Error occurred when running souporcell.

[xliu-ucas]

Hello, a very good tool. But I reported an error when I ran the command. The following are my command: nohup /usr/local/bin/singularity exec \ --cleanenv /data1/xliu/snRNAseq_Trip4_lung/cellranger/souporcell_latest.sif souporcell_pipeline.py \ -i /data1/xliu/scRNA_SKM/xliu_analysis/souporcell/SKM-1-MY/outs/possorted_genome_bam.bam \ -b /data1/xliu/scRNA_SKM/xliu_analysis/souporcell/SKM-1-MY/outs/filtered_feature_bc_matrix/barcodes.tsv \ -f genome.fa \ -t 60 -o /data1/xliu/scRNA_SKM/xliu_analysis/souporcell/SKM-1-MY/res/ \ -k 3 > /data1/xliu/scRNA_SKM/xliu_analysis/souporcell/SKM-1-MY/souporcell_SKM_1.log 2>&1 &

The following are the errors in the log file. merging vcfs running vartrix Traceback (most recent call last): File "/opt/souporcell/souporcell_pipeline.py", line 589, in 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', '/data1/xliu/scRNA_SKM/xliu_analysis/souporcell/SKM-1-MY/res//souporcell_minimap_tagged_sorted.bam', '-c', '/data1/xliu/scRNA_SKM/xliu_analysis/souporcell/SKM-1-MY/outs/filtered_feature_bc_matrix/barcodes.tsv', '--scoring-method', 'coverage', '--threads', '60', '--ref-matrix', '/data1/xliu/scRNA_SKM/xliu_analysis/souporcell/SKM-1-MY/res//ref.mtx', '--out-matrix', '/data1/xliu/scRNA_SKM/xliu_analysis/souporcell/SKM-1-MY/res//alt.mtx', '-v', '/data1/xliu/scRNA_SKM/xliu_analysis/souporcell/SKM-1-MY/res//souporcell_merged_sorted_vcf.vcf.gz', '--fasta', 'genome.fa', '--umi']' returned non-zero exit status 101.

Is there any solution? Looking forward to your reply

[anglixue]

@xliu-ucas Hi, I met the same error today and was wondering if you have any solutions?