Question: Why does Exec RepeatMasker ProcessRepeats Fails?
gravatar for eennadi
4 weeks ago by
eennadi0 wrote:

I am trying to mask repeats using RepeatMasker. The software dies at this stage. I don't seem to have a solution for. No other error message is given.

Exec ~/exe/RepeatMasker/ProcessRepeats -lib ~/maker/mycustom_repeat.fa -orifile ~/22_09_19_flye/racon3x_pilon3x/MUCU_Flye_racon3_pilon3.fasta -maskSource ~/braker_annotation_08092020/RM_406998.WedSep91725412020/MUCU_Flye_racon3_pilon3.fasta ~/braker_annotation_08092020/RM_406998.WedSep91725412020/ failed

About the RepeatMasker I used

RepeatMasker version 4.1.0 Search Engine: NCBI/RMBLAST [ 2.9.0+ ]

INFO: For this species, RepeatMasker is using the new Dfam consensus sequences. These are based on the Dfam seed alignments and may differ from the ones in RepBase.

Master RepeatMasker Database: ~/exe/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: CONS-Dfam_3.1-rb20181026 ) Custom Repeat Library: ~l/mycustom_repeat.fa

sequence software error • 95 views
ADD COMMENTlink modified 4 weeks ago by Michael Dondrup47k • written 4 weeks ago by eennadi0

Could you share your input files, mycustom_repeat.fa, MUCU_Flye_racon3_pilon3.fasta,*

Some ideas:

  • how did you install or invoke RepeatMasker, are you missing some dependencies?
  • system information, OS? Is that Linux? Try to install latest version with Bioconda
  • I think latest version is RepMasker v4.2 now, install the update
  • really no error log, possibly the output is dumped into a log file? Try to run the failing command in a terminal, possible to se more there.
  • why is there a gzip compressed file on the command line, is that intentional?

*You can trust me!™️

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Michael Dondrup47k
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