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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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The log file shows that there are results file output, but I can't find it in the directory #180

Open biology-han opened 2 years ago

biology-han commented 2 years ago

commond : RepeatModeler -pa 32 -database HWDY -engine ncbi > repeatmodeler.log

RepeatClassifier Version 2.0.2 ====================================== Search Engine = rmblast - Looking for Simple and Low Complexity sequences.. - Looking for similarity to known repeat proteins.. Missing /home/dell/Documents/Repo/RepeatMasker/Libraries/RepeatMasker.lib.nsq! Please rerun the configure program in the RepeatMasker directory before running this script. - Looking for similarity to known repeat consensi.. Classification Time: 00:15:30 (hh:mm:ss) Elapsed Time Program Time: 17:24:17 (hh:mm:ss) Elapsed Time Working directory: ${home}/HWDY_ann/Repeat/RM_1146353.WedSep211539232022 may be deleted unless there were problems with the run.
The results have been saved to: HWDY-families.fa - Consensus sequences for each family identified. HWDY-families.stk - Seed alignments for each family identified.
The RepeatModeler stockholm file is formatted so that it can easily be submitted to the Dfam database. Please consider contributing curated families to this open database and be a part of this growing community resource. For more information contact help@dfam.org.

rmhubley commented 1 year ago

Actually it looks like you ran into a problem in the RepeatClassifier step: "Missing /home/dell/Documents/Repo/RepeatMasker/Libraries/RepeatMasker.lib.nsq!". This is indicating that you don't have a correct installation of the RepeatMasker package and it can't find the TE library for comparison. Indeed there still should be a set of discovered families in the ${home}/HWDY_ann/Repeat/RM_1146353.WedSep211539232022 directory under the names "consensi.fa" and "families.stk".