Failed to find test file HG03130.bam

[muhligs]

Hi, I am trying to make the initial test run using singularity in a cluster setting using slurm.

I am getting the following error after running nextflow run main.nf -profile slurm,test :

N E X T F L O W  ~  version 22.10.6
Launching `main.nf` [goofy_goldstine] DSL1 - revision: 6d430c4597
executor >  slurm (5)
[30/33c2ce] process > call_snvs1 (1)  [  0%] 0 of 1
executor >  slurm (5)
[30/33c2ce] process > call_snvs1 (1)  [100%] 1 of 1, failed: 1 ✘
[3f/6f3f90] process > call_snvs2 (1)  [100%] 1 of 1, failed: 1 ✘
[a9/6f8bbd] process > call_sv_del (1) [100%] 1 of 1, failed: 1 ✘
[98/1f3835] process > call_sv_dup (1) [100%] 1 of 1, failed: 1 ✘
[1f/dfb743] process > get_depth (1)   [100%] 1 of 1 ✔
[-        ] process > format_snvs     -
[-        ] process > get_core_var    -
[-        ] process > analyse_1       -
[-        ] process > analyse_2       -
[-        ] process > analyse_3       -
[-        ] process > call_stars      -
Error executing process > 'call_snvs2 (1)'

Caused by:
  Process `call_snvs2 (1)` terminated with an error exit status (134)

Command executed:

  graphtyper genotype hg38/chr22_hg38.fasta --sam=HG03130.bam --sams_index=<(echo HG03130.bam.bai) --region=chr22:42126000-42137500 --output=HG03130_var_2 -a --minimum_extract_score_over_homref=0  
  bcftools concat HG03130_var_2/chr22/*.vcf.gz > HG03130_var_2/chr22/042126000-042137500.vcf       
  bgzip -f HG03130_var_2/chr22/042126000-042137500.vcf
  tabix -f HG03130_var_2/chr22/042126000-042137500.vcf.gz

Command exit status:
  134

Command output:
  (empty)

Command error:
  INFO:    Converting SIF file to temporary sandbox...
  [E::hts_open_format] Failed to open file "/scratch/19864343/graphtyper_230619_102910_chr22_042126000.PLVrLU/bams/HG03130.bam" : No such file or directory
  /home/sennap/git/graphtyper/seqan/include/seqan/hts_io/hts_file.h:97 FAILED!  (Could not open file with filename /scratch/19864343/graphtyper_230619_102910_chr22_042126000.PLVrLU/bams/HG03130.bam)
  .command.sh: line 2: 3641377 Aborted                 (core dumped) graphtyper genotype hg38/chr22_hg38.fasta --sam=HG03130.bam --sams_index=<(echo HG03130.bam.bai) --region=chr22:42126000-42137500 --output=HG03130_var_2 -a --minimum_extract_score_over_homref=0
  INFO:    Cleaning up image...

Work dir:
  /faststorage/project/pharmgene/pharmcat/stellar-software/StellarPGx/work/3f/6f3f905dc33dcb2f86379e3f366690

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

Can anyone help me out?

Thanks,

Morten

[muhligs]

This turned out to be caused by singularity settings following a conda install of singularity. Reverting to the cluster default solved the problem.

[twesigomwedavid]

Glad you found a solution to this. Thanks for sharing it here