add_qiime_labels.py error

[hillar...@gmail.com]

Hi all,

I am attempting to use the command add_qiime_labels.py for 59 individuals ITS2 MiSeq runs. I receive an error message that other users have reported (copied below), but the quoted line with the error does not tell me the entire line name, I am not sure how to sort through millions of reads to find it... 

Traceback (most recent call last):

  File "/usr/local/qiime/py2.7.9/bin/add_qiime_labels.py", line 111, in <module>

    main()

  File "/usr/local/qiime/py2.7.9/bin/add_qiime_labels.py", line 107, in main

    output_dir, count_start)

  File "/usr/local/qiime/py2.7.9/lib/python2.7/site-packages/qiime/add_qiime_labels.py", line 47, in add_qiime_labels

    counter=count_start)

  File "/usr/local/qiime/py2.7.9/lib/python2.7/site-packages/qiime/add_qiime_labels.py", line 144, in write_combined_fasta

    for label, seq in parse_fasta(open(curr_fasta, "U")):

  File "/usr/local/qiime/py2.7.9/lib/python2.7/site-packages/skbio/parse/sequences/fasta.py", line 148, in parse_fasta

    "Found label line without sequences: %s" % rec)

skbio.io._exception.RecordError: Found label line without sequences: ['>M02082:200:000000000-']

I know that in order to fix this error I need to find the label line that consists of "['>M02082:200:000000000-']" but this is the prefix for all of my samples label lines, as below:

>M02082:200:000000000-AUB73:1:1101:13640:1364

GTGAATTGCAGAACTCCGTGA.....

>M02082:200:000000000-AUB73:1:1101:12021:1388

GTGAATTGCAGAACTCCGTGA.....

>M02082:200:000000000-AUB73:1:1101:18934:1403

GTGAATTGCAGAACTCCGTGA.....

Any suggestions are extremely welcome! 

Cheers,

Hillary

[TonyWalters]

Hello Hillary,

There is a non-qiime script that might help you here:

https://gist.github.com/walterst/9457540