[khmer] Paired-end error

C. Titus Brown ctbrown at ucdavis.edu
Fri Oct 30 08:00:43 PDT 2015


Hi Raf,

this sounds like a bug of some sort, but no clear idea of what's
going on, sorry!  I should be able to take a look at this file this
weekend.

thx,
--titus

On Fri, Oct 30, 2015 at 03:37:25PM +0100, Raf Winand wrote:
> 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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> khmer at lists.idyll.org
> http://lists.idyll.org/listinfo/khmer


-- 
C. Titus Brown, ctbrown at ucdavis.edu



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