fanhuan
commented
5 months ago I have the same issue. I was running RepetModeler with -LTRStruct. and it failed at the LTR Structural Analysis part. When I tried to resume the program by using -recoverDir, it also says that my RepeatModeler run is successful. But I do not have database-family.fa. I was able to locate the log for LTR_retriever (for me it was: RM_14.FriJan50358422024/LTR346857.TueJan90142312024/LRET***/LTR_retriever.log) and in thelog it has the command that was run.
Parameters: -repeatmasker /opt/RepeatMasker -blastplus /opt/rmblast/bin -cdhit_path /opt/cd-hit -trf_path /opt/trf -genome seq.fa -inharvest /opt /RM_14.FriJan50358422024/LTR_346857.TueJan90142312024/raw-struct-results.txt -noanno -threads 20
You just need to locate your LTR_retriever in order to restart it. For me it was:
/opt/LTR_retriever/LTR_retriever -repeatmasker /opt/RepeatMasker -blastplus /opt/rmblast/bin -cdhit_path /opt/cd-hit -trf_path /opt/trf -genome seq.fa -inharvest /opt/RM_14.FriJan50358422024/LTR_346857.TueJan90142312024/raw-struct-results.txt -noanno -threads 20
I think it was able to recognize what was done. The previous run stopped at Module 1 (after running for 12h), but this time it was able to move on the modules 2-5 in less than an hour. This finished and I got results like:
##############################
####### Result files #########
##############################
Table output for intact LTR-RTs (detailed info)
seq.fa.pass.list (All LTR-RTs)
seq.fa.nmtf.pass.list (Non-TGCA LTR-RTs)
seq.fa.pass.list.gff3 (GFF3 format for intact LTR-RTs)
LTR-RT library
seq.fa.LTRlib.redundant.fa (All LTR-RTs with redundancy)
seq.fa.LTRlib.fa (All non-redundant LTR-RTs)
seq.fa.nmtf.LTRlib.fa (Non-TGCA LTR-RTs)According to the RepetModeler website, I believe the correct result for a successful RepeatModeler run with the -LTRStruct option should result in things like this instead:
At the succesful completion of a run, three files are generated:
<database_name>-families.fa : Consensus sequences
<database_name>-families.stk : Seed alignments
<database_name>-rmod.log : A summarized log of the runHowever, after finishing the LTR_retriever, I still don't have
Please kindly let me know how I can obtain those files.
My environment:
How did you install RepeatModeler? docker from TE-tools (https://github.com/Dfam-consortium/TETools)
Which version of RepeatModeler do you have? RepeatModeler-2.0.5
Which version of RepeatMasker is this RepeatModeler installation using? 4.1.6
Operating system and version: Ubuntu 22.04
Hi,
I have reported this bug at www.repeatmasker.org, but was hoping to get some input from here as well. Sorry if this is therefore a duplicate.
My issue: LTRHarvest was running on a single core for me, using the binaries downloaded from the software's homepage. I therefore stopped my RepeatModeler run after 7 rounds and while running LTRHarvest, reinstalled LTRHarvest from scratch with
make threads=yes, and restarted my original RepeatModeler run. RepeatModeler then finished within a few seconds, skipping LTRHarvest and any steps following, and reported:My steps for reproducing the issue:
~/programs/RepeatModeler-2.0.3/RepeatModeler -database genome -pa 40 -LTRStruct -genomeSampleSizeMax 729000000 &> run2.out~/programs/RepeatModeler-2.0.3/RepeatModeler -database genome -recoverDir RM_601117.SatMay211407242022 -pa 40 -LTRStruct -genomeSampleSizeMax 729000000 -genometools_dir ~/programs/genometools-1.6.2/bin/ &> restartrun2.outFull log of the re-start:
The content of RM_601117.SatMay211407242022 (dates are not original, as this is a back-up): 4.0K May 24 20:23 LTR_697138.TueMay240229512022 300K May 24 20:23 round-7 136K May 24 20:23 round-6 64K May 24 20:23 round-5 20K May 24 20:23 round-4 4.0K May 24 20:23 round-3 4.0K May 24 20:23 round-2 248K May 24 20:23 round-1 2.5M May 24 20:23 tmpConsensi.fa.masked 2.5M May 24 20:23 tmpConsensi.fa 149M May 24 20:23 families.stk 2.5M May 24 20:23 consensi.fa 7.8K May 24 20:23 rmod.log
Content of subdirectory of LTRHarvest: 503 May 24 20:24 esa_index.prj 0 May 24 20:24 ltrharvest.log 0 May 24 20:24 ltrharvest.out 28G May 24 20:24 esa_index.suf 3.1G May 24 20:24 esa_index.llv 3.5G May 24 20:24 esa_index.lcp 23K May 24 20:23 esa_index.ssp 886M May 24 20:23 esa_index.esq 49K May 24 20:23 esa_index.des 183K May 24 20:23 esa_index.md5 45K May 24 20:23 esa_index.sds 0 May 24 20:23 suffixerator.log
My environment:
How did you install RepeatModeler? Manual installation from repeatmasker.org
Which version of RepeatModeler do you have? RepeatModeler-2.0.3
Which version of RepeatMasker is this RepeatModeler installation using? 4.1.2-p1, standard installation
Operating system and version: Linux 4.18.0-240.1.1.el8_3.x86_64
Some additional context: