Skip to content

GitLab

  • Projects
  • Groups
  • Snippets
  • Help
    • Loading...
  • Help
    • Help
    • Support
    • Community forum
    • Submit feedback
    • Contribute to GitLab
  • Sign in
O
OBITools
  • Project overview
    • Project overview
    • Details
    • Activity
    • Releases
  • Repository
    • Repository
    • Files
    • Commits
    • Branches
    • Tags
    • Contributors
    • Graph
    • Compare
  • Issues 30
    • Issues 30
    • List
    • Boards
    • Labels
    • Service Desk
    • Milestones
  • Merge Requests 0
    • Merge Requests 0
  • Operations
    • Operations
    • Incidents
  • Analytics
    • Analytics
    • Repository
    • Value Stream
  • Wiki
    • Wiki
  • Members
    • Members
  • Collapse sidebar
  • Activity
  • Graph
  • Create a new issue
  • Commits
  • Issue Boards
  • OBITools
  • OBITools
  • Issues
  • #38

Closed
Open
Opened Jan 18, 2019 by Harsh Shukla@harsh.g.shukla

Error in building the reference database

Hi,

Thank you for the wonderful pipeline. I recently downloaded the EMBL release 138 dataset and was trying to build the reference database. But while running the command :

obiconvert --embl -t ./TAXO --ecopcrDB-output=embl_last ./EMBL/*.dat

I encountered an error. The last few lines of log indicating the error are as follows.

Error on sequence : EU394480


Traceback (most recent call last):
  File "/home/uramakri/mousumig/Softwares/OBITools/OBITools-1.2.12/export/bin/obiconvert", line 52, in <module>
    writer(entry)
  File "/home/uramakri/mousumig/Softwares/OBITools/OBITools-1.2.12/lib/python2.7/site-packages/obitools/format/options.py", line 371, in sequen
    writer.put(sequence)
  File "/home/uramakri/mousumig/Softwares/OBITools/OBITools-1.2.12/lib/python2.7/site-packages/obitools/ecopcr/sequence.py", line 173, in put
    self._file.write(self._ecoSeqPacker(sequence))
  File "/home/uramakri/mousumig/Softwares/OBITools/OBITools-1.2.12/lib/python2.7/site-packages/obitools/ecopcr/sequence.py", line 141, in _ecoS
    raise e
struct.error: cannot convert argument to integer

I am also attaching the log for the last obiconvert run. obiconvert.err

I would be quite grateful if someone could help me troubleshoot the error.

Thanking You

With Regards, Harsh

Assignee
Assign to
None
Milestone
None
Assign milestone
Time tracking
None
Due date
None
Reference: obitools/obitools#38