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  • #115

Closed
Open
Opened Aug 22, 2021 by sproft@sproft

obi clean_dms not working properly with obi build_ref_db

After using CTR-C to terminate the command obi build_ref_db, the VIEW db_0.90_matrix.obiview_unfinished is created.

Trying the restart obi build_ref_db creates this ERROR:

bash test.sh
2021-08-22 17:33:50,136 [build_ref_db : INFO ]  obi build_ref_db
Aligning queries with reference database...
DEBUG /tmp/pip-install-mga2jew_/obitools3_8e3958d47e6d408eb4f8316b610f1751/src/obiview.c:1643:obi_new_view, obi_errno = 35, errno = 0 :
Name of new view ('db_0.90_matrix') already exists
DEBUG /tmp/pip-install-mga2jew_/obitools3_8e3958d47e6d408eb4f8316b610f1751/src/obi_lcs.c:531:obi_lcs_align_one_column, obi_errno = 35, errno = 0 :
Error creating the output view when aligning
DEBUG /tmp/pip-install-mga2jew_/obitools3_8e3958d47e6d408eb4f8316b610f1751/src/build_reference_db.c:200:build_reference_db, obi_errno = 35, errno = 0 :
Error aligning the sequences when building a reference database
DEBUG /tmp/pip-install-mga2jew_/obitools3_8e3958d47e6d408eb4f8316b610f1751/src/obiview.c:2087:obi_view_map_file, obi_errno = 35, errno = 2 :
Error opening an obiview file: View db_0.90_matrix does not exist
DEBUG /tmp/pip-install-mga2jew_/obitools3_8e3958d47e6d408eb4f8316b610f1751/src/obiview.c:2040:obi_clone_view_from_name, obi_errno = 21, errno = 2 :
Error: could not open view to clone
DEBUG /tmp/pip-install-mga2jew_/obitools3_8e3958d47e6d408eb4f8316b610f1751/src/build_reference_db.c:230:build_reference_db, obi_errno = 21, errno = 2 :
Error creating the matrix with LCA view when building a reference database
Traceback (most recent call last):
  File "/home/proft/miniconda3/bin/obi", line 62, in <module>
    config[root_config_name]['module'].run(config)
  File "python/obitools3/commands/build_ref_db.pyx", line 90, in obitools3.commands.build_ref_db.run
Exception: Error building a reference database

obi clean_dms does not remove db_0.90_matrix.obiview_unfinished.

You can not restart the command until you have manually deleted the view from the DMS.

Edited Aug 22, 2021 by sproft
To upload designs, you'll need to enable LFS and have an admin enable hashed storage. More information
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Reference: obitools/obitools3#115