RepeatMasker output vanishes

[SheepwormJM]

RepeatMasker runs fine, and outputs files to a temporary folder. However, once completed, all files except the output logfiles generated as part of the bsub command, vanish.

No errors are given, and the logfiles suggest successful completion.

An example command that generated this, using the conda version of RepeatMasker, repeatmasker-4.1.2.p on 18.08.22.

#!/bin/bash
#BSUB -q long
#BSUB -o testmask3.o
#BSUB -e testmask3.e
#BSUB -J testmask3
#BSUB -R "rusage[mem=10000] span[hosts=1] select[mem>10000]"
#BSUB -n 2
#BSUB -M 10000
#BSUB -cwd "/curation/masking_genome/test_mask"

/software/miniconda3/envs/repeatmasker/bin/RepeatMasker -gccalc -par 10 -gff -lib FIRST_TcCANU2.2+SALSA_030822-families.fa FIRST_TcCANU2.2+SALSA_050822.fasta

Note that the families.fa file had been the consensi.fa file RENAMED as this was a test run, and it would save time - it had already done 4 rounds.

FIX: I found a thread on BioStars https://www.biostars.org/p/101994/ where someone had spotted that they got this error when their filenames had a + in them.

Therefore I renamed all my files (input fasta, the database made by RepeatModeler v2.0.2a, the families.fa file) so that the + in the filename was removed, and it worked fine.

Thought I would put it here in case anyone else has the same issue.

[rmhubley]

Oh yes...shell metacharacters like '*', '?', '!', and '+' should be avoided in UNIX filenames/directory names in general. They are technically allowed on most UNIX filesystems but they will cause problems with most UNIX shells/command lines as they will have to be appropriately quoted or escaped.

[SheepwormJM]

Thanks! That's really good to know.

Do you mean that the filenames would have worked if I had put the entire file in "" i.e. "file+name" ? Or would it have needed to be file"+"name? Thanks!

[rmhubley]

It depends on the shell. In some cases you need single quotes and/or backslashes to escape interpretation of these metacharacters.