Hey Nick,
This is the farthest I've got, running your pipeline on the server using the HUM samples to try. I've cloned the pipeline in my personal space, I see I also have it in the .nextflow directory (is it normal to have it twice then?). When I launch it (either using "nextflow run main.nf etc." or "nextflow run nriddiford/nf-lohcator etc."), I get this same error:
N E X T F L O W ~ version 20.10.0
Launching `nriddiford/nf-lohcator` [stoic_saha] - revision: 8de22b788e [master]
===
This is a NEXTFLOW PIPELINE for detecting LOH in matched tumour normal pairs.
Running with the following user-defined options:
--- config ---
--samplePlan: my_sample_plan_tiny_cluster.csv
--outdir: ./results
--condaCacheDir /data/kdi_prod/project_result/948/01.00/Analysis/conda-cache-nextflow/
--- Trimmomatic (v0.39) ---
--adapters [ILLUMINACLIP:] /data/users/asuisse/.nextflow/assets/nriddiford/nf-lohcator/data/adapters.fa
--- Bwa (v0.7.17) ---
--genome /data/kdi_prod/project_result/948/01.00/Analysis/Genomes/Dmel_6/bwa/dmel_6.12.fa
--- Varscan (v2.4.4) ---
--varscan_normal_coverage [--min-coverage-normal] 20
--varscan_tumour_coverage [--min-coverage-tumor] 20
--varscan_tumour_purity [--tumor-purity] 1
--- lohcator (/data/users/asuisse/.nextflow/assets/nriddiford/nf-lohcator/bin/lohcator.py) ---
--sample_ids [--config] /data/users/asuisse/.nextflow/assets/nriddiford/nf-lohcator/data/samples.tsv
--lohcator_chromosome [--chromosome] X
===
executor > pbs (25)
[7a/d39429] process > n_trimmomatic (HUM-6) [100%] 3 of 3 ✔
executor > pbs (25)
[7a/d39429] process > n_trimmomatic (HUM-6) [100%] 3 of 3 ✔
[96/e4315c] process > t_trimmomatic (HUM-7) [100%] 3 of 3 ✔
[44/c989c5] process > index [100%] 1 of 1 ✔
[fd/91d0df] process > align_t (HUM-4) [133%] 4 of 3, failed: 4, retries: 3
[57/79fce6] process > align_n (HUM-6) [150%] 6 of 4, failed: 6, retries: 3 ✘
[- ] process > pileup -
[- ] process > varscan -
[- ] process > lohcator -
[c5/bdae13] process > fastqc (HUM-9) [100%] 6 of 6 ✔
[- ] process > bamstats -
[- ] process > multiqc -
[54/693360] NOTE: Process `align_n (HUM-3)` terminated with an error exit status (127) -- Execution is retried (1)
[97/3014a9] NOTE: Process `align_n (HUM-9)` terminated with an error exit status (127) -- Execution is retried (1)
[ba/c84ebd] NOTE: Process `align_t (HUM-1)` terminated with an error exit status (127) -- Execution is retried (1)
[00/787c26] NOTE: Process `align_t (HUM-4)` terminated with an error exit status (127) -- Execution is retried (1)
[f7/0aa458] NOTE: Process `align_n (HUM-6)` terminated with an error exit status (127) -- Execution is retried (1)
[20/b6cc1e] NOTE: Process `align_t (HUM-7)` terminated with an error exit status (127) -- Execution is retried (1)
Error executing process > 'align_n (HUM-3)'
Caused by:
Process `align_n (HUM-3)` terminated with an error exit status (127)
Command executed:
bwa mem -t 4 dmel_6.12.fa HUM-3.forward.fq.gz HUM-3.reverse.fq.gz | samblaster --addMateTags --removeDups | samtools sort - | samtools view -Sb - > HUM-3.bam
#picard AddOrReplaceReadGroups -INPUT HUM-3.bam -OUTPUT HUM-3.RG.bam -VALIDATION_STRINGENCY LENIENT -RGID HUM-3 -RGLB HUM -RGPL illumina -RGPU 1 -RGSM HUM-3
picard AddOrReplaceReadGroups --INPUT HUM-3.bam --OUTPUT HUM-3.RG.bam --RGID HUM-3 --RGLB HUM --RGPL illumina --RGPU 1 --RGSM HUM-3
samtools index HUM-3.RG.bam
Command exit status:
127
Command output:
(empty)
Command error:
samtools: error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory
samtools: error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory
samblaster: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by samblaster)
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[vfprintf(stdout)] Broken pipe
Work dir:
/bioinfo/users/asuisse/nf-lohcator/work/60/b24f5f7e1d43b2fd3e31c4a92ba409
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
What do you think could be going wrong? I've tried to look into the shared library thing online but I'm going down a rabbit hole of trying to pull the pipeline even though I redownloaded it yesterday... but then it says I can't update it because some files were modified... What do you think?
Thank you for your time :)
Hey Nick,
This is the farthest I've got, running your pipeline on the server using the HUM samples to try. I've cloned the pipeline in my personal space, I see I also have it in the .nextflow directory (is it normal to have it twice then?). When I launch it (either using "nextflow run main.nf etc." or "nextflow run nriddiford/nf-lohcator etc."), I get this same error:
What do you think could be going wrong? I've tried to look into the shared library thing online but I'm going down a rabbit hole of trying to pull the pipeline even though I redownloaded it yesterday... but then it says I can't update it because some files were modified... What do you think?
Thank you for your time :)