Hey Feliks,
it does indeed look a problem with your SAM file as described.
Conceptually the resolve pairs seems like a correct solution, and so I
would contact the author that script or leave report an issue on that
repository's github website.
N
On Wed, Sep 3, 2014 at 9:47 AM, Trakhtenberg, Feliks <
[email protected]> wrote:
> 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 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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