RepeatMasker Run Error

[wjq1981]

Hello. I tried to run 'RepeatMasker -s -gff -lib pn-families.fa -xsmall -pa 64 pn.genome.fasta' and got an error. I thought it was a memory problem. So I split my genome file. When running 'RepeatMasker -s -gff -lib pn-families.fa -xsmall -pa 64 pn.genome.id_Chr1.fasta' there was no problem. But when I run 'RepeatMasker -s -gff -lib pn-families.fa -xsmall -pa 64 pn.genome.id_Chr2.fasta' I get the following error:

Checking for E. coli insertion elements identifying Simple Repeats in batch 2357 of 4637 identifying matches to pn-families.fa sequences in batch 2357 of 4637 identifying Simple Repeats in batch 2343 of 4637

Checking for E. coli insertion elements WARNING: The search engine returned an error (2, status = 2 ) Engine parameters: /home/wangjq/anaconda3/bin/rmblastn -num_alignments 9999999 -db /home/wangjq/anaconda3/share/RepeatMasker/Libraries//general/is.lib -query /hdd/data/wangjq/Genome/newpn/pn.genome.fasta.split/RM_3587272.SatSep112220322021/pn.genome.id_Chr2.fasta_batch-2358.masked -gapopen 12 -gapextend 2 -complexity_adjust -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8 -min_raw_gapped_score 17 -dust no -num_threads 4 -matrix identity.matrix A search phase could not complete on this batch. The batch file will be re-run and if possible the program will resume. WARNING: Retrying batch ( 2358 ) [ 255,, 61203]...

Checking for E. coli insertion elements identifying Simple Repeats in batch 2348 of 4637 WARNING: The search engine returned an error (2, status = 2 ) Engine parameters: /home/wangjq/anaconda3/bin/rmblastn -num_alignments 9999999 -db /home/wangjq/anaconda3/share/RepeatMasker/Libraries//general/is.lib -query /hdd/data/wangjq/Genome/newpn/pn.genome.fasta.split/RM_3587272.SatSep112220322021/pn.genome.id_Chr2.fasta_batch-2358.masked -gapopen 12 -gapextend 2 -complexity_adjust -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8 -min_raw_gapped_score 17 -dust no -num_threads 4 -matrix identity.matrix A search phase could not complete on this batch. The batch file will be re-run and if possible the program will resume. identifying Simple Repeats in batch 2342 of 4637 WARNING: Retrying batch ( 2358 ) [ 255,, 61203]...

Checking for E. coli insertion elements WARNING: The search engine returned an error (2, status = 2 ) Engine parameters: /home/wangjq/anaconda3/bin/rmblastn -num_alignments 9999999 -db /home/wangjq/anaconda3/share/RepeatMasker/Libraries//general/is.lib -query /hdd/data/wangjq/Genome/newpn/pn.genome.fasta.split/RM_3587272.SatSep112220322021/pn.genome.id_Chr2.fasta_batch-2358.masked -gapopen 12 -gapextend 2 -complexity_adjust -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8 -min_raw_gapped_score 17 -dust no -num_threads 4 -matrix identity.matrix A search phase could not complete on this batch. The batch file will be re-run and if possible the program will resume.

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 [ 2.9.0+ ] Command Line: /home/wangjq/anaconda3/bin/RepeatMasker-s -gff -lib pn-families.fa -xsmall -pa 16 pn.genome.id_Chr2.fasta Batch Number: 2358 Disk Space: 文件系统 1K-块 已用 可用 已用% 挂载点 /dev/sda1 19453054212 16451925844 2024520780 90% /hdd

System Memory: MemTotal: 528239704 kB MemFree: 175580020 kB MemAvailable: 483991724 kB Cached: 303084576 kB SwapCached: 104856 kB SwapTotal: 52428796 kB SwapFree: 46754128 kB Further details about this problem may be found in the directory: /hdd/data/wangjq/Genome/newpn/pn.genome.fasta.split/RM_3587272.SatSep112220322021

real 32m51.602s user 864m42.885s sys 7m48.334s (base) wangjq@ubuntu-desktop 22:53:24 /hdd/data/wangjq/Genome/newpn/pn.genome.fasta.split$ (base) wangjq@ubuntu-desktop 22:53:24 /hdd/data/wangjq/Genome/newpn/pn.genome.fasta.split$identifying Simple Repeats in batch 2345 of 4637 identifying Simple Repeats in batch 2346 of 4637 identifying Simple Repeats in batch 2350 of 4637 identifying Simple Repeats in batch 2349 of 4637 identifying Simple Repeats in batch 2344 of 4637 identifying Simple Repeats in batch 2352 of 4637 identifying Simple Repeats in batch 2351 of 4637 identifying Simple Repeats in batch 2353 of 4637

Thank you!

[RanSenn]

Hi，I got the same problem，have you fixed it？>_<

[wjq1981]

Hi，I got the same problem，have you fixed it？>_<

I'm sorry I'm only getting back to you now. I have solved it. The problem was caused by inconsistencies in my rmblast before and after (RepeatModeler, RepeatMasker), you can unify them and you'll be fine.

[RanSenn]

Hi，I got the same problem，have you fixed it？>_<

I'm sorry I'm only getting back to you now. I have solved it. The problem was caused by inconsistencies in my rmblast before and after (RepeatModeler, RepeatMasker), you can unify them and you'll be fine.

Thank you for your reply ！ I've tried the way you told me, and it worked !
Have a nice day !

[rsharris]

How does one solve the problem?

I am also getting that error, from a conda install of repeatmasker-4.1.2.p1, with rmblast-2.2.28.

This was a fresh install of repeatmasker, never been installed on this machine before. Is this an issue with the conda package?

[wjq1981]

How does one solve the problem?

I am also getting that error, from a conda install of repeatmasker-4.1.2.p1, with rmblast-2.2.28.

This was a fresh install of repeatmasker, never been installed on this machine before. Is this an issue with the conda package?

There should be no problem with the conda installation either. 1. You can go ahead and modify the local formulation to use the same version as RepeatModeler; or 2. RepeatMasker with another comparison tool, such as abblast. I am using abblast.

[rsharris]

Thanks.