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hg19 not finishing download #3

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axelitama opened this issue Oct 23, 2024 · 0 comments
Open

hg19 not finishing download #3

axelitama opened this issue Oct 23, 2024 · 0 comments

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@axelitama
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axelitama commented Oct 23, 2024

Whilst running oncodriveclustl with the default genome option, the genome download gets stuck at 100% (after the INFO root: Computing signature... message is printed). The process does not finish, and the downloaded file is not decompressed.

Environment:

  1. python 3.11, bgdata 2.0.4, oncodriveclustl 1.1.4 (current version from this repo);
  2. python 3.10, bgdata 2.0.4, oncodriveclustl 1.1.3 (last version installable from PyPi).

This solved the issue for me (in environment 2, not tested in environment 1)
Before running the programme:

  • delete the bgdata hg19 directory;
  • run bgdata get datasets/genomereference/hg19;
  • manually create the hg19.master file if missing.
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