Hi Shanrong,
Yes, by default SamToFastq does not emit reads that are flagged as
secondary or supplementary.
-Alec
On 7/2/14, 9:48 PM, Zhao, Shanrong wrote:
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
<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)
------------------------------------------------------------------------------
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
_______________________________________________
Samtools-help mailing list
[email protected]
<mailto:[email protected]>
https://lists.sourceforge.net/lists/listinfo/samtools-help
------------------------------------------------------------------------------
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
_______________________________________________
Samtools-help mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/samtools-help
