You should also go to the folks who provided you the BAM and ask for them to
fix it, as this goes against common conventions and best practices.
Unfortunately Picard cannot support BAMs with such problems. I apologize for
your inconvenience.
N
Thumb typed for added typos
> On Sep 5, 2014, at 9:33 AM, Nils Homer <[email protected]> wrote:
>
> 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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>
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