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>obi import Bird-MT_genome/Birds-completeMTgenome.fasta bird/ 2021-02-02 09:14:00,600 [import : INFO ] obi import: imports an object (file(s), obiview, taxonomy...) into a DMS 2021-02-02 09:14:00,600 [import : INFO ] Opened file: Bird-MT_genome/Birds-completeMTgenome.fasta 2021-02-02 09:14:00,649 [import : INFO ] Importing 1603 entries Traceback (most recent call last): File "/usr/local/bin/obi", line 62, in <module> config[root_config_name]['module'].run(config) File "python/obitools3/commands/import.pyx", line 204, in obitools3.commands.import.run NotImplementedError

what i doing wrong ?

changed the description

Hi Mitica,

You need to specify a view name (about the data structure, about the syntax). Try something like:

obi import Bird-MT_genome/Birds-completeMTgenome.fasta bird/MTgenome

Thank you! is working. All the best, Mitica

closed

Hi Celine @mercier,

I am getting the same error although I (hope) I am using the right syntax.

obi import --embl /Volumes/Elements/EMBL/Obitools_databases/OB_dat_EMBL_std_phg /Volumes/Elements/EMBL_dms/fungi_out
2021-04-13 14:38:32,440 [import : INFO ]  obi import: imports an object (file(s), obiview, taxonomy...) into a DMS
2021-04-13 14:39:34,251 [import : INFO ]  Importing 16055 entries
Traceback (most recent call last):
  File "/usr/local/bin/obi", line 62, in <module>
    config[root_config_name]['module'].run(config)
  File "python/obitools3/commands/import.pyx", line 204, in obitools3.commands.import.run
NotImplementedError
(base) Fabians-MacBook-Pro:Obitools_databases fabian$ obi import --taxdump /Volumes/Elements/taxdump.tar.gz /Volumes/Elements/EMBL_dms/taxonomy/my_tax
2021-04-13 18:25:26,689 [import : INFO ]  obi import: imports an object (file(s), obiview, taxonomy...) into a DMS
Traceback (most recent call last):
  File "/usr/local/bin/obi", line 62, in <module>
    config[root_config_name]['module'].run(config)
  File "python/obitools3/commands/import.pyx", line 172, in obitools3.commands.import.run
IndexError: list index out of range

I assume it's a syntax error but couldn't solve it. Any help is highly appreciated!

best

Fabian

Hi Fabian,

This looks weird, I can't see anything wrong with your commands.

It possibly looks like you might already have a normal folder named EMBL_dms in /Volumes/Elements/. I think this produces that kind of error, since the OBITools then try to follow a path inside the existing folder. If so, delete it and try again.

Otherwise, could you copy/paste the output of ls /Volumes/Elements/ here?

Best, Celine

reopened

Hi Celine,

deleting the EMBL_dms folder solved it. I thought I had tried that before but apparently not.

Thanks!

Fabian

All good. Ideally the OBITools3 should handle this case better, I will open an issue for it.

closed