SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Introducing BBMerge: A paired-end read merger Brian Bushnell Bioinformatics 128 02-24-2019 06:49 AM
Questions mkdir Oxford Nanopore 5 07-28-2016 08:52 AM
bbmerge mismatched danova Bioinformatics 3 02-23-2016 11:27 PM
bbmerge ratiomode ? danova Bioinformatics 2 02-16-2016 10:58 AM
Merging paired ends fastq files with BBMerge bi_maniac Illumina/Solexa 19 11-04-2015 01:43 AM

Reply
 
Thread Tools
Old 07-07-2017, 02:49 AM   #1
finswimmer
Member
 
Location: Europe

Join Date: Oct 2016
Posts: 60
Default Questions concerning bbmerge

Hello all,
I have some question concerning bbmerge. I would like to merge overlapping read pairs. For this I use this command:

Code:
bbmerge-auto.sh in1=Sample_L001_R1_001.fastq.gz in2=Sample_L001_R2_001.fastq.gz out=merged/Sample.extendedFrags.fastq.gz outu1=merged/Sample.notCombined_1.fastq.gz outu2=merged/Sample.notCombined_2.fastq.gz qtrim2 trimq=10,20,30 ordered=t ftm=5
When having multiple values for trimq I get the following error

Code:
Exception in thread "Thread-6" java.lang.NullPointerException
	at jgi.BBMerge$MateThread.processReadPair(BBMerge.java:2341)
	at jgi.BBMerge$MateThread.findOverlapInThread(BBMerge.java:1643)
	at jgi.BBMerge$MateThread.processReads(BBMerge.java:1583)
	at jgi.BBMerge$MateThread.run(BBMerge.java:1557)
Output buffer became full; key 1250 waiting on 995.
And the program stop. If I remove the ordered=t option this appears:

Code:
Exception in thread "Thread-7" java.lang.NullPointerException
	at jgi.BBMerge$MateThread.processReadPair(BBMerge.java:2341)
	at jgi.BBMerge$MateThread.findOverlapInThread(BBMerge.java:1643)
	at jgi.BBMerge$MateThread.processReads(BBMerge.java:1583)
	at jgi.BBMerge$MateThread.run(BBMerge.java:1557)
Exception in thread "Thread-9" java.lang.NullPointerException
	at jgi.BBMerge$MateThread.processReadPair(BBMerge.java:2341)
	at jgi.BBMerge$MateThread.findOverlapInThread(BBMerge.java:1643)
	at jgi.BBMerge$MateThread.processReads(BBMerge.java:1583)
	at jgi.BBMerge$MateThread.run(BBMerge.java:1557)
Exception in thread "Thread-6" java.lang.NullPointerException
	at jgi.BBMerge$MateThread.processReadPair(BBMerge.java:2341)
	at jgi.BBMerge$MateThread.findOverlapInThread(BBMerge.java:1643)
	at jgi.BBMerge$MateThread.processReads(BBMerge.java:1583)
	at jgi.BBMerge$MateThread.run(BBMerge.java:1557)
But the program runs fine until it's finished.

What causes this trouble and can I fix it?

Another question is: Can I do quality trimming for reads that do not overlap directly with in this step?

fin swimmer
finswimmer is offline   Reply With Quote
Old 07-07-2017, 03:42 AM   #2
finswimmer
Member
 
Location: Europe

Join Date: Oct 2016
Posts: 60
Default

Ok, I could fix the error messages by setting qtrim2 to one of the values mentioned in the manual for qtrim.

Code:
qtrim=f              Trim read ends to remove bases with quality below minq.
                     Trims BEFORE merging.
                     Values: t (trim both ends), 
                             f (neither end), 
                             r (right end only), 
                             l (left end only).
qtrim2=f             May be specified instead of qtrim to perform trimming 
                     only if merging is unsuccessful, then retry merging.
finswimmer 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 09:36 AM.


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