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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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FastaDB::compact - Error could not locate file /group/pasture/Saila/scanPAV/Kyuss_Imp04_40kb/RepeatMasker_imp04vsKyuss/RM_122929.FriMay61008492022/round-1/sampleDB-1.fa! #169

Closed biowackysci closed 11 months ago

biowackysci commented 2 years ago

**Hello Team,

I am relatively new to repeatModeler,

I am trying to use RepeatModeler on a database that is made up of presence and absence variants in two genomes. I use the following RepeatModeler -database /group/pasture/Saila/scanPAV/Kyuss_Imp04_40kb/pavs_present_in_Imp04_40kb_2kbabovepavs.fasta to run the job. I get an error "FastaDB::compact - Error could not locate file /group/pasture/Saila/scanPAV/Kyuss_Imp04_40kb/RepeatMasker_imp04vsKyuss/RM_86770.FriMay61004432022/round-1/sampleDB-1.fa! at /usr/local/eb/software/generic/RepeatModeler/2.0.1-intel-2019a-Perl-5.28.1/RepeatModeler line 837. "

Looks like the error appears 1000 times with my input file - I think that error is more pertinent to the problem. I think that the code is trying to process the input file, hitting an error lots of times (hence all those lines beginning with 'Error:' ) and failing to build up the .fa file. Once it finishes the first stage, it then tries to read the .fa file and finds it empty, and at that point it throws the error

Can someone please help me to go about it?

Thanks

rmhubley commented 11 months ago

Sorry for the late response. I believe this issue has been resolve, however if you are still experiencing this problem with recent versions of RepeatModeler please let us know.