If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Picard ValidateSam exit status 3
Hello. I am trying to get a better understanding of the exit status codes for ValidateSam. I was running the command within a snakemake pipeline, and clearly there are some errors with the bams themselves, but ValidateSam itself has an exit status of 3, and Im not sure what to do with it.
If I execute the command myself, it will run to completion and produce the summary file, so Im not sure what to make of this and how to move forward. Ultimately Id prefer exit status 0 somehow, because I intend to do stuff with the summary file when there are errors.
[[email protected] ]$ java -Xmx10240m -jar $HOME/software/picard/build/libs/picard.jar ValidateSamFile I=bam_input/work/WO121944/GRCh37/recal.bam O=bam_input/work/WO121944/GRCh37/validation_data.table MODE=SUMMARY IGNORE_WARNINGS=true [Wed Jun 05 13:30:50 EDT 2019] picard.sam.ValidateSamFile INPUT=bam_input/work/WO121944/GRCh37/recal.bam OUTPUT=bam_input/work/WO121944/GRCh37/validation_data.table MODE=SUMMARY IGNORE_WARNINGS=true MAX_OUTPUT=100 VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Wed Jun 05 13:30:50 EDT 2019] Executing as [email protected] on Linux 3.10.0-862.14.4.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_181-b13; Picard version: 2.9.4-7-gd9e5eb9-SNAPSHOT WARNING: BAM index file /home/bwubb/projects/Simpkins_OvCA-Targeted/bam_input/work/WO121944/GRCh37/recal.bai is older than BAM /home/bwubb/projects/Simpkins_OvCA-Targeted/bam_input/work/WO121944/GRCh37/recal.bam INFO 2019-06-05 13:32:41 SamFileValidator Validated Read 10,000,000 records. Elapsed time: 00:01:50s. Time for last 10,000,000: 110s. Last read position: 15:91,347,576 [Wed Jun 05 13:34:07 EDT 2019] picard.sam.ValidateSamFile done. Elapsed time: 3.29 minutes. Runtime.totalMemory()=1515192320 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [[email protected] ]$ echo $? 3
Any comments/advice will likely be very helpful. Thank you