Hi,
I am trying to convert a large BAM file containing genomic DNA sequences to
paired end FASTA files using Picard. I am using the following command:
java -Xmx6g -XX:MaxPermSize=6g -jar
~/bin/broadinstitute-picard-6fd825a/dist/picard.jar SamToFastq
INPUT=$filenamestem.bam FASTQ=$filenamestem.fq
SECOND_END_FASTQ=$filenamestem.2.fq MAX_RECORDS_IN_RAM=1000000
OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false
INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0
INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false
VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false
CREATE_MD5_FILE=false
I consistently get the following error and Picard stops unexpectedly.
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.util.HashMap.resize(HashMap.java:479)
at java.util.HashMap.addEntry(HashMap.java:772)
at java.util.HashMap.put(HashMap.java:402)
at picard.sam.SamToFastq.doWork(SamToFastq.java:171)
at
picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
I tried increasing the RAM size to 6 and tried multiple different options (I
tried it without the -Xmgx and -XX:MaxPermSize and MAX_RECORDS_IN_RAM options),
however, I get the same error.
I have validated my BAM files.
What would be the easiest way to solve this?
Thanks,
Nahal
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