bcbio 1.1.5a fails with GATK with previously ok options re: ExomeSeq

[lento2002]

bcbioadmin@ip-10-0-0-44> bcbio_nextgen.py -v 1.1.5a

bcbioadmin@ip-10-0-0-44> tail bcbio-nextgen.log

[2019-04-15T16:57Z] multiprocessing: calculate_sv_bins [2019-04-15T16:57Z] multiprocessing: calculate_sv_coverage [2019-04-15T16:57Z] multiprocessing: normalize_sv_coverage [2019-04-15T16:57Z] Timing: hla typing [2019-04-15T16:57Z] multiprocessing: call_hla [2019-04-15T16:57Z] Timing: alignment post-processing [2019-04-15T16:57Z] multiprocessing: piped_bamprep [2019-04-15T16:57Z] Timing: variant calling [2019-04-15T16:57Z] multiprocessing: variantcall_sample bcbioadmin@ip-10-0-0-44>

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A USER ERROR has occurred: p is not a recognized option

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Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. Using GATK jar /mnt/fsx/share/bcbio/anaconda/share/gatk4-4.1.1.0-0/gatk-package-4.1.1.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xms681m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=/home/bcbioadmin/X175_exomeseq/config/bcbiotx/tmpegxznm3c -jar /mnt/fsx/share/bcbio/anaconda/share/gatk4-4.1.1.0-0/gatk-package-4.1.1.0-local.jar Mutect2 -R /mnt/fsx/share/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --annotation ClippingRankSumTest --annotation DepthPerSampleHC --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation FisherStrand --annotation MappingQuality --annotation DepthPerAlleleBySample --annotation Coverage --read-validation-stringency LENIENT -I /home/bcbioadmin/X175_exomeseq/config/align/X-tumor/X-tumor-sort.bam --tumor-sample X-tumor -I /home/bcbioadmin/X175_exomeseq/config/align/X-normal/X-normal-sort.bam --normal-sample X-normal -L /home/bcbioadmin/X175_exomeseq/config/mutect2/chr4/X1-chr4_64352556_112622646-regions-nolcr.bed --interval-set-rule INTERSECTION --disable-read-filter NotDuplicateReadFilter -ploidy 2 -O /home/bcbioadmin/X175_exomeseq/config/bcbiotx/tmpegxznm3c/X1-chr4_64352556_112622646-raw.vcf.gz ' returned non-zero exit status 1.X

[naumenko-sa]

Hello, @lento2002 !

Thanks for reporting and sorry about the issues.

Could you please provide a yaml configuration file from your bcbio project?

Sergey

[lento2002]

Sure, see below. Many thanks!

fc_date: '2015-11-18'

fc_name: final upload: dir: ../output details:

• algorithm: aligner: 'bwa' trim_reads: atropos adapters: [illumina] recalibrate: false realign: false remove_lcr: true variantcaller: [mutect2, strelka2, varscan] ensemble: numpass: 2 svcaller: [lumpy, manta] hlacaller: optitype analysis: variant2 description: XX-normal files: [ /mnt/fsx/XXdata/XX-XX-share/XX_data/XX175.017/DNA_XX175_N_11001-017N_normal_dna_reads1.fastq.gz , /mnt/fsx/XXdata/XX-XX-share/XX_data/XX175.017/DNA_XX175_N_11001-017N_normal_dna_reads2.fastq.gz] genome_build: hg38 metadata: batch: XX1 phenotype: normal

  sex: female

• algorithm: aligner: 'bwa' trim_reads: atropos adapters: [illumina] recalibrate: false realign: false variantcaller: [mutect2, strelka2, varscan] ensemble: numpass: 2 svcaller: [lumpy, manta] hlacaller: optitype remove_lcr: true analysis: variant2 description: XX-tumor files: [ /mnt/fsx/XXdata/XX-XX-share/XX_data/XX175.017/DNA_XX175_T_11001-017F_tumor_dna_reads1.fastq.gz, /mnt/fsx/XXdata/XX-XX-share/XX_data/XX175.017/DNA_XX175_T_11001-017F_tumor_dna_reads2.fastq.gz] genome_build: hg38 metadata: batch: XX1 phenotype: tumor

  sex: female

[naumenko-sa]

Thanks! Could you please try to upgrade to the latest stable version (1.1.5) ( it looks like you are on 1.1.5a)?

There was a change in MUTECT syntax: https://github.com/bcbio/bcbio-nextgen/commit/bd13a5683a346a54f3dec048b23b52482109332a

SN

[roryk]

Thanks, this should definitely solve the problem so closing it.