SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to use Picard's MarkDuplicates cliff Bioinformatics 12 01-26-2015 10:56 PM
About Picard Jin Pan Bioinformatics 8 07-15-2014 04:55 AM
picard error seq_GA Bioinformatics 2 07-15-2014 04:50 AM
Picard and GATK poisson200 Bioinformatics 6 08-15-2012 07:04 AM
Picard: HsMetrics Seq84 Bioinformatics 0 04-18-2011 02:24 AM

Reply
 
Thread Tools
Old 04-29-2010, 12:56 PM   #1
bair
Member
 
Location: London

Join Date: Jan 2010
Posts: 65
Default Picard

Hello all,

I merged two ELAND export files by using samtools, but samtools flagstat shows that

191134982 in total
0 QC failure
0 duplicates
139825529 mapped (73.16%)
191134982 paired in sequencing
95567491 read1
95567491 read2
0 properly paired (0.00%)
115989136 with itself and mate mapped
23836393 singletons (12.47%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)

Why it shows 0 properly paired?

Couldn't run picard MarkDuplicates, thread exception:

Exception in thread "main" java.lang.NullPointerException
at net.sf.picard.sam.DiskReadEndsMap.remove(DiskReadEndsMap.java:87)
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:289)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:126)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:143)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:105)

Any help? Many thanks.
bair is offline   Reply With Quote
Old 04-29-2010, 01:58 PM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by bair View Post
Hello all,

I merged two ELAND export files by using samtools, but samtools flagstat shows that

191134982 in total
0 QC failure
0 duplicates
139825529 mapped (73.16%)
191134982 paired in sequencing
95567491 read1
95567491 read2
0 properly paired (0.00%)
115989136 with itself and mate mapped
23836393 singletons (12.47%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)

Why it shows 0 properly paired?
It looks like the converter did not set the "properly paired" bit in the FLAG field.

Quote:
Originally Posted by bair View Post
Couldn't run picard MarkDuplicates, thread exception:

Exception in thread "main" java.lang.NullPointerException
at net.sf.picard.sam.DiskReadEndsMap.remove(DiskReadEndsMap.java:87)
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:289)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:126)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:143)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:105)

Any help? Many thanks.
Looks like a bug to me.

Send both to samtools-help@lists.sourceforge.net
nilshomer is offline   Reply With Quote
Old 07-15-2014, 04:45 AM   #3
Lv Ray
Member
 
Location: GZ,China

Join Date: Jun 2014
Posts: 42
Default

I got the same error. Have you solved your problem, bair or nilshomer?
Lv Ray is offline   Reply With Quote
Reply

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 11:35 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO