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Old 12-09-2019, 02:30 PM   #676
kmavrommatis
Junior Member
 
Location: Bay Area, CA, USA

Join Date: Jul 2013
Posts: 3
Default reformat.sh Failed to auto-detect quality coding

Hi,
when I am running reformat.sh on a set of fastq files downloaded from SRA

Quote:
reformat.sh maxcalledquality=40 out=SRR1_R1.fq.gz qout=33 mincalledquality=2 out2=SRR1_R2.fq.gz qin=auto fixjunk=t in=/RNA-Seq/Raw/fastq.20190712/SRR1_1.fastq.gz in2=/RNA-Seq/Raw/fastq.20190712/SRR1_2.fastq.gz

The program crashes with the following error:

Quote:
Set INTERLEAVED to false
Changed from ASCII-33 to ASCII-64 on input quality 64 for base N while prescanning.
Changed from ASCII-64 to ASCII-33 on input quality 35 while prescanning.
Exception in thread "main" java.lang.AssertionError: Failed to auto-detect quality coding; quitting. Please manually set qin=33 or qin=64.
at stream.FASTQ.testQuality(FASTQ.java:218)
at stream.FASTQ.isInterleaved(FASTQ.java:129)
at stream.ConcurrentReadInputStream.getReadInputStream(ConcurrentRea at stream.ConcurrentReadInputStream.getReadInputStream(ConcurrentReadInputStream.java:119)
at jgi.ReformatReads.process(ReformatReads.java:377)
m(ConcurrentReadInputStream.java:55)
at jgi.ReformatReads.process(ReformatReads.java:377)
at jgi.ReformatReads.main(ReformatReads.java:45)
The version of BBMAP used is 37.64.
Any advice on how to address this issue?
This is part of a bigger pipeline and the intention is to apply it on 100s of files.
Thanks in advance for your help.
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