QIIME 1.9.1 "Invalid qual file. Check the format of the qual files."

[asha febinia]

Hello,

I am experiencing problems with .qual files produced with the split_libraries_fastq.py script. I kept receiving error message that said it's invalid.

For example, with this script:
quality_scores_plot.py -q seqs.qual -o quality_histo_seqs.fna/
Traceback (most recent call last):
  File "/usr/local/bin/quality_scores_plot.py", line 95, in <module>
    main()
  File "/usr/local/bin/quality_scores_plot.py", line 91, in main
    qual_parser=parse_qual_score)
  File "/usr/local/lib/python2.7/dist-packages/qiime/quality_scores_plot.py", line 205, in generate_histogram
    qual_scores = qual_parser(qual_lines)
  File "/usr/local/lib/python2.7/dist-packages/qiime/parse.py", line 746, in parse_qual_score
    id_to_qual = dict([rec for rec in MinimalQualParser(infile, value_cast_f)])
  File "/usr/local/lib/python2.7/dist-packages/qiime/parse.py", line 759, in MinimalQualParser
    "Invalid qual file. Check the format of the qual files.")
qiime.parse.QiimeParseError: Invalid qual file. Check the format of the qual files.

When I checked the format is a bit funny. There is "[" at the beginning and "s" at the end.

>BA001_0 M02082:58:000000000-AENHY:1:1101:14649:1371 1:N:0:1 orig_bc=AAAAAAAAAAAA new_bc=AAAAAAAAAAAA bc_diffs=0
[33 33 33 33 33 33 33 33 33 37 37 37 38 36 30 37 38 36 37 38 38 38 39 38 38
 38 38 38 39 39 39 39 39 38 39 36 37 38 39 39 39 39 39 38 39 38 38 39 38 38
 38 38 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39
 39 38 39 39 39 39 39 38 38 36 36 38 39 39 39 39 37 36 39 38 39 39 39 39 39
 39 39 39 38 39 39 39 39 39 39 39 38 39 39 39 39 39 38 39 39 39 39 39 39 39
 39 39 39 39 39 39 39 39 39 39 37 38 38 38 39 39 38 38 38 38 39 38 38 36 37
 39 38 39 39 38 39 39 38 39 39 39 39 39 39 39 38 39 39 39 39 39 39 38 39 39
 38 39 39 37 38 38 35 37 38 38 37 38 38 38 38 38 36 37 38 39 39 39 37 38 39
 38 37 37 37 38 38 39 39 39 39 39 37 38 38 39 39 37 39 39 38 37 38 39 39 38
 39 38 38 39 37 38 38 38 38 38 38 38 37 38 38 38 37 37 37 37 37 37 37 37 37
 37 33 32s
>BA001_1 M02082:58:000000000-AENHY:1:1101:16444:1440 1:N:0:1 orig_bc=AAAAAAAAAAAA new_bc=AAAAAAAAAAAA bc_diffs=0
[33 33 33 33 33 37 37 33 37 37 37 37 38 37 38 38 38 38 38 36 37 38 39 38 38
 38 36 38 39 38 39 39 39 38 39 39 38 38 39 39 39 39 37 38 39 38 38 38 38 38
 38 38 39 38 38 38 38 38 37 38 39 39 38 39 39 39 39 38 35 38 39 39 39 39 39
 39 39 38 39 38 38 36 36 38 34 38 39 39 39 38 39 35 35 38 39 39 39 39 38 39
 39 38 35 37 38 39 39 39 39 39 39 39 33 38 39 38 35 35 38 39 39 39 39 39 37
 39 37 35 37 38 37 39 39 38 38 38 38 38 39 39 39 38 38 38 38 38 38 38 38 38
 38 38 38 38 37 38 39 39 39 38 38 37 37 38 37 37 37 37 38 37 37 38 37 37 37
 39 37 39 39 37 38 37 37 37 37 37 37 39 37 37 37 38 39 39 37 37 37 36 37 34
 38 38 39 39 38 39 37 37 37 32 30 37 39 39 39 39 37 38 38 37 37 38 38 38 39
 38 38 37 38 38 36 38 37 37 38 37 32 38 35 38 38 37 37 37 37 37 37 37 33 33
 33 33 33s

I got the same invalid qual files with any .fastq input file for the split_libraries_fastq.py script.

Please help?

P.S.
I have the most recent Qiime v1.9.1 virtual box with usearch and usearch61 installed.

[Se Jin Song]

Can you try using 

convert_fastaqual_fastq.py 

instead and then feeding that qual file to quality_scores_plot.py?  Let us know if you get a similar error.

Thanks,
Se Jin