[khmer] normalize-by-median.py Hanging

[Daniel Standage]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.idyll.org/pipermail/khmer/attachments/20140917/9f4f57b6/attachment.htm>