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bbduk.sh AssertionError #18

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yyan823 opened this issue Dec 13, 2018 · 0 comments
Open

bbduk.sh AssertionError #18

yyan823 opened this issue Dec 13, 2018 · 0 comments

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@yyan823
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yyan823 commented Dec 13, 2018

Dear Developers,

I'm trying to use bbduk.sh to remove adapters and do quality trimming in one pair end illumina reads files (in fastq.gz format). I got the following error:

Changed from ASCII-33 to ASCII-64 on input quality @ (Q31) for base N at lines 1 and 3, position 96 while prescanning.
Changed from ASCII-64 to ASCII-33 on input quality 8 (Q-8) for base G at lines 5 and 7, position 9 while prescanning.
Exception in thread "main" java.lang.AssertionError: ASCII encoding for quality (currently ASCII-33) appears to be wrong 
for input quality 25 for base G at lines 5 and 7, position 9.
GTCGTAACTATGGTCAACGTTCAAGAACTAATCAACTCCGATGATGTAGTCGTCTTCAGCAAGTCCTACTGCCCTTTCTGTGTCCGCGCAAAGACTNNNN
@SRR3734914.2 HWI-ST942:114:C11YJACXX:3:1101:1963:2179 length=100
[64, 83, 82, 82, 51, 55, 51, 52, 57, 49, 52, 46, 50, 32, 72, 87, 73, 45, 83, 84, 57, 52, 50, 58, 49, 49, 52, 58, 67, 49, 49, 89, 74, 65, 67, 88, 88, 58, 51, 58, 49, 49, 48, 49, 58, 49, 57, 54, 51, 58, 50, 49, 55, 57, 32, 108, 101, 110, 103, 116, 104, 61, 49, 48, 48]
	at stream.FASTQ.testQuality(FASTQ.java:231)
	at stream.FASTQ.isInterleaved(FASTQ.java:131)
	at stream.FastqReadInputStream.<init>(FastqReadInputStream.java:58)
	at stream.ConcurrentReadInputStream.getReadInputStream(ConcurrentReadInputStream.java:121)
	at stream.ConcurrentReadInputStream.getReadInputStream(ConcurrentReadInputStream.java:55)
	at jgi.BBDukF.spawnProcessThreads(BBDukF.java:1674)
	at jgi.BBDukF.process2(BBDukF.java:1058)
	at jgi.BBDukF.process(BBDukF.java:967)
	at jgi.BBDukF.main(BBDukF.java:71)

Could you please help to see what does this mean and potentially how to solve this?

Thank you!

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