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Old 02-01-2018, 12:51 PM   #1
Junior Member
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

Exception in thread "main" picard.PicardException: Sequence '1' was not found in the sequence dictionary
at picard.util.BedToIntervalList.doWork(
at picard.cmdline.CommandLineProgram.instanceMain(
at picard.cmdline.PicardCommandLine.instanceMain(
at picard.cmdline.PicardCommandLine.main(

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

The fasta file I downloaded from UCSC ( 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
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Location: Stanford, CA

Join Date: Feb 2018
Posts: 4

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.

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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