Problem setting PASA MySQL

[eggrandio]

Hello,

I am trying to use funannotate train with --pasa_db mysql but I am not able.

I have set up the MySQL database following the steps described here.

Then, when I run funannotate train, all the steps up to the PASA step work properly, but then I get this error:

pasa-assembly.log

-connecting to MySQL db: Penicillium_paxilli_pasa
Use of uninitialized value in pattern match (m//) at /home/eggrandio/miniconda3/envs/funannotate/opt/pasa-2.5.3/Launch_PASA_pipeline.pl line 281.
-*** Running PASA pipeine:
* [Sun Dec 14 11:32:48 2025] Running CMD: /home/eggrandio/miniconda3/envs/funannotate/opt/pasa-2.5.3/scripts/create_mysql_cdnaassembly_db.dbi -c /mnt/e/seq_data/2025_04_21_Ppax_genome/funannotate/ppax/training/pasa/alignAssembly.txt -S '/home/eggrandio/miniconda3/envs/funannotate/opt/pasa-2.5.3/schema/cdna_alignment_mysqlschema' -r
Error, need all method parameters (server, db, username, password) for mysql  at /home/eggrandio/miniconda3/envs/funannotate/opt/pasa-2.5.3/PerlLib/DB_connect.pm line 66.
	DB_connect::connect_to_db(undef, "", undef, undef) called at /home/eggrandio/miniconda3/envs/funannotate/opt/pasa-2.5.3/scripts/create_mysql_cdnaassembly_db.dbi line 57
Error, cmd: /home/eggrandio/miniconda3/envs/funannotate/opt/pasa-2.5.3/scripts/create_mysql_cdnaassembly_db.dbi -c /mnt/e/seq_data/2025_04_21_Ppax_genome/funannotate/ppax/training/pasa/alignAssembly.txt -S '/home/eggrandio/miniconda3/envs/funannotate/opt/pasa-2.5.3/schema/cdna_alignment_mysqlschema' -r died with ret 65280 No such file or directory at /home/eggrandio/miniconda3/envs/funannotate/opt/pasa-2.5.3/PerlLib/Pipeliner.pm line 187.
	Pipeliner::run(Pipeliner=HASH(0x5cc255105d60)) called at /home/eggrandio/miniconda3/envs/funannotate/opt/pasa-2.5.3/Launch_PASA_pipeline.pl line 1061

It seems that it cannot fetch the MySQL parameters from the config file (DB_connect::connect_to_db(undef, "", undef, undef)), but the alignAsembly.txt file created in the training/pasa directory seems to be fine (I've tried to include the database settings after # database settings and it still does not work):

./training/pasa/alignAsembly.txt

DATABASE=Penicillium_paxilli_pasa
MYSQL_SERVER=localhost
MYSQL_RW_USER=pasa_write
MYSQL_RW_PASSWORD=pasa_write_pwd
MYSQL_RO_USER=pasa_access
MYSQL_RO_PASSWORD=pasa_access

## templated variables to be replaced exist as <__var_name__>

# database settings


# PASA alignment assembly configuration file
## templated variables to be replaced exist as <__var_name__>

#######################################################
# Parameters to specify to specific scripts in pipeline
# create a key = "script_name" + ":" + "parameter"
# assign a value as done above.

#script validate_alignments_in_db.dbi

validate_alignments_in_db.dbi:--NUM_BP_PERFECT_SPLICE_BOUNDARY=3
validate_alignments_in_db.dbi:--MIN_PERCENT_ALIGNED=90
validate_alignments_in_db.dbi:--MIN_AVG_PER_ID=95

#script subcluster_builder.dbi
subcluster_builder.dbi:-m=50

What could be causing this issue? I am using the conda version of funannotate