ReorderSam.jar problem

[wijota]

Hi

I'm trying to use GATK RealignerTargetCreator but got an error message saying "Lexicographically sorted human genome sequence detected in reads."

$ java -jar /local/software/rh53/GATK/Sting/dist/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /temp/wjt/EXOME/OXC/Z1905/GATK/hg18.fa -I /temp/wjt/EXOME/OXC/Z1905/BAM/Z1905_novoalign.bam -o /temp/wjt/EXOME/OXC/Z1905/BAM/Z1905.intervals

I've got a ref dictionary file (hg18.dict) and ran ReorderSam.jar which seemed to work ok (output below) but when rerunning GATK RealignerTargetCreator with the resorted bam I get the same error message.

$ java -jar /local/software/rh53/GATK/Sting/dist/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /temp/wjt/EXOME/OXC/Z1905/GATK/hg18.fa -I /temp/wjt/EXOME/OXC/Z1905/BAM/Z1905_novoalignRS.bam -o /temp/wjt/EXOME/OXC/Z1905/BAM/Z1905.intervals

"Lexicographically sorted human genome sequence detected in reads."

Thanks for any help regarding this query.

Will

ReorderSam.jar output:
$ java -jar ReorderSam.jar INPUT=/temp/wjt/EXOME/OXC/Z1905/BAM/Z1905_novoalign.bam OUTPUT=/temp/wjt/EXOME/OXC/Z1905/BAM/Z1905_novoalignRS.bam REFERENCE=/temp/wjt/EXOME/OXC/Z1905/GATK/hg18.fa

Executing as wjt@blue32 on Linux 2.6.18-164.6.1.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_16-b01; Picard version: 1.64(1146)
INFO 2012-03-13 15:14:41 ReorderSam SAM/BAM file
INFO 2012-03-13 15:14:41 ReorderSam SN=%s LN=%d%nchr10135374737
INFO 2012-03-13 15:14:41 ReorderSam SN=%s LN=%d%nchr10_random113275
.
.
INFO 2012-03-13 15:14:41 ReorderSam Reordering SAM/BAM file:
INFO 2012-03-13 15:14:41 ReorderSam Reordering read contig chr10 [index=0] to => ref contig chr10 [index=0]
INFO 2012-03-13 15:14:41 ReorderSam Reordering read contig chr10_random [index=1] to => ref contig chr10_random [index=1]
.
.
INFO 2012-03-13 15:14:41 ReorderSam Reordering read contig chrX_random [index=47] to => ref contig chrX_random [index=47]
INFO 2012-03-13 15:14:41 ReorderSam Reordering read contig chrY [index=48] to => ref contig chrY [index=48]
INFO 2012-03-13 15:14:41 ReorderSam Writing reads...
INFO 2012-03-13 15:14:41 ReorderSam Processing chr10
INFO 2012-03-13 15:15:33 ReorderSam Wrote 2877802 reads
INFO 2012-03-13 15:15:33 ReorderSam Processing chr10_random
.
.
INFO 2012-03-13 15:36:09 ReorderSam Wrote 6465436 reads
[Tue Mar 13 15:36:09 GMT 2012] net.sf.picard.sam.ReorderSam done. Elapsed time: 21.48 minutes.
Runtime.totalMemory()=1055588352

[msarotti]

Hi

I've got the same problem here

When trying to use RealignerTargetCreator, GATK tells me that the sequence is in Lexicographically, so i tried to solve with ReorderSam which it works fine.
But when I run RealignerTargetCreator on the sorted bam, i find the same error.

Hope someone can help,
Thanks!!

Marco

[yuelincoln]

i also confront this problem, have you solve it?