Question: Mikado prepare error
0
gravatar for Kay
6 months ago by
Kay0
Liverpool, UK
Kay0 wrote:

I am trying to use Mikado, a software for identifying a better set of transcripts from multiple assemblies. Been having these error in the congihuration/prepare phase.

2017-12-18 12:26:47,372 - prepare - prepare.py:67 - INFO - setup - MainProcess - Command line: /anaconda3/bin/mikado prepare --json-conf configuration.yaml
2017-12-18 12:26:47,517 - prepare - prepare.py:430 - ERROR - prepare - MainProcess - list index out of range
Traceback (most recent call last):
  File "/anaconda3/lib/python3.6/site-packages/Mikado/preparation/prepare.py", line 409, in prepare
    min_length=args.json_conf["prepare"]["minimum_length"])
  File "/anaconda3/lib/python3.6/site-packages/Mikado/preparation/prepare.py", line 280, in load_exon_lines
    strand_specific=strand_specific)
  File "/anaconda3/lib/python3.6/site-packages/Mikado/preparation/annotation_parser.py", line 387, in load_from_gtf
    for row in gff_handle:
  File "/anaconda3/lib/python3.6/site-packages/Mikado/parsers/GTF.py", line 397, in __next__
    return GtfLine(line)
  File "/anaconda3/lib/python3.6/site-packages/Mikado/parsers/GTF.py", line 55, in __init__
    GFAnnotation.__init__(self, line, my_line, header=header)
  File "/anaconda3/lib/python3.6/site-packages/Mikado/parsers/gfannotation.py", line 78, in __init__
    self._parse_attributes()
  File "/anaconda3/lib/python3.6/site-packages/Mikado/parsers/GTF.py", line 70, in _parse_attributes
    self.attributes[info[0]] = info[1].replace('"', '')
IndexError: list index out of range
2017-12-18 12:26:47,519 - prepare - prepare.py:432 - ERROR - prepare - MainProcess - Mikado has encountered an error, exiting
2017-12-18 12:26:47,519 - prepare - prepare.py:442 - INFO - prepare - MainProcess - Finished

Not sure if there is a limit to the length of the transcript the software can handle. Or my input files aren't conformed to what d software requires.

anyone with ideas?

rna-seq assembly genome • 286 views
ADD COMMENTlink modified 5 months ago by colindaven700 • written 6 months ago by Kay0
1

Why not ask in a github issue, the authors are friendly and quick to reply!

ADD REPLYlink written 5 months ago by colindaven700
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