FileExistsError in initialize_genome

[stolarczyk]

that's odd, I'm 100% sure nothing has changed in that regard. Maybe failing jobs left the lock in place and that's the issue.I noticed there are a couple of logs with errors other than the RuntimeError, did you look into these? For example: /project/shefflab/deploy/plantref/genomes/submission/refgenie_Arabidopsis_lyrata__JGI_v2_1-fasta.log

There has been a FileExistsError raised, that I need to resolve anyway, even if it's not related.

Originally posted by @stolarczyk in https://github.com/refgenie/refgenconf/issues/105#issuecomment-682032052

Compute node: udc-aj38-14c0
Start time: 2020-08-27 10:15:21
Bulker config: /project/shefflab/rivanna_config/bulker.yaml
Activating crate: databio/refgenie:0.7.6

Using 'default' as the default tag for 'Ostreococcus_lucimarinus_JGI_2_0/fasta'
Recipe validated successfully against a schema: /home/ns5bc/.local/lib/python3.6/site-packages/refgenie/schemas/recipe_schema.yaml
Building 'Ostreococcus_lucimarinus_JGI_2_0/fasta:default' using 'fasta' recipe
Initializing genome: Ostreococcus_lucimarinus_JGI_2_0
Loaded AnnotatedSequenceDigestList (21 sequences)
Traceback (most recent call last):
  File "/home/ns5bc/.local/bin/refgenie", line 10, in <module>
    sys.exit(main())
  File "/home/ns5bc/.local/lib/python3.6/site-packages/refgenie/refgenie.py", line 713, in main
    refgenie_build(gencfg, asset_list[0]["genome"], asset_list, recipe_name, args)
  File "/home/ns5bc/.local/lib/python3.6/site-packages/refgenie/refgenie.py", line 543, in refgenie_build
    alias=ori_genome)
  File "/home/ns5bc/.local/lib/python3.6/site-packages/refgenconf/refgenconf.py", line 1342, in initialize_genome
    os.makedirs(os.path.dirname(pth))
  File "/apps/software/standard/core/anaconda/5.2.0-py3.6/lib/python3.6/os.py", line 220, in makedirs
    mkdir(name, mode)
FileExistsError: [Errno 17] File exists: '/project/shefflab/deploy/plantref/genomes/data/c1e1639e59337dec9e0bd1e585de0608ba2a804f06476403'