Error downloading GRCm38.p6

[peterch405]

$genomepy install GRCm38.p6 Ensembl
downloading from ftp://ftp.ensembl.org/pub/release-92/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.toplevel.fa.gz...
done...
name: GRCm38.p6
local name: GRCm38.p6
fasta: /media/chovanec/My_Passport/genomes/GRCm38.p6/GRCm38.p6.fa
Traceback (most recent call last):
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/pyfaidx/__init__.py", line 351, in __init__
    if mutable else 'rb')
IsADirectoryError: [Errno 21] Is a directory: 'GRCm38.p6'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/genomepy/functions.py", line 282, in __init__
    super(Genome, self).__init__(name)
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/pyfaidx/__init__.py", line 962, in __init__
    rebuild=rebuild)
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/pyfaidx/__init__.py", line 360, in __init__
    "Cannot read FASTA file %s" % filename)
pyfaidx.FastaNotFoundError: Cannot read FASTA file GRCm38.p6

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/chovanec/anaconda3/bin/genomepy", line 11, in <module>
    load_entry_point('genomepy==0.5.1', 'console_scripts', 'genomepy')()
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/click/core.py", line 696, in main
    rv = self.invoke(ctx)
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/click/core.py", line 889, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/genomepy/cli.py", line 38, in install
    regex=regex, invert_match=not(match), annotation=annotation)
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/genomepy/functions.py", line 200, in install_genome
    g = Genome(name, genome_dir=genome_dir)
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/genomepy/functions.py", line 304, in __init__
    os.path.join(genome_dir, name)
FileNotFoundError: no *.fa files found in genome_dir GRCm38.p6/GRCm38.p6

[simonvh]

Thanks for reporting. I tried the same command on my system, which works fine. That means it will be somewhat harder to debug but I'll try. Can you post the contents of the directory /media/chovanec/My_Passport/genomes/GRCm38.p6/? Do other genomes from Ensembl work? You can try with a small genome, for instance:

$ genomepy install WBcel235 Ensembl

[peterch405]

The smaller genome installed no problem. I tried GRCm38.p6 again, same error. I am not sure why its doubling the dir path to GRCm38.p6/GRCm38.p6

$ls /media/chovanec/My_Passport/genomes/GRCm38.p6/
GRCm38.p6.fa  README.txt

These are my dependency versions:

pytest==2.9.2
click==6.6
pyfaidx==0.5.3
norns==0.1.2
xmltodict==0.9.2
msgpack==0.5.6
bucketcache==0.12.0
requests==2.13.0
appdirs==1.4.3

Python 3.5.5

[simonvh]

Thanks for posting the dependencies. I have created an environment with the same versions, and that seems to work on my side. Is the GRCm38.p6.fa that is created a valid & correct FASTA file? Can you post the contents of ~/.config/genomepy/genomepy.yaml?

[peterch405]

Yes seems to be a valid fasta. I do not have the genomepy.yaml file. When I was trying to generate it I got this error so I kinda gave up there:

$ genomepy config generate
Traceback (most recent call last):
  File "/home/chovanec/anaconda3/bin/genomepy", line 11, in <module>
    load_entry_point('genomepy==0.5.1', 'console_scripts', 'genomepy')()
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/click/core.py", line 696, in main
    rv = self.invoke(ctx)
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/click/core.py", line 889, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/genomepy/cli.py", line 64, in config
    genomepy.functions.manage_config(command)
  File "/home/chovanec/anaconda3/lib/python3.5/site-packages/genomepy/functions.py", line 37, in manage_config
    with open(fname, "w") as fout:
FileNotFoundError: [Errno 2] No such file or directory: '/home/chovanec/.config/genomepy/genomepy.yaml'

I instead edited the default.yaml to get a custom genome directory. Maybe I broke something :S

[simonvh]

Ah, that is a bug that a should fix in any case. What are the contents of default.yaml?

[peterch405]

genome_dir: /media/chovanec/My_Passport/genomes/
plugin:
- gaps
- sizes

[simonvh]

That config looks fine, but I think I might have found the error. Is there a directory called GRCm38.p6 in the directory from which you run genomepy? If so, genomepy should run fine when you run it from a different directory. This a situation that I had somehow not considered, a bug that I will fix for the next release.

[simonvh]

Should be fixed in 0.5.4. Feel free to re-open or post another issue if this is not the case.