[khmer] interleave-reads.py error

[Titus Brown]

Hi Dacotah, thank you for the report! We should have fixed this in the 1.4 release (the latest). Please let us know if that works for you (or not)!

--
Titus Brown, ctbrown at ucdavis.edu

> On Jul 1, 2015, at 10:32 AM, Dacotah Melicher <dacotahm at gmail.com> wrote:
> 
> 
> Precisely describe what you are trying to do. Reread it from the perspective of someone else trying to reproduce your task.
> Copy-and-paste the exact command that is causing the problem. Include the steps you performed leading up to the issue.
> 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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