[khmer] normalize-by-median.py Hanging

Daniel Standage daniel.standage at gmail.com
Fri Sep 19 05:30:21 PDT 2014


Ok sorry for the scare, it looks like it was a transient I/O issue. Second
time it ran through successfully. Thanks!


--
Daniel S. Standage
Ph.D. Candidate
Computational Genome Science Laboratory
Indiana University

On Thu, Sep 18, 2014 at 9:25 AM, C. Titus Brown <ctb at msu.edu> wrote:

> If it's not responding to kill -9, then it's an OS-level hang on I/O, most
> likely; that's probably not khmer's fault!
>
> If it responds to kill -9 but not Ctrl-C, then it's a threading issue,
> which would not be unheard of.
>
> cheers,
> --titus
>
> On Wed, Sep 17, 2014 at 04:53:09PM -0400, Daniel Standage wrote:
> > I don't know if this helps, but: the command is not responding to Ctrl-c
> or
> > kill -9 as root.
> >
> >
> > --
> > Daniel S. Standage
> > Ph.D. Candidate
> > Computational Genome Science Laboratory
> > Indiana University
> >
> > On Wed, Sep 17, 2014 at 4:38 PM, Daniel Standage <
> daniel.standage at gmail.com>
> > wrote:
> >
> > > Here it is: https://gist.github.com/standage/4222de94bd695f23f673
> > >
> > > Forgot to mention, running khmer 1.1
> > >
> > > Thanks,
> > > Daniel
> > >
> > >
> > > --
> > > Daniel S. Standage
> > > Ph.D. Candidate
> > > Computational Genome Science Laboratory
> > > Indiana University
> > >
> > > On Wed, Sep 17, 2014 at 4:31 PM, C. Titus Brown <ctb at msu.edu> wrote:
> > >
> > >> On Wed, Sep 17, 2014 at 04:27:09PM -0400, Daniel Standage wrote:
> > >> > Before running norm-by-median, I
> > >> >
> > >> >    - Downloaded SRA file
> > >> >    - Used fastq-dump to create paired Fastq files
> > >> >    - used interleave-reads to create a Fastq file in the One True
> Format
> > >> >
> > >> > All of the Fastq files seem to be fine i.e. none appear truncated.
> > >> Memory
> > >> > usage is remaining constant, CPU utilization is 100%, but the weird
> > >> thing
> > >> > is that as far as I can tell the norm-by-median script is complete.
> It
> > >> has
> > >> > processed all the input, given a final report, and all of the kept
> reads
> > >> > have been written to output: except the last read is missing and the
> > >> second
> > >> > to last read is cut off.
> > >>
> > >> Sounds like a classic fencepost error :(.
> > >>
> > >> Could you send me (on or off the list) the SRA commands you used and
> > >> the command line you ran with diginorm?  Then we'll see if we can
> > >> replicate
> > >> on our own hardware.
> > >>
> > >> cheers,
> > >> --titus
> > >>
> > >> > On Wed, Sep 17, 2014 at 4:21 PM, C. Titus Brown <ctb at msu.edu>
> wrote:
> > >> >
> > >> > > Hi Daniel,
> > >> > >
> > >> > > sounds like an infinite loop of some sort :(.
> > >> > >
> > >> > > A few questions --
> > >> > >
> > >> > > What version of khmer are you using?
> > >> > >
> > >> > > Have you run the reads file through any other software?  I'm
> worried
> > >> > > that the file is truncated in some way.
> > >> > >
> > >> > > Do you know how far through your reads file it's gotten?
> > >> > >
> > >> > > Is memory usage increasing or remaining constant?
> > >> > >
> > >> > > thanks,
> > >> > > --titus
> > >> > >
> > >> > > On Wed, Sep 17, 2014 at 04:16:37PM -0400, Daniel Standage wrote:
> > >> > > > Hi all,
> > >> > > >
> > >> > > > I am seeing some strange behavior running
> normalize-by-median.py.
> > >> The
> > >> > > > program seemed to complete successfully after 30-45 minutes, but
> > >> then it
> > >> > > > just hung there. It's now been at least 90 minutes and it's
> > >> continuing to
> > >> > > > hang. The output file seems to contain all the data except the
> last
> > >> > > record,
> > >> > > > and the second-to-last record is cut off.
> > >> > > >
> > >> > > > (khmer-env)[standage at bggnomic qc] tail SRR494178_int.fastq.keep
> > >> > > > +
> > >> > > >
> > >> > >
> > >>
> GBGED>>E##################################################################################
> > >> > > > @SRR494178.12090255/1
> > >> > > >
> > >> > >
> > >>
> TCGAGGACNACCTTTTGACCCTTCTGCAACCTTTGAATTTCAGACATCAAACTCTCCCTCTGTCGTGTCTCCNNCAATGATGGGTCGGGC
> > >> > > > +
> > >> > > >
> > >> > >
> > >>
> IIIIIGGG#GGGGGGIIIIIIIIIIIIIIIIGIHIIIIIGIIIIIIIIIIIIIHIIIIHIEGHHIFIHII=?##?;9>>;IGBFFGBD8G
> > >> > > > @SRR494178.12090255/2
> > >> > > >
> > >> > >
> > >>
> GATTCCGTCACCGAGGAGTATCCGTTGCCGAGGTTGTGCGTCTGTCGAACCTGGCCGTTCTTTTTGACCGTGTAGGTGCCGCCGTTGATC
> > >> > > > +
> > >> > > > IIIIIIHIIIIIIIIIBIHHIIIGIIIIIII(khmer-env)[standage at bggnomic
> qc]
> > >> > > >
> > >> > > > Any ideas as to what could be causing this?
> > >> > > >
> > >> > > > Thanks,
> > >> > > > Daniel
> > >> > > >
> > >> > > > PS.
> > >> > > >
> > >> > > >    - OS: Fedora 20 with lots o RAM (100s of GB)
> > >> > > >    - Command: normalize-by-median.py -k 17 -p -N 4 -x 8e9
> > >> > > >    SRR494178_int.fastq
> > >> > > >    - Data: http://www.ncbi.nlm.nih.gov/sra/?term=SRR494178
> > >> > > >
> > >> > > >
> > >> > > > --
> > >> > > > Daniel S. Standage
> > >> > > > Ph.D. Candidate
> > >> > > > Computational Genome Science Laboratory
> > >> > > > Indiana University
> > >> > >
> > >> > > > _______________________________________________
> > >> > > > khmer mailing list
> > >> > >
> > >> > > --
> > >> > > C. Titus Brown, ctb at msu.edu
> > >> > >
> > >>
> > >> --
> > >> C. Titus Brown, ctb at msu.edu
> > >>
> > >
> > >
>
> --
> C. Titus Brown, ctb at msu.edu
>
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