Hello, I want to use SamToFastq on BAM produced by Tophat. I am getting Illegal
Mate State error, details below. Setting VALIDATION_STRINGENCY to LENIENT or to
SILENT did not solve the issue, even if I first pre-filter to unique reads
using samtools view -bq 4 accepted_hits.bam > filtered.bam.
Same issue was reported here https://github.com/jeff-k/resolvepairs explaining
that the error is due to more than one pair of reads having the same query
name. The proposed solution was to add unique id to the names of reads
belonging to the same mate pair using the Resolvepair script, which failed for
me on line 94 due to syntax error. Would appreciate a solution, thank you.
Java version 1.7. Program report (Command line included below):
Job </opt/java/jdk1.7.0_45/bin/java -jar /opt/picard-tools-1.79/SamToFastq.jar
VALIDATION_STRINGENCY=SILENT INPUT=filtered_old.bam FASTQ=read_1.fastq
SECOND_END_FASTQ=read_2.fastq> was submitted from host <mezzanine.orchestra> by
user <ft42> in cluster <hms_orchestra>.
Job was executed on host(s) <clarinet002-164.orchestra>, in queue <mini>, as
user <ft42> in cluster <hms_orchestra>.
</home/ft42> was used as the home directory.
</groups/benowitz/BamToFastq> was used as the working directory.
Started at Wed Sep 3 09:31:24 2014
Results reported at Wed Sep 3 09:31:27 2014
Your job looked like:
------------------------------------------------------------
# LSBATCH: User input
/opt/java/jdk1.7.0_45/bin/java -jar /opt/picard-tools-1.79/SamToFastq.jar
VALIDATION_STRINGENCY=SILENT INPUT=filtered_old.bam FASTQ=read_1.fastq
SECOND_END_FASTQ=read_2.fastq
------------------------------------------------------------
Exited with exit code 1.
Resource usage summary:
CPU time : 1.36 sec.
The output (if any) follows:
[Wed Sep 03 09:31:26 EDT 2014] net.sf.picard.sam.SamToFastq
INPUT=filtered_old.bam FASTQ=read_1.fastq SECOND_END_FASTQ=read_2.fastq
VALIDATION_STRINGENCY=SILENT OUTPUT_PER_RG=false RE_REVERSE=true
INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0
INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false
COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false
CREATE_MD5_FILE=false
[Wed Sep 03 09:31:26 EDT 2014] Executing as
ft42@clarinet002-164<mailto:ft42@clarinet002-164> on Linux
3.2.41-bpo.4-ritg1-amd64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_45-b18;
Picard version: 1.79(1282)
[Wed Sep 03 09:31:27 EDT 2014] net.sf.picard.sam.SamToFastq done. Elapsed time:
0.01 minutes.
Runtime.totalMemory()=1140850688
FAQ: http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page
Exception in thread "main" net.sf.picard.PicardException: Illegal mate state:
HWI-ST1006:65:C0VRNACXX:2:1102:15430:43570
at net.sf.picard.sam.SamToFastq.assertPairedMates(SamToFastq.java:325)
at net.sf.picard.sam.SamToFastq.doWork(SamToFastq.java:146)
at
net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
at net.sf.picard.sam.SamToFastq.main(SamToFastq.java:119)
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