AB-BLAST version is not detected when blastp warns about mismatched libxml version

[jebrosen]

Copied from https://github.com/rmhubley/RepeatMasker/issues/50#issuecomment-766803634 by @Tiramisu023:

RepeatMasker version 4.1.1
WUBlastSearchEngine::setPathToEngine( /public2/users/liyulong/software/ab-blast-20200317-linux-x64/blastp ): Cannot determine engine variant and version!
 at /public2/users/liyulong/software/RepeatMasker-4.1.1/RepeatMasker line 518.`

This is the information of blastp in the ab-blast software.

(base) [liyulong@node1 ab-blast-20200317-linux-x64]$ ./blastp -h                       
Warning: program compiled against libxml 209 using older 207
Warning: program compiled against libxml 209 using older 207
BLASTP 3.0 [2020-03-17] [linux-x64 2020-03-19T22:57:46]
Copyright (C) 2020 Warren R. Gish.  All rights reserved.
This software is available only under license from Advanced Biocomputing, LLC.
Any unlicensed use, reproduction or distribution is strictly prohibited.
This software is licensed to [Yulong Li] until [2022-01-14]
at [Sun Yat-sen University] for nonprofit use only.
Reference:  Gish, W. (1996-2020) https://blast.advbiocomp.com

Thanks for reporting this. It looks like those extra Warning: lines are a problem.

Can you try this possible fix (on either RepeatMasker 4.1.0 or 4.1.1) and let us know if AB-BLAST then works successfully for you?

Change line 287 of WUBlastSearchEngine.pm by adding an m:

Old line: if ( $result =~ /^(BLAST[PN]) (\S+ \[.*\])/ ) {
New line: if ( $result =~ /^(BLAST[PN]) (\S+ \[.*\])/m ) {

[Tiramisu023]

Yes, it really works. Thanks so much.

[jebrosen]

Thanks for testing it! This fix will be incorporated into the next RepeatMasker release.

[jebrosen]

The fix for this bug was included in the RepeatMasker 4.1.2 release!

[carlosgonzalezcobo]

Hello! I have the same issue than jebrosen. I have installed RepeatMasker 4.1.5 and I checked line 287 of WUBlastSearchEngine.pm and it was already in the newer version.

WUBlastSearchEngine::setPathToEngine( /groups/nordborg/user/carlos.gonzalez/software/AB-Blast/ab-blast-20200317-linux-x64/blastp ): Cannot determine engine variant and version! at /groups/nordborg/user/carlos.gonzalez/software/miniconda3/envs/transposon_annotation/bin/RepeatMasker line 541.

I also tried to run again the /configure file and stablish ABBlast as the search engine, but it seems it didn't work.

Any solution? Thank you in advance

Carlos