Output: VCFs/, VCFs/, VCFs/ RuleException:ĬalledProcessError in line 28 of /data/data/Samples/snakemake-example/WGS-test/step7.smk:Ĭommand ' set -euo pipefail gatk -java-options -Xmx16g VariantRecalibrator -R /data/data/reference/refs/ ta -V VCFs/ -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /data/data/variant_call /hapmap_3.3. -resource:omni,known=false,training=true,truth=false,prior=12.0 /data/data/variant_call/1000 G_omni2.5. -resource:1000G,known=false,training=true,truth=false,prior=10.0 /data/data/variant_call/1000G _ -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /data/data/ variant_call/dbsnp_ -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP -O VCFs/CHS. Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (-java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to p rint the stack trace. an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR \ SNPS="/data/data/variant_call/1000G_"ĭBSNP="/data/data/variant_call/dbsnp_" I am new in using snakemake, I have an issue when doing the step gatk VariantRecalibrator on snakemake, it generated error but the script can run without error when not in snakemake format.
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