[khmer] Issue interleaving reads with cutadapt processed fastq

[Will Shoemaker]

Hello,

I am unable to merge pairs of MiSeq reads using the khmer scrip
interleave-reads.py in khmer version 1.3. The R1 and R2 files have had the
first 10 bases trimmed off and have been quality filtered using cutadapt
v1.9.

Using the command zcat file_name.fastq.gz | echo $((`wc -l`/4)) on each set
of reads, I found that the number of reads in R1 and R2 is the same.

The command I'm running is:
interleave-reads.py -o output.fastq.gz R1.fastq.gz R2.fastq.gz   (file
names changed for readability)

My OS is Linux 2.6.32-573.3.1.el6.x86_64 x86_64

Attached is a txt file of the khmer output.

Could this be an issue of cutadapt changing the file format? I am able to
run assemblies on cutadapt processed reads.


Best,
Will Shoemaker
-- 
Will Shoemaker
Indiana University
Graduate Student: Lennon Lab
Evolution, Ecology, & Behavior Program
Jordan Hall 238
wrshoema at umail.iu.edu
@shoemakah <https://twitter.com/shoemakah>
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|| This is the script 'interleave-reads.py' in khmer.
|| You are running khmer version 1.3-366-g3ed54b8
|| You are also using screed version 0.8-rc4
||
|| If you use this script in a publication, please cite EACH of the following:
||
||   * MR Crusoe et al., 2014. http://dx.doi.org/10.6084/m9.figshare.979190
||
|| Please see http://khmer.readthedocs.org/en/latest/citations.html for details.

Interleaving:
	GSF911-711_S1_L001_R1_001_U10_Q30.fastq
	GSF911-711_S1_L001_R2_001_U10_Q30.fastq
... 0 pairs
ERROR: Input files contain different number of records.