SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
CollectGcBiasMetrics.jar doc2r Bioinformatics 1 10-23-2013 08:06 AM
Problems Running Picard's ReorderSam tatinhawk Bioinformatics 3 08-26-2012 07:57 PM
ReorderSam.jar in picard and GATK wisekh Bioinformatics 0 12-12-2011 07:27 AM
Estimatelibrarycomplexity.jar in Picard Jin Pan Bioinformatics 0 12-02-2011 06:46 AM
Myrna new reference jar middlemale RNA Sequencing 2 01-10-2011 02:39 PM

Reply
 
Thread Tools
Old 03-13-2012, 09:45 AM   #1
wijota
Junior Member
 
Location: Salisbury

Join Date: Mar 2012
Posts: 1
Default ReorderSam.jar problem

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 [email protected] 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
wijota is offline   Reply With Quote
Old 02-26-2014, 07:01 AM   #2
msarotti
Junior Member
 
Location: Milano

Join Date: Feb 2014
Posts: 2
Default

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
msarotti is offline   Reply With Quote
Old 11-10-2014, 05:26 AM   #3
yuelincoln
Junior Member
 
Location: hK

Join Date: Jun 2014
Posts: 5
Default

i also confront this problem, have you solve it?
yuelincoln is offline   Reply With Quote
Reply

Tags
reorder sam

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:03 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO