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Dfam-consortium / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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How to solve the ERROR: "The assumed RepeatMasker: /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. "? #257

Closed nguyenvantuananh99 closed 2 months ago

nguyenvantuananh99 commented 5 months ago

Describe the issue 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 https://anaconda.org/bioconda/maker Then, I run maker as in tutorial http://gmod.org/wiki/MAKER_Tutorial#Running_MAKER_with_example_data

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

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`

How Can I solve this error ? Thank you everyone

rmhubley commented 2 months ago

Please submit this to the "Maker" developers. We are not associated with their tool.