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Old 06-11-2019, 04:01 AM   #223
bwubb
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Location: Philadelphia

Join Date: Jan 2012
Posts: 58
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Greetings,

I have a seemingly simple problem, that Im sure bbmap can help with, but Im unclear what steps must be taken for success.

I have several bams from paired end sequencing where some number of mates have been removed. The remaining read still says it is paired so every tool seems to throw an error. Samtools or picard fixmate does not correct it, at best they yell the read names in question.

I am trying to use reformat.sh to remove those mates that remain, but I also seem to get a java exception, even when just trying to convert to fastq.

Code:
[bwubb@node107 disambres]$ reformat.sh -Xmx5g in=qsortA.bam out1=reads1.fq out2=reads2.fq ow
java -ea -Xmx5g -cp /home/bwubb/software/bbmap/current/ jgi.ReformatReads -Xmx5g in=qsortA.bam out1=reads1.fq out2=reads2.fq ow
Executing jgi.ReformatReads [-Xmx5g, in=qsortA.bam, out1=reads1.fq, out2=reads2.fq, ow]

Set INTERLEAVED to true
Found samtools 1.9
Input is being processed as paired
Exception in thread "Thread-2" java.lang.AssertionError: K00315:202:H577WBBXY:7:1101:1438:38767 13      -1      -       57328513        57328662        1000000100000000011     1       0  60       TCCAGAAAGAGAGTTCTTGAAAGAAAGAGGCGCTATCATTTTGACACAGATGGNAAGGGCTCGATTCACGATCAAAAAGGCTCCAAAAANAAAAAAAATTCTGTTTGTTNTNCTTTTTCCTCCNGATTCTAGTTTTTTTNTTATNTTTTG  AAFFFFFAJJJJJ7FFFJJ7JJ7FJJJJJFFJJJJJFJJJJJF-A-AAFFJFA!AF---AAJJ-AJF<FF-AAFAF<AAAJJJJFA-7A!--77-<A<JJ<A--7A<FJ!J!<FJJJJA<FF7!)7AJF---7AFJJFJ!JF--!7-7<F      .       30      C68m28Nm53      .

K00315:202:H577WBBXY:7:1101:1438:38767  113     19      57328582        60      68S82M  1       176081441       0       CAAAANATAANAAAAAAACTAGAATCNGGAGGAAAAAGNANAACAAACAGAATTTTTTTTNTTTTTGGAGCCTTTTTGATCGTGAATCGAGCCCTTNCCATCTGTGTCAAAATGATAGCGCCTCTTTCTTTCAAGAACTCTCTTTCTGGA      F<7-7!--FJ!JFJJFA7---FJA7)!7FF<AJJJJF<!J!JF<A7--A<JJ<A<-77--!A7-AFJJJJAAA<FAFAA-FF<FJA-JJAA---FA!AFJFFAA-A-FJJJJJFJJJJJFFJJJJJF7JJ7JJFFF7JJJJJAFFFFFAA      NM:i:1  MD:Z:28C53      MC:Z:150M       AS:i:80 XS:i:21 SA:Z:1,176081357,+,81S62M7S,54,7;       RG:Z:FGC2033.7
flag=1110001

        at stream.SamReadInputStream.toReadList(SamReadInputStream.java:136)
        at stream.SamReadInputStream.fillBuffer(SamReadInputStream.java:89)
        at stream.SamReadInputStream.hasMore(SamReadInputStream.java:53)
        at stream.ConcurrentGenericReadInputStream$ReadThread.readLists(ConcurrentGenericReadInputStream.java:643)
        at stream.ConcurrentGenericReadInputStream$ReadThread.run(ConcurrentGenericReadInputStream.java:635)

I thought I could make read1.fq reads2.fq and use repair.sh Clearly it finds the two problem reads. I have tried other arguments with the reformat.sh, and a few other tools, but none want to correct the MATE_NOT_FOUND problem. It would seem impossible that I am the first person to run into this issue. Thank you very much for any advice/help.

-bwubb

EDIT: Sorry if this post shows up multiple times. I literally tried making it three times and nothing showed up for a full day. Tried a quick reply and it showed up immediately.
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