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hoffmangroup / genomedata

The Genomedata format for storing large-scale functional genomics data.
https://genomedata.hoffmanlab.org/
GNU General Public License v2.0
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genomedata-load-seq error #41

Open EricR86 opened 6 years ago

EricR86 commented 6 years ago

Original report (archived issue) by Anonymous.

When I run genomedata-load-seq using the following command:

genomedata-load-seq -f embl87Galgal5.genomedata embl87Galgal5.dna.fa

I got the following error message:

Traceback (most recent call last): File "/usr/local/bin/genomedata-load-seq", line 9, in load_entry_point('genomedata==1.3.6', 'console_scripts', 'genomedata-load-seq')() File "/usr/local/lib/python2.7/dist-packages/genomedata/_load_seq.py", line 319, in main mode=args.mode, seqfile_type=args.seqfile_type) File "/usr/local/lib/python2.7/dist-packages/genomedata/_load_seq.py", line 233, in load_seq assert not gdpath.exists() AssertionError

EricR86 commented 6 years ago

Original comment by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

It looks this issue comes from trying to create a genomedata archive in file mode when the file already exists. Does embl87Galgal5.genomedata already exist when you attempted that command? It looks like you just need to remove the embl87Galgal5.genomedata folder first then re-run the command.

There should be a better message for this case. I re-raised this as Issue #42.