missing a space between flag and file name

[fulabgenomics]

Hi there, Thanks for the great tool! I followed the manual for calling the somatic mutations

path="/SNV/Monopogen"
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${path}/apps
#python  ${path}/src/Monopogen.py  preProcess -b bam.list3 -o bm  -a ${path}/apps -t 2
python ${path}/src/Monopogen.py  germline  -a ${path}/apps  -r region.lst \
 -p ./  -t 22 \
 -g  genome.fa  -m 3 -s all  -o bm

with bam.list3 like this $cat bam.list3 bm,/SNV/Monopogen/test/chr20.maester_scRNA.bam

I successfully have the bm_chr20.filter.bam from the first step, then I got errors

Exception in thread "main" java.lang.IllegalArgumentException: Missing line (#CHROM ...) after meta-information lines
File source: bm/germline/chr20.germline.vcf

when I double-check the script file that it automatically generated,

$cat bm/Script/runGermline_chr20.sh /SNV/Monopogen/apps/samtools mpileup -bout/Bam/chr20.filter.bam.lst -f chr20_2Mb.hg38.fa -r chr20 -q 20 -Q 20 -t DP -d 10000000 -v | .....

I think the correct code should be -b out/Bam/chr20.filter.bam.lst .... but somehow there is no space between the -b and the file name, maybe a space in line 77 of Monopogen.py is needed.

Thanks!

[fulabgenomics]

and when I ran the next step with

python  ${path}/src/Monopogen.py  somatic  \
    -a   ${path}/apps  -r  region.lst  -t 50 \
    -i  bm  -l  CB_7K.maester_scRNA.csv   -s featureInfo     \
    -g  refdata-gex-GRCh38-2020-A/fasta/genome.fa 

I go error

[E::idx_find_and_load] Could not retrieve index file for 'bm/germline/chr20.phased.vcf.gz'
[W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.)
[E::idx_find_and_load] Could not retrieve index file for 'bm/germline/chr20.gl.vcf.gz'

Right now I tried manually indexing the files to get around it, can the index step be added to the runGermline_chr20.sh? in the future? Thank you so much!

[jinzhuangdou]

Thanks. It is weired that there is no space in the -b option. The index process has been fixed now.

[fulabgenomics]

Thank you very much for your prompt response! The pipeline now works perfectly with my data, so I will go ahead and close this comment. Thanks for the tool once again.