[khmer] Paired-end error

Raf Winand raf.winand at esat.kuleuven.be
Fri Oct 30 07:37:25 PDT 2015


Hi

I'm trying out some of the examples I found on the internet and am now
working on part of the data that comes with walk-through called Kalamazoo
Metagenome Assembly protocol. The data set I'm currently trying out is
SRR492065. After running trimmomatic I end up with two PE files that I
interleave using the script 'interleave-reads.py'. When I run
'normalize-by-median.py' with the --paired option on this interleaved file,
it gives an error (output below). I also used the script
'extract-paired-reads.py' on the interleaved file and when it finishes it
says "DONE; read 10264272 sequences, 5132136 pairs and 0 singletons" so the
original file was probably fine. Running the normalization again on the
output of 'extract-paired-reads.py' gives the exact same error as before.

Do you have any idea what might be causing this?

Best regards
Raf


|| This is the script normalize-by-median.py in khmer.
|| You are running khmer version 2.0+36.g799039f
|| 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., 2015.
http://dx.doi.org/10.12688/f1000research.6924.1
||   * CT Brown et al., arXiv:1203.4802 [q-bio.GN]
||
|| Please see http://khmer.readthedocs.org/en/latest/citations.html for
details.


PARAMETERS:
 - kmer size =    20 (-k)
 - n tables =     4 (-N)
 - max tablesize = 8e+09 (-x)

Estimated memory usage is 3.2e+10 bytes (n_tables x max_tablesize)
--------
making countgraph
... kept 100000 of 100000 or 100.0% sofar
... in file SRR492065_trim_combined.fastq.pe
... kept 199984 of 200000 or 100.0% sofar
... in file SRR492065_trim_combined.fastq.pe
... kept 299832 of 300000 or 99.9% sofar
... in file SRR492065_trim_combined.fastq.pe
... kept 399356 of 400000 or 99.8% sofar
... in file SRR492065_trim_combined.fastq.pe
** ERROR: Unpaired reads when require_paired is set!
** Failed on SRR492065_trim_combined.fastq.pe:
** Exiting!




-- 
Raf Winand
PhD student
Faculty of Engineering - ESAT/STADIUS
Bioinformatics Group
Kasteelpark Arenberg 10 bus 2446
3001 Heverlee
BELGIUM
Tel: +32 16 32 86 43
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