Comments (8)
from edta.
Yes. There are files being produced in the folder '*.fa.mod.EDTA.raw/TIR/Module3_New/TIR-Learner'. I'll keep waiting.
Thank you for the quick reply.
Augusto
from edta.
Hi Augusto,
Just want to check back, did you finish the run successfully?
Thanks,
Shujun
from edta.
Hi Shujun,
Unfortunately, I had to kill the process because after 30 days it didn't finish running. I'm dealing with a large polyploid genome and the assembly is highly fragmented. When I run EDTA.pl on a small slice of contigs, it works fine. What do you think about running the pipeline on subsets of contigs?
Thanks,
Augusto
from edta.
Hi Augusto,
Thanks for your feedback. Both genome size and fragment number are deterministic for the run time of TIR-Learner. I've run through the chromosomal-scaffold wheat genome and the TIR part took about 26 days (#61). I also tested on the apple genome which is not big but with 127k sequences and it took about 10 days with large memory (>128Gb and I allocate 1 TB on it). You may split the genome into different batches such as split by ploidy, and combine them afterward (also see #61 and other issues).
Best,
Shujun
from edta.
Close due to no activity. Please reopen if the issue persists.
from edta.
Hi @oushujun,
I have approximately the same problem, except that I have 0 process corresponding to the program. I don't have any error message either. Penaeus vanamei genome (1.6 Gb)
nohup singularity exec -B /mystore /biolo/EDTA/1.9.5/edta.sif EDTA.pl --genome GCF_003789085.1_ASM378908v1_genomic.fna --overwrite 1 --sensitive 1 --anno 1 --evaluate 1 --threads 48 > run_EDTA.out 2>&1 &
########################################################
Extensive de-novo TE Annotator (EDTA) v1.9.4
Shujun Ou ([email protected])
########################################################
Mon Mar 15 16:45:20 CET 2021 Dependency checking:
All passed!
Mon Mar 15 16:45:34 CET 2021 The longest sequence ID in the genome contains 136 characters, which is longer than the limit (15)
Trying to reformat seq IDs...
Attempt 1...
Mon Mar 15 16:45:42 CET 2021 Seq ID conversion successful!
Mon Mar 15 16:45:42 CET 2021 Obtain raw TE libraries using various structure-based programs:
Mon Mar 15 16:45:42 CET 2021 EDTA_raw: Check dependencies, prepare working directories.
Mon Mar 15 16:45:47 CET 2021 Start to find LTR candidates.
Mon Mar 15 16:45:47 CET 2021 Identify LTR retrotransposon candidates from scratch.
from edta.
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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