Hello all,
I have some question concerning bbmerge. I would like to merge overlapping read pairs. For this I use this command:
When having multiple values for trimq I get the following error
And the program stop. If I remove the ordered=t option this appears:
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
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
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.
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)
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
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