Failed to auto-detect quality coding
deblac...@gmail.com
this time I have another issue with JAFFA version 1.08. See the follow output
================================= Stage get_unmapped (ERR1294578) ==================================
5136176 reads; of these:
5136176 (100.00%) were unpaired; of these:
3457835 (67.32%) aligned 0 times
1678341 (32.68%) aligned exactly 1 time
0 (0.00%) aligned >1 times
32.68% overall alignment rate
java -ea -Xmx200m -cp /media/mdhdd/richard/genfusion/JAFFA-version-1.08/tools/bbmap/current/ jgi.ReformatReads in=ERR1294578/unmapped.fastq out=ERR1294578/temp.fasta threads=10
Executing jgi.ReformatReads [in=ERR1294578/unmapped.fastq, out=ERR1294578/temp.fasta, threads=10]
Set threads to 10
Changed from ASCII-33 to ASCII-64 on input quality 66 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.FastqReadInputStream.<init>(FastqReadInputStream.java:61)
at stream.ConcurrentReadInputStream.getReadInputStream(ConcurrentReadInputStream.java:119)
at stream.ConcurrentReadInputStream.getReadInputStream(ConcurrentReadInputStream.java:55)
at jgi.ReformatReads.process(ReformatReads.java:364)
at jgi.ReformatReads.main(ReformatReads.java:43)
ERROR: Command failed with exit status = 1 :
/media/mdhdd/richard/genfusion/JAFFA-version-1.08/tools/bin/reformat in=ERR1294578/unmapped.fastq out=ERR1294578/temp.fasta threads=10 ; /media/mdhdd/richard/genfusion/JAFFA-version-1.08/tools/bin/dedupe in=ERR1294578/temp.fasta out=ERR1294578/ERR1294578.fasta threads=10 absorbcontainment=f ; rm ERR1294578/temp.fasta ERR1294578/unmapped.fastq 2> /dev/null
========================================= Pipeline Failed ==========================================
One or more parallel stages aborted. The following messages were reported:
Branch ERR1294578 in stage Unknown reported message:
Command failed with exit status = 1 :
/media/mdhdd/richard/genfusion/JAFFA-version-1.08/tools/bin/reformat in=ERR1294578/unmapped.fastq out=ERR1294578/temp.fasta threads=10 ; /media/mdhdd/richard/genfusion/JAFFA-version-1.08/tools/bin/dedupe in=ERR1294578/temp.fasta out=ERR1294578/ERR1294578.fasta threads=10 absorbcontainment=f ; rm ERR1294578/temp.fasta ERR1294578/unmapped.fastq 2> /dev/null
Use 'bpipe errors' to see output from failed commands.
tanks you for your help
kids regards