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
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
Comment