gravatar for Peter Chung

2 hours ago by

Hong Kong

I have a paired end fastq file and when I ran trim galore, the error said lengths of bases and qualities do not match,
so I searched the solution and recommended to using bbtools reformat.sh to discard reads that have mismatching lengths of bases and qualities:

reformat.sh in=pair_1.fq.gz in2=pair_2.fq.gz out=fixed_1.fq.gz out2=fixed_2.fq.gz tossbrokenreads=t

The error
Set INTERLEAVED to false
Input is being processed as paired
pigz: abort: read error on pair_1.fq.gz (Input/output error)
java.lang.AssertionError:
There appear to be different numbers of reads in the paired input files.
The pairing may have been corrupted by an upstream process. It may be fixable by running repair.sh.
at stream.ConcurrentGenericReadInputStream.pair(ConcurrentGenericReadInputStream.java:497)
at stream.ConcurrentGenericReadInputStream.readLists(ConcurrentGenericReadInputStream.java:362)
at stream.ConcurrentGenericReadInputStream.run0(ConcurrentGenericReadInputStream.java:206)
at stream.ConcurrentGenericReadInputStream.run(ConcurrentGenericReadInputStream.java:182)
at java.lang.Thread.run(Thread.java:745)

so I tried to repair it by using bbtools repairs.sh

repair.sh in1=pair_1.fq.gz in2=pair_2.fq.gz out1=fixed_1.fq.gz out2=fixed_2.fq.gz outs=singletons.fq repair

Set INTERLEAVED to false
Started output stream.
pigz: abort: read error on pair_1.fq.gz (Input/output error)
java.lang.Exception:
Mismatch between length of bases and qualities for read 107893745 (id=ST-E00126:1085:HF3YVCCX2:1:2106:16620:58339 1:N:0:TAAGCTCC+AGATCTCG).

AAFFFFJJJJJJJJJJJJJJJJJJ
GTGTAGGACATCCATTTTATCAAGTTTCTGCTACAAGAAATGAAAAAATGAGACACTTGATTACTACAGGCAGACCAACCAAAGTCTTTGTTCCACCTTTTAAAACTAAATCGCATTTTCACAGAGTTGAACAGTGTGTTAGGAATATTA

This can be bypassed with the flag 'tossbrokenreads' or 'nullifybrokenquality'
at shared.KillSwitch.kill(KillSwitch.java:96)
at stream.Read.validateQualityLength(Read.java:214)
at stream.Read.validate(Read.java:104)
at stream.Read.<init>(Read.java:76)
at stream.Read.<init>(Read.java:50)
at stream.FASTQ.quadToRead_slow(FASTQ.java:809)
at stream.FASTQ.toReadList(FASTQ.java:646)
at stream.FastqReadInputStream.fillBuffer(FastqReadInputStream.java:107)
at stream.FastqReadInputStream.nextList(FastqReadInputStream.java:93)
at stream.ConcurrentGenericReadInputStream$ReadThread.readLists(ConcurrentGenericReadInputStream.java:680)
at stream.ConcurrentGenericReadInputStream$ReadThread.run(ConcurrentGenericReadInputStream.java:656)

but the error said tossbrokenreads again, it kinda fall into a loop.

Anyone has experience this, please advice. Thanks.

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modified 1 hour ago

written
2 hours ago
by

Peter Chung120



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