yml
"NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK":
sdrf-pipelines: $(parse_sdrf --version 2>&1 | awk -F ' ' '{print $2}')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
touch: cannot touch '.command.trace': Permission denied

Work dir:
/Users/emiljohansson/R/CB2110/lab1/work/87/a4b657405d49abcd7ab2a3d93d687c

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

-- Check '.nextflow.log' file for details