Tutorial Somatic Variant Calling Error for the cellScan step. Different output for different input to -t and -w? Potentially different reference file?

[hannahkimincompbio]

Dear Monopogen developers,

I am currently running the somatic variant calling part of your tutorial.

(monopogen) [hk Monopogen]$ hk/anaconda3/bin/python ${mpath}/src/Monopogen.py somatic -a ${mpath}/apps -t 5 -w 50MB -r ${mpath}/t_conditions/region.lst -i hk/tools/Monopogen/bm -l ${mpath}/t_conditions/CB_7K.maester_scRNA.csv -s cellScan -g hk/tools/Monopogen/t_conditions/chr20.hg38.fa 
...
hk/tools/samtools-1.2/samtools mpileup -b hk/tools/Monopogen/bm/Bam/split_bam/cell.bam.lst -f hk/tools/Monopogen/t_conditions/chr20.hg38.fa -r chr20 -q 20 -Q 20 -t DP4 -d 10000 -v  | hk/tools/bcftools-1.8/bcftools view  | hk/tools/bcftools-1.8/bcftools norm -m-both -f hk/tools/Monopogen/t_conditions/chr20.hg38.fa | grep -v "<X>" | grep -v INDEL |hk/tools/htslib-1.9/bgzip -c > hk/tools/Monopogen/bm/somatic/chr20.cell.gl.vcf.gz
[mpileup] fail to load index for hk/tools/Monopogen/bm/Bam/split_bam/AGAGAGCTCGCCACTT.bam
Failed to open -: unknown file type
Failed to open -: unknown file type
hk/tools/bcftools-1.8/bcftools concat -o hk/tools/Monopogen/bm/somatic/chr20.cell.gl.vcf.gz  -O z
...
ValueError: invalid file `b'hk/tools/Monopogen/bm/somatic/chr20.cell.gl.vcf.gz'` (mode=`b'r'`) - is it VCF/BCF format?

The only things that are different are: (1) the input to -t and -w, because I could not manipulate ulimit in my hpc system. (2) reference file https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/

Should changing the input to -t and -w change the output as well? If so, what is the difference anticipated? Also, is this the format/source of reference file that is expected to be used?

Best,

Hannah Kim

[jjializhu]

I also met the same problem. Have you solved it?

[jinzhuangdou]

Please try the new version v1.6.0.