Re: [Samtools-help] Picard release 1.46

[Alec W. <al...@br...>]

Hi Robin,

I will improve this error message so it is clearer. 
Homo_sapiens_assembly19.rRNA.interval_list has 25 sequences, and 
s_1_2_pefca_2_sorted.bam has 85.  You may need to edit the interval list 
so that it has all the sequences in your bam, and uses the same naming 
convention.

-Alec

On 5/26/11 2:09 PM, mei ge wrote:
> Hi Alec:
> I used your ribosomal interval file and I got an error as follow:
> [Thu May 26 13:50:45 EDT 2011] 
> net.sf.picard.analysis.CollectRnaSeqMetrics 
> REF_FLAT=/home/gtf/hg19/refFlat_table_for_picard.txt 
> RIBOSOMAL_INTERVALS=/home/gtf/ribosomal_RNA/Homo_sapiens_assembly19.rRNA.interval_list 
> STRAND_SPECIFICITY=NONE
> INPUT=/s_1_2_pefca_2/s_1_2_pefca_2_sorted.bam 
> OUTPUT=/s_1_2_pefca_2/s_1_2_pefca_2_RNAseq_metrics.txt 
> REFERENCE_SEQUENCE=/databases/hs_chromosomes/hg19.fa ASSUME_SORTED=true
> VALIDATION_STRINGENCY=SILENT
> STOP_AFTER=0
> VERBOSITY=INFO
> QUIET=false
> COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false 
> CREATE_MD5_FILE=false
> INFO 2011-05-26 13:50:46 CollectRnaSeqMetrics Loaded 21987 genes.
> [Thu May 26 13:50:46 EDT 2011] 
> net.sf.picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.03 
> minutes.
> Runtime.totalMemory()=165347328
> Exception in thread "main" 
> net.sf.samtools.util.SequenceUtil$SequenceListsDifferException: 
> Sequence dictionaries are not the same size (25, 85)
> at 
> net.sf.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:84)
> at 
> net.sf.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:126)
> at 
> net.sf.picard.analysis.CollectRnaSeqMetrics.setup(CollectRnaSeqMetrics.java:86)
> at 
> net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:101)
> at 
> net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:54)
> at 
> net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
> at 
> net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:118)
> at 
> net.sf.picard.analysis.CollectRnaSeqMetrics.main(CollectRnaSeqMetrics.java:77)
>
>
> --- On *Thu, 5/26/11, Alec Wysoker /<al...@br...>/* wrote:
>
>
>     From: Alec Wysoker <al...@br...>
>     Subject: Re: [Samtools-help] Picard release 1.46
>     To: "mei ge" <rge...@ya...>
>     Cc: "Sam...@li..."
>     <Sam...@li...>
>     Date: Thursday, May 26, 2011, 10:58 AM
>
>     Hi Robin,
>
>     Human HG19 is attached.  I don't have one for mouse.  I just
>     extracted these from gencode GTF file.  Presumably you could do
>     the same for mouse. Interval list format described here:
>     http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html
>
>     Note that this file is not required by CollectRnaSeqMetrics, but
>     if you do not provide it the program will not be able to determine
>     when reads map to rRNA.
>
>     -Alec
>
>     On 5/26/11 9:54 AM, mei ge wrote:
>>     Hi Alec:
>>     I am looking for human (hg19) and mouse(mm9).
>>     Thanks
>>     Robin
>>
>>     --- On *Wed, 5/25/11, Alec Wysoker /<al...@br...>
>>     <http://us.mc388.mail.yahoo.com/mc/compose?to=al...@br...>/*
>>     wrote:
>>
>>
>>         From: Alec Wysoker <al...@br...>
>>         <http://us.mc388.mail.yahoo.com/mc/compose?to=al...@br...>
>>         Subject: Re: [Samtools-help] Picard release 1.46
>>         To: "mei ge" <rge...@ya...>
>>         <http://us.mc388.mail.yahoo.com/mc/compose?to=rge...@ya...>
>>         Cc: "samtools help" <sam...@li...>
>>         <http://us.mc388.mail.yahoo.com/mc/compose?to=sam...@li...>
>>         Date: Wednesday, May 25, 2011, 4:52 PM
>>
>>         Hi Mei,
>>
>>         Are you looking for human?  If so, what genome build?
>>
>>         -Alec
>>
>>         On 5/25/11 3:15 PM, mei ge wrote:
>>>         Hi Alec,
>>>         I use the CollectRnaSeqMetrics in the new release Picard.  I
>>>         don't know where to get the Ribosomal_intervals file.  Can
>>>         you point a place for the file?
>>>         Thanks
>>>         Mei
>>>