Question: PICARD ValidateSamFile terminating prematurely, without errors, processes only portion of total reads
0
gravatar for freuv
24 months ago by
freuv20
freuv20 wrote:

Hi,

I am processing ~200 million WGS aligned reads with Picard's ValidateSamFile, with the following options:

MODE=VERBOSE MAX_OUTPUT=10000000 TMP_DIR=[/local2/tmp] IGNORE_WARNINGS=false VALIDATE_INDEX=true 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

However, the job ends prematurely without any errors and says it is complete -- after processing only 300K or so reads.

I have used this tool before without any issues for alignments with multimillions of reads.

Please advise, any help would be much appreciated!

freuv

sequencing assembly genome • 661 views
ADD COMMENTlink written 24 months ago by freuv20

version of picard ? full command line ?

ADD REPLYlink written 24 months ago by Pierre Lindenbaum124k

Picard 1.67

Command Line:

java -Xmx12G -Xms12G -jar ValidateSamFile.jar I=input.bam MODE=VERBOSE O=results.txt MAX_OUTPUT=10000000 TMP_DIR=/local2/tmp

ADD REPLYlink written 24 months ago by freuv20

your version of picard is outdated. 1.67 there is more than 500 bug fixes/commit since 1.67. Update picard and try again please. https://github.com/broadinstitute/picard/releases/tag/2.16.0

ADD REPLYlink modified 24 months ago • written 24 months ago by Pierre Lindenbaum124k

I am unable to install the latest version, as the cluster I work on has java v-1.7.0_151. Please advise.

Thanks! F

ADD REPLYlink written 24 months ago by freuv20

java 1..7 has been deprecated: http://www.oracle.com/technetwork/java/javase/downloads/java-se-jre-7-download-432155.html

This release is no longer the most current release of Java SE

update java to 1.8...

ADD REPLYlink written 24 months ago by Pierre Lindenbaum124k
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