hang during `Processing Splicing Graph`

Brought to you by: juntaosdu

hang during `Processing Splicing Graph`

Forum: General Discussion

Creator: Matt MacManes

Created: 2016-02-22

Updated: 2016-02-22

Matt MacManes - 2016-02-22

I am trying to assembly a test dataset consisting of 20 million PE reads.

/share/BinPacker_binary/BinPacker -o rcorr20M -s fq -p pair -m RF -k 25 -g 200 \ -l skewer.20M.rcorr-trimmed-pair1.fastq \ -r skewer.20M.rcorr-trimmed-pair2.fastq

BinPacker reproducibly hangs at

Processing Splicing Graph: comp29397.rg.debug ... Processing Splicing Graph: comp29398.rg.debug ... Processing Splicing Graph: comp29399.rg.debug ... Processing Splicing Graph: comp2939.rg.debug ... Processing Splicing Graph: comp293.rg.debug ...

It has been at this point for 12 hours, without progress. A single active process is evident when using top

This comp is available here: https://www.dropbox.com/s/yrsxsctqeohptmx/comp293.rg.debug.gz
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- Juntaosdu - 2016-02-22
  
  Please redownload it and type -q in your command for quickly running mode as follows:
  share/BinPacker_binary/BinPacker -o rcorr20M -s fq -p pair -m RF -k 25 -g 200 -l skewer.20M.rcorr-trimmed-pair1.fastq -r skewer.20M.rcorr-trimmed-pair2.fastq -q
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

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