Entering edit mode
4.7 years ago
ewelinarubin
▴
10
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>
main()
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
command.run(command_line, 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'
Hello,
Has someone solved this issue because I get the same problem when running KisSplice?
Thanks
Pascaline
It's been years since this post was created, I'd recommend that you create a new post and add a link to this one so if yours get solved, people stumbling on to this post would know where to look for a solution.