Missing RepeatMasker output? Literally nothing.

[marct]

It is a real head-scratcher for me.

After no errors and completely running through all cycles, RepeatMasker finishes but there are no output files. The only trace of the analysis is the rmblastdb.log file in the RepeatMasker/Libraries directory which reads:

Building a new DB, current time: 05/29/2014 10:54:02
New DB name: /home/mtollis/RepeatMasker/Libraries/20140131/anolis/specieslib
New DB title: /home/mtollis/RepeatMasker/Libraries/20140131/anolis/specieslib
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 100% ambiguous nucleotides (shouldn't be over 40%)
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 100% ambiguous nucleotides (shouldn't be over 40%)
Adding sequences from FASTA; added 776 sequences in 0.108892 seconds.

Perhaps the makeblastdb "error" is harmless and maybe it is merely coincidental that my analysis fails. I don't see how either true ambiguities or line endings (as in a Unix to Mac or vice-versa) are the problem, as my database is hardly novel: I am using the RepBase update and the -species command. the command appears to work, as it creates the species specific library as well as the general library in the RepeatMasker/Libraries directory.

Does anyone know why RepeatMasker would run without throwing any errors and then leave no output files whatsoever?

[GenoMax]

Have you tried to run some test data through to see if the install of repeatmasker is working as expected?

[marct]

Yes, a smaller test data set worked and produced the expected output. So it rules out the makeblastdb error as the source (i think). Perhaps it's the size and number of sequences in the full data set? It's an NGS genome assembly with several thousand scaffolds. Although I have run RepeatMasker on similar data sets in the past with no problems.

[marct]

Happened again, found this error in the standard output.

Can't call method "getScore" on unblessed reference at /home/mtollis/RepeatMasker/PRSearchResult.pm line 164.

[marct]

Problem solved

From the RepeatMasker developer, who suggested the following two fixes:

"The culprit is the processing of the alignment data using the "-a" flag. I tracked it down to a bug
in a routine which handles joining DNA transposons. The ugly match set was:

334 C21533332 2812 2859 + HAT1_DR#DNA/hAT-Ac 598 645
299 C21533332 2812 2859 C hAT-N76_DR#DNA/hAT 2324 2371

And the line in ProcessRepeats is ( line 7852 )

# add fused element to our derived from list
if ( $options{'source'} ) {
$lastAnnot->addDerivedFromAnnot( $member );
}

This should be:

# add fused element to our derived from list
if ( $options{'source'} ) {
$lastAnnot->addDerivedFromAnnot( $member->{'annot'} );
}
"

"I found something which causes ProcessRepeats to go into an infinite loop. It keeps expanding an array until the computer runs out of memory and the process is killed. It didn't print the
"Can't call method "getScore" on unblessed reference at /home/mtollis/RepeatMasker/PRSearchResult.pm line 164"
You have seen before though. I am not sure how you got that a second time. In any case I fixed this problem and I wondered if you might rerun this file on your system. The fix is in the PRSearchResult.pm module. You can download a patched copy of the module here:

http://www.repeatmasker.org/~rhubley/PRSearchResult.pm.gz

Copy this into your RepeatMasker directory, backup your old file and unzip this one:

mv PRSearchResult.pm PRSearchResult.pm.bak
gunzip PRSearchResult.pm.gz

I hope this fixes your problem. Thanks for reporting this!"

[GenoMax]

Thank you for taking the time to come back to an old thread to submit the solution.