Comments (7)
Thanks for the heads-up Shujun - I just pulled it and turned it on, it's currently running and will probably run for a few days (plant genome) :)
from edta.
Hi @hsiaopei ,
Thanks for testing EDTA
! Currently we encounter some issues with TIR-Learner, so the first module EDTA_raw.pl
, as well as the EDTA.pl
, are under a test mode. I am working with @weijiaweijia, the author of TIR-Learner
and co-author of the EDTA manuscript, to resolve this issue. It should be fixed within this week. Sorry for the inconvenience.
Best,
Shujun
from edta.
Dear @hsiaopei, @gabyrech, and @philippbayer,
Thank you for using EDTA. I just finished a major upgrade for the program including fixing the TIR-Learner
issue. Please reinstall the EDTA package and help to test with your genomes. Please ignore the FASTA-Reader error (e.g. FASTA-Reader: Ignoring invalid residues at position(s): On line 252: 520-746
) and cp
rm
errors for now. They are harmless to the result.
Please kindly let me know if you encounter any other errors. Thank you!
Best,
Shujun
from edta.
I've now have had it running for about 24 hours:
perl EDTA/EDTA.pl -genome ragoo.fasta -threads 15
currently it's hanging at this step:
perl <snip>/EDTA/bin/LTR_retriever/bin/LTR.identifier.pl ragoo.fasta -list ragoo.fasta.retriever.scn -seq ragoo.fasta.retriever.scn.extend.fa -anno ragoo.fasta.retriever.scn.extend.fa.aa.anno -flanksim 60 -flankmiss 25 -flankaln 0.6 -minlen 100 -u 1.3e-8 -threads 15 -blastplus /ws/00089503/anaconda/envs/EDTA/bin/ -motif TCCA TGCT TACA TACT TGGA TATA TGTA TGCA > ragoo.fasta.defalse
and is not consuming memory or CPU, and it hasn't written output in about 12 hours. The last file written was ragoo.fasta.defalse
(my input is ragoo.fasta
). Have you observed this before?
Last output in ragoo.fasta.defalse:
Chr0_RaGOO:14387060..14401218 false motif:TGAA TSD:TCAG 14387056..14387059 14401219..14401222 IN:14387558..14400719 0.9779 ? unknown NA 862315 Adjust: NO lLTR: 498 rLTR: 499 Alignment regions: 1, 498, 13661, 14158 LTR coordinates: 14387060, 14387557, 14400720, 14401218 TSD-LTR overlap: 0 Boundary missing: 0
from edta.
from edta.
Dear All,
Sorry for the delay of response. I just push a bulk update to EDTA and have tested it in different servers - it seems to work now. But I have not tested it in macOS, so some tiny differences could cause problems.
For testing purposes, please use a small file, ie. 20 Mb, for faster turn around. Please let me know if there are any issues.
Best,
Shujun
from edta.
I consider this issue is fixed. Please reopen it if the problem is persistent, or open new issues if you found new problems.
Best,
Shujun
from edta.
Related Issues (20)
- stats file is null HOT 6
- I have a question, why are the.mod.edta.teanno.gff3 and.mod.EDTA.TEanno.out lines different HOT 4
- error: LTR_retriever is not found in the LTR_retriever path ./! HOT 1
- Question about threads HOT 2
- Question about MITEs HOT 1
- Empty sum file, gff2bed errors HOT 3
- There are many overlapping regions of TE
- Many overlapping regions of TE HOT 1
- CACTA HOT 4
- LAI values from LTRRetrivar HOT 1
- LAI HOT 2
- Multiple EDTAs in parallel HOT 1
- LTR_retriever": No such file or directory at /home/ubuntu/deru/EDTA/EDTA_raw.pl line 307. HOT 6
- Are "Unknowns" Unknown TEs or generally unknown repeats? HOT 3
- Further classification HOT 4
- SLURM-specific behavior: repeat content dramatically reduced but no errors HOT 12
- genome.fa problem HOT 7
- Error when running panEDTA HOT 3
- CACTA HOT 1
- lib-test.pl -std and -tst must have different input file name HOT 1
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from edta.