jwli-code
commented
2 weeks ago I encountered the same issue and am unsure if there is a solution.
Open etwatson opened 3 weeks ago
jwli-code
commented
2 weeks ago I encountered the same issue and am unsure if there is a solution.
oushujun
commented
2 weeks ago 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.
— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/517#issuecomment-2456529799, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NGOJQSTZWXZVJBEOXLZ7B6QTAVCNFSM6AAAAABRCA7HGCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJWGUZDSNZZHE . You are receiving this because you are subscribed to this thread.Message ID: @.***>
etwatson
commented
1 week ago 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?
oushujun
commented
1 week ago 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?
— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/517#issuecomment-2468579446, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NG6I6WFFXCWSM745IT2ADLTNAVCNFSM6AAAAABRCA7HGCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINRYGU3TSNBUGY . You are receiving this because you commented.Message ID: @.***>
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 list