Question: Kissplice -- error - AttributeError: 'NoneType' object has no attribute 'returncode'
gravatar for ewelinarubin
10 months ago by
ewelinarubin0 wrote:

I am running

This is KisSplice, version 2.5.0

The command line was:     

  /gpfs/runtime/opt/kissplice/2.5.0/bin/kissplice -r sample_example/reads1.fa -r sample_example/reads2.fa

Using the read files:       sample_example/reads1.fa sample_example/reads2.fa

Results will be stored in:  /gpfs/data/epscor/erubin/SNPtest/peach/results

Summary log file will be saved in:  /gpfs/data/epscor/erubin/SNPtest/peach/results/kissplice_log_summary_09-08-07_16-04-2020_109982

I am getting this error:

09:08:07 16/04/2020] --> Building de Bruijn graph...
Graph will be written in results/graph_reads1_reads2_k41.[edges/nodes]
Traceback (most recent call last):
  File "/gpfs/runtime/opt/kissplice/2.5.0/bin/kissplice", line 999, in <module>
  File "/gpfs/runtime/opt/kissplice/2.5.0/bin/kissplice", line 875, in main
    build_graph(KS_SEC_EXEC_PATH, workdir, readfiles, kval, graphfile, min_cov, options.nbprocs, options.verbose)
  File "/gpfs/runtime/opt/kissplice/2.5.0/bin/kissplice", line 238, in build_graph
    subprocessLauncher(command_line, verbose=verbose)
  File "/gpfs/runtime/opt/kissplice/2.5.0/bin/kissplice", line 154, in subprocessLauncher, out_file, mode, verbose, timeout)
  File "/gpfs/runtime/opt/kissplice/2.5.0/bin/kissplice", line 126, in run
    if self.process.returncode == -15:
AttributeError: 'NoneType' object has no attribute 'returncode'
snp • 227 views
ADD COMMENTlink modified 10 months ago by GenoMax96k • written 10 months ago by ewelinarubin0
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