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Resfinder download fails #494

@smdabdoub

Description

@smdabdoub

Expected Behavior

The Resfinder database is downloaded and an mmseqs2 index is created.

Current Behavior

Fails at the download extraction step.

Steps to Reproduce (for bugs)

mmseqs databases Resfinder db/rf tmp

MMseqs Output (for bugs)

databases Resfinder db/rf tmp

MMseqs Version: 13.45111
Force restart with latest tmp false
Remove temporary files false
Compressed 0
Threads 48
Verbosity 3

--2021-10-08 14:50:24-- https://api.bitbucket.org/2.0/repositories/genomicepidemiology/resfinder_db/commit/master?fields=hash,date
Resolving api.bitbucket.org (api.bitbucket.org)... 18.205.93.8, 18.205.93.6, 18.205.93.7, ...
Connecting to api.bitbucket.org (api.bitbucket.org)|18.205.93.8|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 89 [application/json]
Saving to: 'tmp/9391455786971071082/version'

tmp/9391455786971071082/version 100%[=================================================================================================>] 89 --.-KB/s in 0s

2021-10-08 14:50:24 (13.7 MB/s) - 'tmp/9391455786971071082/version' saved [89/89]

--2021-10-08 14:50:24-- https://bitbucket.org/genomicepidemiology/resfinder_db/get/master.tar.gz
Resolving bitbucket.org (bitbucket.org)... 104.192.141.1, 2406:da00:ff00::22c3:9b0a, 2406:da00:ff00::34cc:ea4a, ...
Connecting to bitbucket.org (bitbucket.org)|104.192.141.1|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 457328 (447K) [application/x-tar-gz]
Saving to: 'tmp/9391455786971071082/master.tar.gz'

tmp/9391455786971071082/master.tar.gz 100%[=================================================================================================>] 446.61K --.-KB/s in 0.07s

2021-10-08 14:50:25 (5.88 MB/s) - 'tmp/9391455786971071082/master.tar.gz' saved [457328/457328]

tar: .fsa: not found in archive
createdb tmp/9391455786971071082/
.fsa db/rf --compressed 0 -v 3

Input tmp/9391455786971071082/*.fsa does not exist
Error: createdb died

Context

Your Environment

Include as many relevant details about the environment you experienced the bug in.

  • Git commit used (The string after "MMseqs Version:" when you execute MMseqs without any parameters): h95f258a
  • Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.): singularity container downloaded from Biocontainers
  • Server specifications (especially CPU support for AVX2/SSE and amount of system memory): Intel Xeon 8268, 192GB RAM
  • Operating system and version: RHEL 7.9

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