Shared libraries problem in samtool

[asuisse]

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 :)

[nriddiford]

Hi Annabelle, I've only just got round to seeing this - sorry for the big delay!

It looks like this might help. I'll see if I can get round to this in the coming weeks. Do you still have the same issue?