Test is failing after install #517
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I encountered the same issue and am unsure if there is a solution. |
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Hi I don’t see anything wrong with your test run, can you please articulate?
Shujun
…On Tue, Nov 5, 2024 at 3:27 AM jwli ***@***.***> wrote:
I encountered the same issue and am unsure if there is a solution.
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The test produces no results, which seems pretty confusing if that is expected. How am I to be certain if the software is working properly if it produces no result for the provided test data? |
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It produced your result:
Sat 02 Nov 2024 07:56:31 PM UTC EDTA final stage finished! You may check out:
The final EDTA TE library: genome.fa.mod.EDTA.TElib.fa
Please check manual
Shujun
…On Mon, Nov 11, 2024 at 11:30 AM Eric Watson ***@***.***> wrote:
The test produces no results, which seems pretty confusing if that is
expected. How am I to be certain if the software is working properly if it
produces no result for the provided test data?
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I followed these instructions with a fresh miniforge install, but I am still getting the warning that others experienced in this thread #487. For me, it seems to stem from the ltr pipeline. Also, I get this warning following your different instructions for using EDTA and EDTA2. No matter what, I can't seem to get it to work.
mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython cd-hit coreutils genericrepeatfinder genometools-genometools glob2 tir-learner ltr_finder_parallel ltr_retriever mdust multiprocess muscle openjdk perl perl-text-soundex r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr tesorter samtools bedtools LTR_HARVEST_parallel HelitronScannermamba activate EDTA2.2cd /home/EDTAgit checkout EDTA2git branchI then ran EDTA on the test data:
$ /home/EDTA/EDTA.pl --genome /home/EDTA/test/genome.fa --cds /home/EDTA/test/genome.cds.faHere is what I have installed in the mamba env:
$ mamba listThe text was updated successfully, but these errors were encountered: