[khmer] interleave-reads.py error

[Dacotah Melicher]

   1. Precisely describe what you are trying to do. Reread it from the
   perspective of someone else trying to reproduce your task.
   2. Copy-and-paste the exact command that is causing the problem. Include
   the steps you performed leading up to the issue.
   3. Include the complete error message; if it is large, include a link to
   a file.


Linux 3.19.0-15-generic x86_64 (Virtualbox guest on a Windows 7 host)

Python 2.7.9

Khmer1.1

Hello,

I'm trying to work through trimming and normalizing a data set and I
receive the following error from *interleave-reads.py* after running
Trimmomatic.  I have successfully run this data set through on another
machine as-is and with the same commands but now I receive this error.


Input Read Pairs: 3995957 Both Surviving: 838881 (20.99%) Forward Only
Surviving: 3157067 (79.01%) Reverse Only Surviving: 0 (0.00%) Dropped: 9
(0.00%)
TrimmomaticPE: Completed successfully

|| This is the script 'interleave-reads.py' in khmer.
|| You are running khmer version 1.1
|| You are also using screed version 0.9
||
|| If you use this script in a publication, please cite EACH of the
following:
||
||   * MR Crusoe et al., 2014. doi: 10.6084/m9.figshare.979190
||
|| Please see the CITATION file for details.

Interleaving:
    s1_pe
    s2_pe
... 0 pairs
Traceback (most recent call last):
  File "/usr/local/share/khmer/scripts/interleave-reads.py", line 124, in
<module>
    main()
  File "/usr/local/share/khmer/scripts/interleave-reads.py", line 115, in
main
    "This doesn't look like paired data! %s %s" % (name1, name2)
AssertionError: This doesn't look like paired data!
M00366:65:000000000-ABGLH:1:1101:10774:1303 1:N:0:6/1
M00366:65:000000000-ABGLH:1:1101:10774:1303 2:N:0:6/2


Thanks!

Dacotah
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