Resfinder download fails

[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

[milot-mirdita]

This is quite confusing. For whatever reason your system's tar doesn't use the default --wildcards option. It seems to be having --no-wildcards set as the default mode. I don't have access to RHEL, but in the centos 7.9 docker image this doesn't seem to happen.

You can probably get around this issue by doing:

TAR_OPTIONS="--wildcards" mmseqs databases Resfinder db/rf tmp

[smdabdoub]

Ah, ok that actually does make sense. It's not using the OS tar because I was running it through a singularity container. So I'm guessing whatever tar was built into the container had the issue. I tried the standard command again but with a conda install of mmseqs2 and it worked fine. Thanks!

[milot-mirdita]

Is this a public container? I would like to know how exactly this failed to improve the script for the future.

[smdabdoub]

It is. The container was created by the BioContainers people. Although I can never get their registry to load. So I downloaded it from quay.io using this link: https://quay.io/repository/biocontainers/mmseqs2?tab=tags