gatk-variant template non-zero exit status 250

[alongalor]

Hello!

I am using the gatk-variant template and have encountered some issues I would really appreciate any help with.

Upon executing the following command:

bcbio_nextgen.py /n/data1/hms/dbmi/park/alon/software/bcbio/project2/config/project2.yaml -t ipython -n 64 -s lsf -q park_long

things run smoothly for a few hours and then an error appears.

the bcbio-nextgen-debug.log is attached. bcbio-nextgen-debug.log

The commands I used are as follows:

# Installation
mkdir /n/data1/hms/dbmi/park/alon/software/bcbio
cd /n/data1/hms/dbmi/park/alon/software/bcbio
wget https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
python ./bcbio_nextgen_install.py /n/data1/hms/dbmi/park/alon/software/bcbio/share/bcbio-nextgen --tooldir=/n/data1/hms/dbmi/park/alon/software/bcbio --genomes GRCh37 --aligners bwa
gatk-register /n/data1/hms/dbmi/park/alon/software/gatk/GenomeAnalysisTK-3.8-0.tar.bz2 
bcbio_setup_genome.py -f /n/data1/hms/dbmi/park/alon/software/gatk/human_g1k_v37_decoy.fasta -i bwa -n hs37d5 -b hs37d5

# gatk-variant pipeline
cd /n/data1/hms/dbmi/park/alon/software/bcbio/
bcbio_nextgen.py -w template gatk-variant project2
# manually edit template file: /n/data1/hms/dbmi/park/alon/software/bcbio/project2/config/project2-template.yaml, eddited as shown below*
nano /n/data1/hms/dbmi/park/alon/software/bcbio/project2.csv
# enter the following:
samplename,batch,sex
A10_S10_L008,batch1,male
bcbio_nextgen.py -w template /n/data1/hms/dbmi/park/alon/software/bcbio/project2/config/project2-template.yaml /n/data1/hms/dbmi/park/alon/software/bcbio/project2.csv /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/ReferenceTissueProject/sourceData/fastq/Vaccarino/A10_S10_L008_R1_001.fastq.gz /n/data1/hms/dbmi/park/DATA/BSMCommonExperiment/ReferenceTissueProject/sourceData/fastq/Vaccarino/A10_S10_L008_R2_001.fastq.gz 
cd /n/data1/hms/dbmi/park/alon/software/bcbio/project2/work
bcbio_nextgen.py /n/data1/hms/dbmi/park/alon/software/bcbio/project2/config/project2.yaml -t ipython -n 64 -s lsf -q park_long

*for reference, my project2-template.yaml reads as follows:

# Template for whole genome Illumina variant calling with GATK pipeline
---
details:
  - analysis: variant2
    genome_build: GRCh37
    # to do multi-sample variant calling, assign samples the same metadata / batch
    # metadata:
    #   batch: your-arbitrary-batch-name
    algorithm:
      aligner: bwa
      mark_duplicates: true
      recalibrate: gatk
      realign: gatk
      variantcaller: false
      # for targetted projects, set the region
      # variant_regions: /path/to/your.bed

Thanks a lot for your help!

Alon

[roryk]

Hi Alon,

I think this is a bug in GATK, see https://gatkforums.broadinstitute.org/gatk/discussion/comment/42836#Comment_42836-- they should have a release fixing it soon. @chapmanb might know better, though. It looks like it might be something that you could try rerunning and it might only happen randomly. bcbio will pick up where it left off if you start again to see if it fails in the same spot.

[alongalor]

Ah interesting! Thanks for the quick reply Rory! Much appreciated!

[roryk]

Alternatively you could turn on GATK4 instead and run with that and it shouldn't have this issue. See Brad's GATK4 validation here (https://github.com/bcbio/bcbio_validations/tree/master/gatk4). You can turn on GATK4 with this: http://bcbio-nextgen.readthedocs.io/en/latest/contents/configuration.html (search for GATK4). Adding tools_on: [gatk4] to your configuration template will turn on GATK4.

[alongalor]

Great suggestion. Thanks again!

[PatrickJReed]

Hi Alon, side note, should your genome_build be hs37d5 in your project template?

[alongalor]

Haha hey Patrick, thanks for jumping in! Just running a test here, but in general I am!

[PatrickJReed]

cool, cheers!

[roryk]

Thanks, hopefully this was all set, closing for now.