error about genome size / bad lexical cast when using a non-human reference genome

[sdvie]

I try to run strelka using a fasta file and matching bam files containing both human and mouse chromosomes.
After ok validation of the sequences in the bam and fasta files, I immediately get an error:

INFO: Scanning reference genome
INFO: Scanning reference genome complete

ERROR: Failed system call: '/apps/STRELKA/1.0.14/libexec/strelka2 -clobber -filter-unanchored -min-paired-align-score 20 -min-single-align-score 10 -min-qscore 0 -report-range-begin 25000001 -report-range-end 50000000 -samtools-reference 'hsapiens_mmusculus.hg38_GRCm38.fasta' -max-window-mismatch 3 20 -print-used-allele-counts -bam-seq-name '2' -genome-size 5582397882 -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 0.000001 --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 49combined.bam --tumor-bam-file 47combined.bam --somatic-snv-file strelkaAnalysis/chromosomes/2/bins/0001/somatic.snvs.unfiltered.vcf --somatic-indel-file strelkaAnalysis/chromosomes/2/bins/0001/somatic.indels.unfiltered.vcf --variant-window-flank-file 50 strelkaAnalysis/chromosomes/2/bins/0001/somatic.indels.unfiltered.vcf.window --ignore-conflicting-read-names --report-file strelkaAnalysis/chromosomes/2/bins/0001/strelka.stats >| strelkaAnalysis/chromosomes/2/bins/0001/strelka.stdout 2>| strelkaAnalysis/chromosomes/2/bins/0001/strelka.stderr'

 at /apps/STRELKA/1.0.14/libexec/../lib/Utils.pm line 37
        Utils::errorX('Failed system call: \'/apps/STRELKA/1.0.14/libexec/strelka2 -...') called at /apps/STRELKA/1.0.14/libexec/../lib/Utils.pm line 50
        Utils::executeCmd('/apps/STRELKA/1.0.14/libexec/strelka2 -clobber -filter-unanch...', 0) called at /apps/STRELKA/1.0.14/libexec/callSomaticVariants.pl line 218
make: *** [strelkaAnalysis/chromosomes/2/bins/0001/task.complete] Error 1

above mentioned strelka.stderr file says:

******** COMMAND-LINE ERROR:: argument after flag -genome-size (5582397882) cannot be parsed to expected type: bad lexical cast: source type value could not be interpreted as target ********


The standard output says the following:

Successfully configured analysis and created makefile '/scratch/production/sderdak/parzival_RDC5/SCGRES_02/OVA150/OVA150_L2_combined/strelkaAnalysis/Makefile'.
To run the analysis locally using make, run:
make -C strelkaAnalysis

...or:

cd strelkaAnalysis
make

make: Entering directory `strelkaAnalysis'
/apps/STRELKA/1.0.14/libexec/callSomaticVariants.pl --config=strelkaAnalysis/config/run.config.ini --chrom=2 --bin=0001 && touch strelkaAnalysis/chromosomes/2/bins/0001/task.complete
make: Leaving directory `strelkaAnalysis'


I am using strelka version 1.0.14.

Is this a problem of the genome size (bigger than usual human genome)?

Any suggestions for fixes/workarounds will be very much appreciated.

Thanks a lot,
Sophia

[Jingzhong Xie]

I face the same problem. Any solution for it now? 

Thanks.

Jingzhong