What command did you issue?
Copy/paste the command used.
Logfiles
Command error:
-------------------------------------------------------
[Mar 09 12:42 PM]: OS: Debian GNU/Linux 10, 64 cores, ~ 132 GB RAM. Python: 3.8.12
[Mar 09 12:42 PM]: Running funannotate v1.8.9
[Mar 09 12:42 PM]: GeneMark not found and $GENEMARK_PATH environmental variable missing. Will skip GeneMark ab-initio prediction.
[Mar 09 12:42 PM]: Skipping CodingQuarry as $QUARRY_PATH not found as ENV
[Mar 09 12:42 PM]: Parsed training data, run ab-initio gene predictors as follows:
Program Training-Method
augustus busco
glimmerhmm busco
snap busco
[Mar 09 12:42 PM]: Loading genome assembly and parsing soft-masked repetitive sequences
[Mar 09 12:42 PM]: Genome loaded: 22 scaffolds; 20,738,633 bp; 17.30% repeats masked
[Mar 09 12:42 PM]: Mapping 556,382 proteins to genome using diamond and exonerate
[Mar 09 01:13 PM]: Found 192,293 preliminary alignments --> aligning with exonerate
[Mar 09 01:20 PM]: Exonerate finished: found 663 alignments
[Mar 09 01:20 PM]: Running BUSCO to find conserved gene models for training ab-initio predictors
[Mar 09 01:20 PM]: BUSCO training of Augusus failed, check busco logs, exiting
When I open the log file, there is message exactly like #229:
INFO ****************** Start a BUSCO 2.0 analysis, current time: 03/09/2023 03:59:13 ******************
ERROR Impossible to read funannotate/dikarya
ERROR BUSCO analysis failed !
INFO Check the logs, read the user guide, if you still need technical support, then please contact mailto:support@orthodb.org
. So I feel that's error in reading symlink. As if I use conda, with absolute path of database, that's not happen. (Although after that, we also encounter various errors #103 #776 )
Are you using the latest release? Yes
Describe the bug I run the funannotate code on HPC by nextflow, this is the code
What command did you issue? Copy/paste the command used.
Logfiles
When I open the log file, there is message exactly like #229:
. So I feel that's error in reading symlink. As if I use conda, with absolute path of database, that's not happen. (Although after that, we also encounter various errors #103 #776 )
OS/Install Information