Marker protein search failed! about platon HOT 8 CLOSED

Hello @aaa-meituo-aaa ,
it seems that platon is not able to find any protein from its internal database. This could be due to the assembly itself (rare species which is not covered very well by the marker proteins (MPS) in the database or this could also be a technical issue.

Could please provide the log file along with some more information on the species?

from platon.

I also have the same error. (This might also be related to #10.)
I'm using macOS.

$ platon --db db test.fasta
Marker protein search failed!
$ tail -3 test.log
2020-08-29 08:42:10,751 - main - INFO - ORF detection: # ORFs=4467
2020-08-29 08:42:10,751 - main - INFO - ORF contig filter disabled! # passed contigs=63
2020-08-29 08:42:39,797 - main - ERROR - diamond execution failed! diamond-error-code=-4

When I ran diamond itself, it failed as follows.

$ diamond blastx -d db/mps -q test.fasta --verbose
.
.
.
Searching alignments... Illegal instruction: 4

The release page of diamond v0.9.33 (https://github.com/bbuchfink/diamond/releases/tag/v0.9.33) says "Fixed various issues related to Illegal instruction errors on macOS.".
Because platon uses diamond v0.9.32, macOS seems to suffer from this problem and this might be the reason why platon returns an error.

from platon.

@ryotag Thank you very much for the hint, excellent! I'll have a look at that and update the diamond version upon successful tests. I'll let you know...

from platon.

Thanks @oschwengers!
I'm looking forward to it.

from platon.

@aaa-meituo-aaa , @ryotag a first test with diamond v2.0.4 was successful on Linux. Unfortunately, I have no access to a MacOS system for testing/debugging purposes. I submitted a PR to Bioconda in order to update diamond there as well. Until, the merge is public, you can also use the GitHub-based installation of platon containing the latest diamond version as explained in the readme. Please, let me know, if this fixes the issue.

from platon.

@aaa-meituo-aaa , @ryotag I successfully tested platon with diamond=2.0.4 on Linux. An updated is pushed to BioConda and public. Please, drop me line if this fixes the issue on MacOS, as I don't have any MacOS system in order to debug this myself.

from platon.

@oschwengers I confirmed that current version of Platon works well on macOS.
Thanks a lot!

from platon.

@ryotag Great! Thanks a lot again for the hint and for the quick reply!

from platon.