[khmer] FW: khmer problem

Amy Rebecca Ellison are35 at cornell.edu
Wed Nov 6 11:25:56 PST 2013

Forwarded as requested.

Thanks, Amy

From: Amy Rebecca Ellison
Sent: 06 November 2013 11:57
To: titus at idyll.org
Subject: khmer problem

Dear Prof. Brown,

I am trying to run khmer script normalize-by-median.py but I keep getting this error at the same point in the process:

 kept 561892 of 99000000 , or 0 %
... in file Aga_all.fq.gz
... kept 561906 of 99100000 , or 0 %
... in file Aga_all.fq.gz
... kept 561921 of 99200000 , or 0 %
... in file Aga_all.fq.gz
Traceback (most recent call last):
  File "/programs/khmer/scripts/normalize-by-median.py", line 156, in <module>
  File "/programs/khmer/scripts/normalize-by-median.py", line 85, in main
    for n, batch in enumerate(batchwise(screed.open(input_filename), batch_size)):
  File "/usr/local/lib/python2.7/site-packages/screed-0.7-py2.7.egg/screed/fastq.py", line 52, in fastq_iter
    raise IOError('sequence and accuracy strings must be '\
IOError: sequence and accuracy strings must be of equal length

I wonder if you have had this issue previously and have any recommendations? Thank you for your time.

Dr. Amy Ellison PhD
Postdoctoral Research Associate

Department of Ecology & Evolutionary Biology
E221 Corson Hall
Cornell University
Ithaca, NY 14853
are35 at cornell.edu

More information about the khmer mailing list