FATAL ERROR: RepeatMasker giving up. One or more batches failed!
Entering edit mode
4 days ago
Carla ▴ 10

Hello, I'm using a Virtual box version 6.1 with Ubuntu 21.04.

I'm trying to compute an ab initio gene prediction with the largest contig of Drosophila buzzatii. My contig is in fasta format and my search engine is RMBlast. When I try to perform the analysis I get back the following error:

FATAL ERROR: RepeatMasker giving up. One or more
batches failed!  Unfortunately this type of error
cannot be recovered from. Please submit the following
details to the feedback page at the repeatmasker
website: http://www.repeatmasker.org

RepeatMasker Version: 4.1.2-p1
Library Version: 
Search Engine: ncbi [ 2.12.0+ ]
Command Line: /home/osboxes/anaconda3/envs/annotation/bin/RepeatMasker-pa 3 -e rmblast -lib /home/osboxes/Documents/NGS_assembly_Sonia/Assembly_Assignment/assembly_annotation/configurationFiles/fly_repeats/specieslib -dir /home/osboxes/Documents/NGS_assembly_Sonia/Assembly_Assignment/assembly_annotation/316/316_annotation/RepeatMasker -norna -cutoff 250 -xsmall -gff /home/osboxes/Documents/NGS_assembly_Sonia/Assembly_Assignment/assembly_annotation/316/316.fasta

Batch Number: 1
Disk Space:
Filesystem     1K-blocks     Used      Available       Use%     Mounted on 
/dev/sda4       277708868  14725668     248806688       6%      /home

System Memory:
MemTotal:        5465104 kB
MemFree:         2508952 kB
MemAvailable:    3768496 kB
Cached:          1403368 kB
SwapCached:            0 kB
SwapTotal:       8787964 kB
SwapFree:        8787964 kB

The detailed error within the new directory is the following:

Warning:  Number of threads was reduced to 1 to match the number of available CPUs
Aborted (core dumped)

Can someone tell me the possible error here? Thank you!

fatal batch threads RepeatMasker error • 98 views
Entering edit mode
4 days ago
Carla ▴ 10

Hi everyone! I solved the problem.

First of all, this error occurred in the conda environment that I created with the default python (which was python 3.10). Nevertheless it seems that latest version of conda is not working properly with this version of python. So, I decided to create another environment with python 3.9.

Afterwards I downloaded the previous version of RepeatMasker (v 4.1.1) because there is a recent release of rmblast v 2.11 (my search engine) which is not accesible by conda and pip. So, rmblast latest version allowed by conda is v 2.10. On the whole, the new environment was settled with:

  • Python 3.9
  • RepeatMasker 4.1.1
  • rmblast 2.10

Then the one-liner was run and everything worked! The contig has been successfully masked.



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