File "/usr/local/bioinfsoftware/python/current/bin/split_libraries_fastq.py", line 391, in <module>
File "/usr/local/bioinfsoftware/python/current/bin/split_libraries_fastq.py", line 370, in main
for fasta_header, sequence, quality, seq_id in seq_generator:
File "/usr/local/bioinfsoftware/python/current/lib/python2.7/site-packages/qiime-1.9.1.dev0-py2.7.egg/qiime/split_libraries_fastq.py", line 317, in process_fastq_single_end_read_file
parse_fastq(fastq_read_f, strict=False, phred_offset=phred_offset)):
File "/usr/local/bioinfsoftware/python/current/lib/python2.7/site-packages/skbio/parse/sequences/fastq.py", line 174, in parse_fastq
skbio.parse.sequences._exception.FastqParseError: Failed qual conversion for seq id: M01176:175:000000000-AJRBC:1:1101:15763:1979 1:N:0:1. This may be because you passed an incorrect value for phred_offset.
That seq id is the first in the files.
I get the same error message with and without --store_demultiplexed_fastq; with --phred_offset 33 and with --phred_offset 64 ; with and without -q 20
Looking at the code that generated the message, line 174 of fastq.py, the line that is triggering the error is
if enforce_qual_range and ((qual < 0).any() or (qual > 62).any())
which is concerning because the output of FastQC on reads.fastq shows quality scores up to 76
Edit: I have attached the output of qiime_config -t , and the 1st read and barcode, which are enough to show the error
Thanks for your time,
I presume where 2 calls agree the scores are summed?