strelka is not well a tested

[jason-weirather]

It doesn't look like strelka is covered in the test cases included with polysolver. we don't have any current errors in it, but it was not a straitforward build since vcftools never seemed to get where it was supposed to go on its own, and we are running off a bioconda perl vcf tools.

[hygine]

To run the analysis locally using make, run:

make -C /share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/strelka.hla_c_03_04_01_02

...or:

cd /share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/strelka.hla_c_03_04_01_02 make

make: Entering directory `/share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/strelka.hla_c_03_04_01_02' /home/linhj/anaconda2/envs/polysolver/share/strelka/libexec/callSomaticVariants.pl --config=/share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/strelka.hla_c_03_04_01_02/config/run.config.ini --chrom=hla_c_03_04_01_02 --bin=0000 && touch /share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/strelka.hla_c_03_04_01_02/chromosomes/hla_c_03_04_01_02/bins/0000/task.complete

ERROR: Failed system call: '/home/linhj/anaconda2/envs/polysolver/share/strelka/libexec/strelka2 -clobber -filter-unanchored -min-paired-align-score 40 -min-single-align-score 10 -min-qscore 0 -report-range-begin 1 -report-range-end 25000000 -samtools-reference '/home/linhj/anaconda2/envs/polysolver/share/polysolver_data/abc_complete.fasta' -max-window-mismatch 3 20 -print-used-allele-counts -bam-seq-name 'hla_c_03_04_01_02' -genome-size 22375332 -max-indel-size 50 -indel-nonsite-match-prob 0.5 --min-contig-open-end-support 35 --somatic-snv-rate 0.000001 --shared-site-error-rate 0.0000005 --shared-site-error-strand-bias-fraction 0.5 --somatic-indel-rate 0.000001 --shared-indel-error-rate 0.0000001 --tier2-min-single-align-score 5 --tier2-min-paired-align-score 5 --tier2-single-align-score-rescue-mode --tier2-mismatch-density-filter-count 10 --tier2-no-filter-unanchored --tier2-indel-nonsite-match-prob 0.25 --tier2-include-singleton --tier2-include-anomalous -bam-file /share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/type.hla_c_03_04_01_02.bam --tumor-bam-file /share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/type.hla_c_03_04_01_02.tumor.bam --somatic-snv-file /share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/strelka.hla_c_03_04_01_02/chromosomes/hla_c_03_04_01_02/bins/0000/somatic.snvs.unfiltered.vcf --somatic-indel-file /share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/strelka.hla_c_03_04_01_02/chromosomes/hla_c_03_04_01_02/bins/0000/somatic.indels.unfiltered.vcf --variant-window-flank-file 50 /share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/strelka.hla_c_03_04_01_02/chromosomes/hla_c_03_04_01_02/bins/0000/somatic.indels.unfiltered.vcf.window --max-input-depth 10000 --eland-compatibility --report-file /share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/strelka.hla_c_03_04_01_02/chromosomes/hla_c_03_04_01_02/bins/0000/strelka.stats >| /share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/strelka.hla_c_03_04_01_02/chromosomes/hla_c_03_04_01_02/bins/0000/strelka.stdout 2>| /share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/strelka.hla_c_03_04_01_02/chromosomes/hla_c_03_04_01_02/bins/0000/strelka.stderr'

at /home/linhj/anaconda2/envs/polysolver/share/strelka/libexec/../lib/Utils.pm line 37. Utils::errorX("Failed system call: '/home/linhj/anaconda2/envs/polysolver/sh"...) called at /home/linhj/anaconda2/envs/polysolver/share/strelka/libexec/../lib/Utils.pm line 50 Utils::executeCmd("/home/linhj/anaconda2/envs/polysolver/share/strelka/libexec/s"..., 0) called at /home/linhj/anaconda2/envs/polysolver/share/strelka/libexec/callSomaticVariants.pl line 213 make: *** [/share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/strelka.hla_c_03_04_01_02/chromosomes/hla_c_03_04_01_02/bins/0000/task.complete] Error 1 make: Leaving directory /share/nas1/linhj/bin/software/hla-polysolver-master/BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/strelka.hla_c_03_04_01_02' cp: cannot stat ./BMK181214-O873-0101-4-Human-Tumor-Exom/hla_mutations_X01_X02/strelka.hla_c_03_04_01_02/results/all.somatic.indels.vcf': 没有那个文件或目录