I have difficulty in doing this simple thing using PICARD. I tried the latest
version as well as an older version 1.110, but got the same error message
below. I simply don't how to walk around this issue.
[Tue Jul 01 20:22:44 EDT 2014] net.sf.picard.sam.SamToFastq
INPUT=LP6005799-DNA_A02.bam FASTQ=LP6005799-DNA_A02_1.fastq
SECOND_END_FASTQ=LP6005799-DNA_A02_2.fastq
UNPAIRED_FASTQ=LP6005799-DNA_A02.unpaired.fastq OUTPUT_PER_RG=false
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 MAX_RECORDS_IN_RAM=500000
CREATE_INDEX=false CREATE_MD5_FILE=false
[Tue Jul 01 20:22:44 EDT 2014] Executing as zhao...@amrndhl460.pfizer.com on
Linux 2.6.32-358.11.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM
1.7.0_25-mockbuild_2013_06_26_07_26-b00; Picard version: 1.110(1752)
IntelDeflater
INFO 2014-07-01 20:23:04 SamToFastq Processed 1,000,000
records. Elapsed time: 00:00:19s. Time for last 1,000,000: 18s. Last read
position: chrM:13,788
[Tue Jul 01 20:23:06 EDT 2014] net.sf.picard.sam.SamToFastq done. Elapsed time:
0.38 minutes.
Runtime.totalMemory()=3668639744
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" net.sf.samtools.SAMFormatException: SAM validation
error: ERROR: Record 1179125, Read name C30BLACXX_0:5:1313:824748:0, bin field
of BAM record does not equal value computed based on alignment start and end,
and length of sequence to which read is aligned
at net.sf.samtools.SAMUtils.processValidationErrors(SAMUtils.java:449)
at
net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:621)
at
net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:606)
at
net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:576)
at
net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:774)
at
net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:752)
at net.sf.picard.sam.SamToFastq.doWork(SamToFastq.java:139)
at
net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:179)
at net.sf.picard.sam.SamToFastq.main(SamToFastq.java:127)
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