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Picard ValidateSam exit status 3

bwubbbwubb Member ✭✭

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

-bwubb

Best Answer

Answers

  • bshifawbshifaw Member, Broadie, Moderator admin

    You can set the --VERBOSITY argument to DEBUG to generate more log messages.

    Also your using a very old version of the tool, try running the latest release of the tool Picard 2.20.2.

  • bwubbbwubb Member ✭✭

    @cnorman said:
    @bwubb Return code 3 mean errors were found, but no warnings. See more details here.

    Thank you for the details.

    That is very confusing to me, because whether the bam has errors or not has no bearing on the execution of the java. I dont suppose there is anyway to suppress that? Snakemake will be looking to see if there is a non-zero exit; deleting the output in such situations. The summary output is all the error indication one should need, imo.

    Otherwise I guess Ill just have to code around. Thank you both.

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