Error with somaticseq_parallel.py

[joonlee3]

Hi,

I tried to run somaticseq (v3.2.1) with the following command line

~/.pyenv/versions/3.6.1/bin/python ${SomaticSeq_home}/somaticseq_parallel.py paired \
-outdir ${vcf_output_path}/SomaticSeq_new \
--genome-reference /site/ne/home/wings/ref_data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa \
-nbam ${bam_n} \
-tbam ${bam_t} \
--threads 8 \
--mutect2-vcf ${tumour_id}.mutect2.pass.vcf \
--vardict-vcf ${tumour_id}.vardict.pass.vcf \
--strelka-snv ${tumour_id}.strelka2.snvs.pass.vcf \
--strelka-indel ${tumour_id}.strelka2.indels.pass.vcf

At the end, I've got the following error - somaticseq_parallel.py: error: the following arguments are required: -ref/--genome-reference

If you have suggestions, please let me know.

Thank you, Joon

[litaifang]

Hi Joon,

The options/arguments for -outdir and --genome-reference and --threads should be placed before paired.

Try,

~/.pyenv/versions/3.6.1/bin/python ${SomaticSeq_home}/somaticseq_parallel.py \
-outdir ${vcf_output_path}/SomaticSeq_new \
--genome-reference /site/ne/home/wings/ref_data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa \
--threads 8 \
paired \
-nbam ${bam_n} \
-tbam ${bam_t} \
--mutect2-vcf ${tumour_id}.mutect2.pass.vcf \
--vardict-vcf ${tumour_id}.vardict.pass.vcf \
--strelka-snv ${tumour_id}.strelka2.snvs.pass.vcf \
--strelka-indel ${tumour_id}.strelka2.indels.pass.vcf

To see what goes before paired and what goes after: before: somaticseq_parallel.py -h after: somaticseq_parallel.py paired -h

[litaifang]

--threads should go before paired as well.

[litaifang]

Looks like the issue is taken care of.