souporcell: vartrix problem

Hi @wheaton5

I ran the souporcell_latest.sif pipeline (using singularity) successfully for 14 of my 16 libraries. In two of them I got an error and tracked back to vartrix (in the vartrix.err). The error is this:

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', '/home/yaraScratch/souporcell-F1678CM-AB2-Sc-4-1/souporcell_minimap_tagged_sorted.bam', '-c', '/home/yara/Scratch/souporcell-F1678CM-AB2-Sc-4-1/barcodes.tsv', '--scoring-method', 'coverage', '--threads', '8', '--ref-matrix', '/home/yara/Scratch/souporcell-F1678CM-AB2-Sc-4-1/ref.mtx', '--out-matrix', '/home/yara/Scratch/souporcell-F1678CM-AB2-Sc-4-1/alt.mtx', '-v', '/home/yara/Scratch/souporcell-F1678CM-AB2-Sc-4-1/souporcell_merged_sorted_vcf.vcf.gz', '--fasta', '/home/yara/Scratch/references/refdata-cellranger-GRCh38-3.0.0/fasta/genome.fa', '--umi']' returned non-zero exit status 101.

I emailed the crash reports to the authors and they replied that I should try with a newest version of vartrix (https://github.com/10XGenomics/vartrix/releases/tag/v1.1.22). So, my questions are: is there a way around this? how could I do this? would it be possible for you to add this to the souporcell_latest.sif?

Many thanks for your help!