oushujun
commented
2 years ago Hi, after the structural filter, it will go through other filters such as protein blast, Which may take some time for a single step. You may check Which file was written lately, i.e. find ./ -mmin 100, to see Which step it is on. Or check what perl commands are running at the moment, ie, ps aux|grep perl.
If it's stuck at a step, You may need to rerun the program. This happens in a busy system in which other programs are alao consuming CPUs.
Best, Shujun
On Tue, Dec 21, 2021 at 12:14 AM yangfty @.***> wrote:
I tried to analyze a genome about 3G, and the program have been running for more than 48, the last line of output on the screen was “Intact LTR-RT found: 47765”, then nothing changed, and the latest file was "genome.fa.defalse", my command was "LTR_retriever -genome genome.fa -inharvest genome.fa.rawLTR.scn -threads 40", I found that it was not normal to have no results for such a long time. I hope to know how to get the results.
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I tried to analyze a genome about 3G, and the program have been running for more than 48, the last line of output on the screen was “Intact LTR-RT found: 47765”, then nothing changed, and the latest file was "genome.fa.defalse", my command was "LTR_retriever -genome genome.fa -inharvest genome.fa.rawLTR.scn -threads 40", I found that it was not normal to have no results for such a long time. I hope to know how to get the results.