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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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BuildDatabase error on big genome #101

Open AlenaKizenko opened 4 years ago

AlenaKizenko commented 4 years ago

I'm trying to run RepeatModeler v2 BuildDatabase script on genome 4,9G, but it fails. Nevertheless, RepeatModeler v1 can manage to build a database. BuildDatabase script works on different parts of genome file, but not on a whole file, which means that problem is not in the file format.

Error: Building database euprymna: Reading Lachesis_assembly.fasta... The makeblastdb program did not generate the file euprymna.nsq. Please check your input file(s) for potential formating errors. /apps/rmblast/2.9.0-p2/bin/makeblastdb returned:

Building a new DB, current time: 09/11/2020 11:58:49 New DB name: /scratch/kizenko_hydra_project/cephalopods/euprymna/euprymna New DB title: ./7RMRo_I_mB Sequence type: Nucleotide Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 1735 sequences in 113.391 seconds.

The command used was: /apps/rmblast/2.9.0-p2/bin/makeblastdb -blastdb_version 4 -out euprymna -parse_seqids -dbtype nucl -in ./7RMRo_I_mB 2>&1

jebrosen commented 4 years ago

This was fixed in #67, but it isn't in a released version yet. Here is a direct link to the the latest fixed BuildDatabase script: https://raw.githubusercontent.com/Dfam-consortium/RepeatModeler/708c53ddc23d8cc1b967f440be2130d4988c85b8/BuildDatabase

cement-head commented 4 years ago

Awesome! I have this same problem; new script solves problem for me.

huangziyan11111 commented 3 years ago

@jebrosen Hi, I can not open this website 'https://raw.githubusercontent.com/Dfam-consortium/RepeatModeler/708c53ddc23d8cc1b967f440be2130d4988c85b8/BuildDatabase'. Has this changed the position?

jebrosen commented 3 years ago

That link is still working for me. Does either of https://raw.githubusercontent.com/Dfam-consortium/RepeatModeler/c4a9d519e9da160b5aadc00fb06ccbf7beadf96e/BuildDatabase, or https://github.com/Dfam-consortium/RepeatModeler/blob/c4a9d519e9da160b5aadc00fb06ccbf7beadf96e/BuildDatabase, work?