Hi everyone,

I am going to do the gene prediction and annotation for my rice genome assembled sequence. I installed RepeatModeler via conda and built and Made a repeat library for my rice-assembled genome fasta file. I also installed MAKER version 3.01.03 via Conda enter link description here Then, I run MAKER as in the tutorial enter link description here

These are commands that I used to run MAKER:

maker -CTL  
export ZOE=/opt/home/sony/miniconda3/envs/MAKER2/bin/snap 
export AUGUSTUS_CONFIG_PATH=/opt/home/sony/miniconda3/envs/MAKER2/bin/augustus/config

I run MAKER with a script

mpiexec -n 4 maker -base En_Pan_MaS_R1 maker_opts.ctl maker_bopts.ctl maker_exe.ctl
bash ./round1_run_maker.sh 2>&1 | tee round1_run_maker.log

However, I encountered this error:

setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_kG9F4R; /opt/home/sony/miniconda3/envs/MAKER2/bin/RepeatMasker /opt/data/sony/thesis/Repeat_Oi_Nip/MaSuRCA/En_Pan_MaS_R1.maker.output/En_Pan_MaS_R1_datastore/CC/6F/scf7180000020707//theVoid.scf7180000020707/0/scf7180000020707.0.rice.rb -species rice -dir /opt/data/sony/thesis/Repeat_Oi_Nip/MaSuRCA/En_Pan_MaS_R1.maker.output/En_Pan_MaS_R1_datastore/CC/6F/scf7180000020707//theVoid.scf7180000020707/0 -pa 1
#-------------------------------#
doing repeat masking
doing repeat masking
The assumed RepeatMasker installation directory
    /opt/home/sony/miniconda3/envs/MAKER2/share/RepeatMasker
does not appear to be correct.  E.g it does not
contain a 'Libraries' or 'Matrices' subdirectory.
This can occur if hard links are used to invoke
this script.
ERROR: RepeatMasker failed
--> rank=3, hostname=hpz6
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:scf7180000020707

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:scf7180000020707

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: scf7180000020709
Length: 2066
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking

I already check the presence of 'Libraries' or 'Matrices' in /opt/home/sony/miniconda3/envs/MAKER2/share/RepeatMasker , these are available.

How can I solve these error? This is my first time doing gene prediction and annotation. Thank you everyone for any suggestions.