AttributeError

[marbeno]

Hi, I am trying to run nextSV, but I get the following error

[12/14/2017 16:58:24] program started
[12/14/2017 16:58:24] reading config file
[12/14/2017 16:58:24] creating output directories
[12/14/2017 16:58:24] checking samtools version
[12/14/2017 16:58:24] samtools sort version is new
[12/14/2017 16:58:24] reading input files list
[12/14/2017 16:58:24] checking input files
[12/14/2017 16:58:24] generating tasks
[12/14/2017 16:58:24] generating tasks for NGMLR/Sniffles
Traceback (most recent call last):
  File "/home/nextsv/nextsv.py", line 998, in <module>
    main()
  File "/home/nextsv/nextsv.py", line 123, in main
    ngmlr_sniffles_tasks = generate_tasks_ngmlr_sniffles(settings)
  File "/home/nextsv/nextsv.py", line 702, in generate_tasks_ngmlr_sniffles
    align_bam_dir = os.path.join(out_dir, '1_align_bam')
  File "/usr/lib/python2.7/posixpath.py", line 70, in join
    elif path == '' or path.endswith('/'):
AttributeError: 'NoneType' object has no attribute 'endswith'

[fangli80]

Hi, Thanks for using NextSV. Can you please upload your config file?

[marbeno]

1678_nextSV.config.zip

Hi, here's the file

[fangli80]

The problem is fixed. Please clone the latest version of NextSV and try again. If you still have the issue, please let me know.

[marbeno]

Hi, now it works. Thank you very much.

[fangli80]

You are welcome.