Alec,
Thank you. It works, and you save my headache.
I assume a read pair is written out once, though the pair can be mapped to
multiple location. Is this true?
Thanks again,
Shanrong
From: Alec Wysoker [mailto:[email protected]]
Sent: Wednesday, July 2, 2014 8:30 AM
To: Zhao, Shanrong; [email protected]
Subject: Re: [Samtools-help] BAM to faatsq
Hi Shanrong,
You can try one or all of these:
* Add option VALIDATION_STRINGENCY=LENIENT or VALIDATION_STRINGENCY=SILENT
to the SamToFastq command line.
* Investigate the way your BAM file was created, to try to understand why
an invalid bin field was put into the file.
* Convert BAM to SAM and then back to BAM again. Unfortunately, this is
the only way I know of to fix the bin fields in a BAM file.
-Alec
On 7/1/14, 9:08 PM, Zhao, Shanrong wrote:
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
[email protected]<mailto:[email protected]> 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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Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
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Samtools-help mailing list
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