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Old 02-01-2018, 12:51 PM   #1
gacarson
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Location: Stanford, CA

Join Date: Feb 2018
Posts: 4
Default Picard tools error: Sequence not found in dictionary

I'm currently troubleshooting the use of Picard's BedToIntervalList with an odd error that I don't quite understand. I wonder if one of you can help me.

My input:
java -jar picard.jar BedToIntervalList I=Covered_hg38.bed O=list.interval_list SD=reference.dict

Error:
Exception in thread "main" picard.PicardException: Sequence '1' was not found in the sequence dictionary
at picard.util.BedToIntervalList.doWork(BedToIntervalList.java:155)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:269)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)

Can anyone help me make sense of this error?

if useful...

The bed file I downloaded from Agilent, and converted from hg19 to hg38 using https://uswest.ensembl.org/Homo_sapi...verter?db=core

The fasta file I downloaded from UCSC (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/) and fed that to CreateSequenceDictionary (java -jar picard.jar CreateSequenceDictionary R=reference.fasta)

format of the bed file:
1 11107307 11107584 ref|MTOR,ref|NM_004958,ens|ENST00000376838,ens|ENST00000473471,ens|ENST00000490931,ens|ENST00000361445,mRNA|AB209995,mRNA|BC117166,mRNA|L34075,mRNA|AK304273,mRNA|AK302863,mRNA|AK126762,mRNA|U88966

format of the .dict file:
@HD VN:1.5
@SQ SN:chr1 LN:248956422 M5:2648ae1bacce4ec4b6cf337dcae37816 UR:file:/Users/gacarson/picard/build/libs/reference.fasta

Last edited by gacarson; 02-01-2018 at 01:19 PM.
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Old 02-01-2018, 01:31 PM   #2
gacarson
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Location: Stanford, CA

Join Date: Feb 2018
Posts: 4
Default

solved!
The ensembl converter I had used was the culprit. I instead used CrossMap to convert the Agilent supplied (hg19) annotated bed file to hg38, and then fed that file back to BedToIntervalList and things seem to have worked.

Input:
java -jar picard.jar BedToIntervalList I=hg38.bed O=list.interval_list SD=reference.dict

After, I see my list.interval_list file!
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