vartrix error

[liym0758]

Hi, @wheaton5
Thank you for developing the pipeline!
I'm getting the same issue as thishttps://github.com/wheaton5/souporcell/issues/126.
The issue above was solved by updating vartrix, but I'm using the latest version (vartrix 1.1.22), still having the same problem. The version of singularity that I'm using is 3.8.6, which can also meet the requirements.
This is my code:
singularity exec /biosoft/souporcell/souporcell_latest.sif souporcell_pipeline.py -i /data/lib34_check/merged_lib34.bam -b /data/lib34_check/raw_merged_barcode.tsv -f /data/reference/hg38.fa -t 8 -o /data/lib34_check/souporcell/merged_output/ -k 7
and the error report is exactly the same as vartrix problem
#126
running vartrix Traceback (most recent call last): File "/opt/souporcell/souporcell_pipeline.py", line 589, in <module> vartrix(args, final_vcf, bam) File "/opt/souporcell/souporcell_pipeline.py", line 512, in vartrix subprocess.check_call(cmd, stdout = out, stderr = err) File "/usr/local/envs/py36/lib/python3.6/subprocess.py", line 311, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['vartrix', '--mapq', '30', '-b', '/data/lib34_check/souporcell/merged_output//souporcell_minimap_tagged_sorted.bam', '-c', '/data/lib34_check/raw_merged_barcode.tsv', '--scoring-method', 'coverage', '--threads', '8', '--ref-matrix', '/data/lib34_check/souporcell/merged_output//ref.mtx', '--out-matrix', '/data/lib34_check/souporcell/merged_output//alt.mtx', '-v', '/data/lib34_check/souporcell/merged_output//souporcell_merged_sorted_vcf.vcf.gz', '--fasta', '/data/reference/hg38.fa', '--umi']' returned non-zero exit status 101.
There're quite few information online about this error. I've tried to update the version of singularity and vartrix, but that didn't work.
Do you know what is the cause this error? And how can I solve this problem?
Apologies if this is a basic question. I just began to learn bioinformatics.
Thank you very much!