Maker Failed while doing repeat masking

Question

[jamie.pike]

I'm having a problem with MAKER2, it's producing the following error message for all contigs and I can't work out how to fix it. Initially, it had a problem finding RepBase, so I set the following environmental variable before invoking maker export REPEATMASKER_LIB_DIR=/path/to/my/repeatmasker/lib (recommended here). Have I missed something stupid? How do I fix this?

Possible precedence issue with control flow operator at /shared/software/miniconda3/envs/maker/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 845.
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/home/u1983390/Fusarium_data/MAKER_annotations/VLOF01.1.maker.output/VLOF01.1_datastore

To access files for individual sequences use the datastore index:
/home/u1983390/Fusarium_data/MAKER_annotations/VLOF01.1.maker.output/VLOF01.1_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: VLOF01000001.1
Length: 2369
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_aMxeYi; /shared/software/miniconda3/envs/maker/bin/RepeatMasker /home/u1983390/Fusarium_data/MAKER_annotations/VLOF01.1.maker.output/VLOF01.1_datastore/D2/F7/VLOF01000001.1//theVoid.VLOF01000001.1/0/VLOF01000001%2E1.0.all.rb -species all -dir /home/u1983390/Fusarium_data/MAKER_annotations/VLOF01.1.maker.output/VLOF01.1_datastore/D2/F7/VLOF01000001.1//theVoid.VLOF01000001.1/0 -pa 1
#-------------------------------#
Died at /shared/software/miniconda3/envs/maker/share/RepeatMasker/LibraryUtils.pm line 332.
ERROR: RepeatMasker failed
--> rank=NA, hostname=vettel
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:VLOF01000001.1

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:VLOF01000001.1

examining contents of the fasta file and run log



--Next Contig--

[Maria]

Same problem. Any updates?

[lieven.sterck]

Are either of you able to run repeatmasker itself, so not in the MAKER pipeline but just run that command in your terminal?

[Rilla_xy]

Yes ,I also have same problem. I can run repeatmasker in my terminal ,but not in the MAKER pipeline. Do you know how to solve this error ? Thank you .

Answer 1

[Juke34]

A way to solve this problem I have used is to first run MAKER with repeatmasker only (do not perform any other task e.g. evidence alignement or prediction) setting the chunck size to a lower value (max_dna_len parameter).

Then you can run MAKER normally ( with normal max_dna_len and parameters you wish e.g. alignment, gene prediction, etc...) but without repeatmasking setp. Instead you provide the gff file from the repeat output of the previous run.