Docker version: Error in execution of HMMsearch in RunHMMSearchForLowConservedGenes subroutine

[ckeeling]

Hello @natacha-beck

I am using the Docker version with apptainer.

I get the following error at step 13:

...
12) Identify start codons; identify gene fusions...
13) Find extra genes with HMM
Error in execution of HMMsearch in RunHMMSearchForLowConservedGenes subroutine
... 41 additional times ...
Error in execution of HMMsearch in RunHMMSearchForLowConservedGenes subroutine
Can't call method "get_resume" on an undefined value at /mfannot/mfannot line 7148.

Unlike in issue #13 , I do have a resulting .orf file. Any suggestions where I can look next? I have the following environmental variables assigned by MFannot_env-file.txt:

EGC="/MFannot_data/EGC"
MFANNOT_HOME="/mfannot"
MFANNOT_EXT_CFG_PATH="/MFannot_data/config"
MFANNOT_MOD_PATH="/MFannot_data/models"
ERPIN_MOD_PATH="/MFannot_data/models/Erpin_models"
MFANNOT_LIB_PATH="/MFannot_data/protein_collections"

RNAFINDER_CFG_PATH="/"
MF2SQN_LIB="/mf2sqn/lib/"
BLASTMAT="/BLASTMAT/"
ERPIN_MOD_PATH="/MFannot_data/models/Erpin_models/"
PIR_DATAMODEL_PATH="/PirModels"
PATH="/bin:/usr/bin:/usr/local/bin"
PATH="/mfannot:$PATH"

My command is as follows:

apptainer exec --env-file MFannot_env-file.txt -B /project -B /scratch -B /localscratch ~/scratch/APPTAINER/IMAGES/mfannot_latest.sif mfannot contig.fa --genetic 5 --logfile logfile.txt --outputfile outputfile.txt -T /home/ckeeling/scratch/APPTAINER/IMAGES/tmp_dir

Thanks!

Chris