RepeatMasker fails upon finishing

[DrPintoThe2nd]

Hi,

I'm trying out the program on a few new genomes and am caught on a RepeatMasker error that I can't quite figure out. I haven't been able to find much in terms of checking logs. I'm running Ubuntu 22.04 WSL (with conda) on a medium-powered PC (32 cores, 64Gb RAM). I first hit this error running 24 cores and then replicated it at 16 cores. I have successfully run RepeatMasker/RepeatModeler independently in the past on this machine for other genomes about the same size (~2.5Gb), but this is my first experience using EarlGrey. Thanks!!!!!

...
Checking for E. coli insertion elements
identifying Simple Repeats in batch 41278 of 41278
identifying matches to Gila_monster-families.fa.strained sequences in batch 41275 of 41278
identifying matches to Gila_monster-families.fa.strained sequences in batch 41273 of 41278
identifying Simple Repeats in batch 41259 of 41278
identifying Simple Repeats in batch 41260 of 41278
identifying matches to Gila_monster-families.fa.strained sequences in batch 41278 of 41278
identifying Simple Repeats in batch 41278 of 41278

forksys:  Program terminated by a signal 9.
The executing command was:  /home/user/miniconda3/envs/earlgrey/share/RepeatMasker/ProcessRepeats -a -lib /mnt/e/test/earlgrey_hap1/test_EarlGrey/test_strainer/test-families.fa.strained -lcambig -source -orifile /mnt/e/test/test_ctg.finalfasta.prep -maskSource /mnt/e/test/earlgrey_hap1/test_EarlGrey/test_RepeatMasker_Against_Custom_Library/RM_1276.FriJun71728352024/test_ctg.finalfasta.prep /mnt/e/test/earlgrey_hap1/test_EarlGrey/test_RepeatMasker_Against_Custom_Library/RM_1276.FriJun71728352024/test_ctg.finalfasta.prep.cat.gz
ERROR: RepeatMasker failed, please check logs

[TobyBaril]

Hi,

In this case it looks like your system is killing the process for some reason (sig 9 is a kill signal from the kernel). This step is running a classic RepeatMasker run with nothing special - can you replicate the error if you run RepeatMasker with the custom library generated by Earl Grey (e.g RepeatMasker -lib Gila_monster-families.fa.strained)?

This is failing right at the processing step of RepeatMasker, where all the annotations are read into memory and processed to generate the summaries. How big is the genome? How large do the intermediate annotation files look? There is the potential that your system is killing the process due to out of memory issues, and treating the conda processes differently somehow (weird, but sometimes happens!). Generally, the genome size won't matter as much as the TE content, so it could be case that this genome has just enough TEs to cause a problem.

[DrPintoThe2nd]

Apologies for the delay, this didn't come through via email. I'm running this now and will get back to you ASAP.

Thank you!!

[DrPintoThe2nd]

Okay, just finished. Same error, different spot.. starting to look like it could be a RAM issue, but also I think it may have finished and errored out at the same time? First, the only output files it left behind:

2934578658 Jun 22 05:03 genome.fasta.cat.gz
 977638034 Jun 22 05:03 genome.fasta.out

And then the error itself,

identifying matches to Gila_monster-families.fa.strained sequences in batch 41275 of 41278
identifying matches to Gila_monster-families.fa.strained sequences in batch 41273 of 41278
identifying Simple Repeats in batch 41259 of 41278
identifying Simple Repeats in batch 41260 of 41278
identifying matches to Gila_monster-families.fa.strained sequences in batch 41278 of 41278
identifying Simple Repeats in batch 41278 of 41278
processing output:
cycle 1 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cycle 2 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cycle 3 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cycle 4 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cycle 5
cycle 6 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cycle 7 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cycle 8 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cycle 9 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cycle 10 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Generating output... 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forksys:  Program terminated by a signal 9.
The executing command was:  /home/bjp004/miniconda3/envs/RepAnno/share/RepeatMasker/ProcessRepeats -lib earlgrey_hap1/Gila_monster_EarlGrey/Gila_monster_strainer/Gila_monster-families.fa.strained -orifile genome.fasta -maskSource ~/RM_1434.FriJun211144432024/genome.fasta ~/RM_1434.FriJun211144432024/genome.fasta.cat.gz

[TobyBaril]

This definitely looks like a RAM issue. The run itself is finished but it looks like there isn't enough memory to successfully load and parse the file to generate the RepeatMasker summaries

[TobyBaril]

Closing for the moment, but feel free to reopen is more help is needed