IOError: [Errno 24] Too many open files:

[GoogleCodeExporter]

What steps will reproduce the problem?
2014-03-11 22:31:04,573 - root - INFO - Sorting BEDPE file
Traceback (most recent call last):
  File "/usr/local/bin/chimerascan_run.py", line 1002, in <module>
    main()
  File "/usr/local/bin/chimerascan_run.py", line 999, in main
    sys.exit(run_chimerascan(runconfig))
  File "/usr/local/bin/chimerascan_run.py", line 659, in run_chimerascan
    tmp_dir=tmp_dir)
  File "/usr/local/lib64/python2.6/site-packages/chimerascan/pipeline/discordant_reads_to_bedpe.py", line 92, in sort_bedpe
    tempdirs=tempdirs)
  File "/usr/local/lib64/python2.6/site-packages/chimerascan/lib/batch_sort.py", line 46, in batch_sort
    output_chunk = open(os.path.join(tempdir,'%06i'%len(chunks)),'w+b',64*1024)
IOError: [Errno 24] Too many open files: 
'/home/calogero/Documents/data/fusion_comparison/positive.tests/MCF-7/illu/1st/t
mp/001020'

It seems that the there is a limits in the number of files that Python can open.


What is the expected output? What do you see instead?
No output the program stops because of the above error


What version of the product are you using? On what operating system?
chimerascan-0.4.5 on Suse Enterprise



Please provide any additional information below.
I attached the nohup.out file of the run.
I also add the commands used to run chimerascan
nohup chimerascan_run.py /home/calogero/bin/chimerascan-0.4.5/index -v -p 64 
--filter-unique-frags=2  --library-type=fr-firststrand 
/home/calogero/Documents/data/fusion_comparison/positive.tests/MCF-7/illu/MCF7w4
e8spikesmrna_S1_L001_R1_001.fastq 
/home/calogero/Documents/data/fusion_comparison/positive.tests/MCF-7/illu/MCF7w4
e8spikesmrna_S1_L002_R1_001.fastq 
/home/calogero/Documents/data/fusion_comparison/positive.tests/MCF-7/illu/1st &

nohup chimerascan_run.py /home/calogero/bin/chimerascan-0.4.5/index -v -p 64 
--filter-unique-frags=2  --library-type=fr-secondstrand 
/home/calogero/Documents/data/fusion_comparison/positive.tests/MCF-7/illu/MCF7w4
e8spikesmrna_S1_L001_R1_001.fastq 
/home/calogero/Documents/data/fusion_comparison/positive.tests/MCF-7/illu/MCF7w4
e8spikesmrna_S1_L002_R1_001.fastq 
/home/calogero/Documents/data/fusion_comparison/positive.tests/MCF-7/illu/2nd &

Original issue reported on code.google.com by raffaele...@gmail.com on 12 Mar 2014 at 6:46

Attachments:

• nohup.out