I meet the problem with mmseqs database GTDB

[shaodongyan]

Expected Behavior

I met problem with mmseqs database GTDB .The problem in mmseqs tar2db gtdb.tar.gz tardb --tar-include 'faa$'. It can't work in "faa$" paramater. But if i delete "$" it can work.

mmseqs tar2db gtdb.tar.gz tardb --tar-include 'faa$' tar2db gtdb.tar.gz tardb --tar-include faa$

MMseqs Version: 14.7e284 Output database type 12 Tar Inclusion Regex faa$ Tar Exclusion Regex ^$ Compressed 0 Threads 56 Verbosity 3

Time for merging to tardb: 0h 0m 0s 57ms Time for merging to tardb.lookup: 0h 0m 0s 72ms Time for processing: 0h 0m 44s 946ms but results are empty.

mmseqs tar2db gtdb.tar.gz tardb --tar-include 'faa' tar2db gtdb.tar.gz tardb --tar-include faa

MMseqs Version: 14.7e284 Output database type 12 Tar Inclusion Regex faa Tar Exclusion Regex ^$ Compressed 0 Threads 56 Verbosity 3

this can work.

Current Behavior

Steps to Reproduce (for bugs)

Please make sure to execute the reproduction steps with newly recreated and empty tmp folders.

MMseqs Output (for bugs)

Please make sure to also post the complete output of MMseqs. You can use gist.github.com for large output.

Context

Providing context helps us come up with a solution and improve our documentation for the future. I think the problem with paramater "faa$" should be solved again.

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):
• MMseqs 14.7e284
• Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.):
• Statically-compiled
• Server specifications (especially CPU support for AVX2/SSE and amount of system memory):
• 56GB 2TB
• Operating system and version: Centos

[shaodongyan]

and it's same in version 390457d87ed7049d918e46bc8b0571ac4034aae4.

~/program/mmseqs/bin/mmseqs tar2db gtdb.tar.gz tardb --tar-include 'faa$' tar2db gtdb.tar.gz tardb --tar-include faa$

MMseqs Version: 390457d87ed7049d918e46bc8b0571ac4034aae4 Output database type 12 Tar Inclusion Regex faa$ Tar Exclusion Regex ^$ Compressed 0 Threads 56 Verbosity 3

it can't work too

[jmtsuji]

@shaodongyan Your issue might be resolved now in the latest master branch of mmseqs. I hope this helps!