EDTA

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Use of unitialized value $chr_pre in has element call_seq_by_list.pl line 87

3

Hello Shujun, I was running EDTA v2.0.0 on a small cranberry genome and got the following error: `Use of uninitialized value $chr_pre in hash element at /mnt/home/teresisc/anaconda3/envs/EDTA/share/LTR_retriever/bin/call_seq_by_list.pl line 87.` The...

sjteresi

No intact LTR's passed through in combine stage

5

Hi Shujun, I noticed on my run through of EDTA 1.9.9 that none of the LTRs in the final combined library produced by EDTA had internal and LTR regions annotated...

mason-linscott

"mdb_env_open: Cannot allocate memory" and "singularity version can't find the input file"

6

Dear Shujun, Sorry to bother you again. I had got successful runs in June 2021 with EDTA, but now no idea why EDTA complains about `RMblast engine is not installed`....

zmz1988

TIR learner error - Illegal instructions

10

I'm getting this error in TIR learner when running the test genome. Fri Dec 10 16:15:45 EST 2021 Identify TIR candidates from scratch. ``` Species: others /Users/benweinberg/GitHub/EDTA/bin/TIR-Learner2.5/TIR-Learner2.5.sh: line 290: 39174...

benweinberg89

LINES vs LTR content

2

Hi @oushujun, I have been running the EDTA pipeline on several mollusc genomes to compare repeat content between species. My primary focus has been on examining how LTR content differs...

mason-linscott

make_panTE.pl has a sequence limit (>1Kb) that throws a bug of segmentation fault in blastn?

8

sh: line 2: 2474030 Aborted bash -c 'timeout 188s /home/omendivi/.conda/envs/EDTA_1.9.9/bin/blastn -query TE_00071658_INT#LTR/unknown TCTGGTATCAGAGCAATCATTCCAGGGGATTTGTTCTATGTCTTTTTTTTCAACATAATCAAGCAATCACTCCATCACCATTTTCCCTTCATCGTAGTCTCGCATCAAACAAACATCCACCACCTGACGCTACACACGCAATAGAAATAACAGAACTCGCTGCATAGTGAAATAAAAATACCCATAATCTACGTGCGTAGAAGACACAGTGAGCTACTTAACGAAGAATTCATAGATAACTAGCAATTATCGATGTGGTAGAAGTGAGTTAAAAATAATTCTAGATCTTCCACTTGCAAAAAATCATATCGACGAATATTTTTCAAAGCGATTCAACACTCAATTCTCGGCACAAACATCATCTCCGATGAATAACCCAAGAAATTGGTGAAAATAAAATAAAAATTAAAAATAAAACTAAGGTTTAATATTTTTCTATTCATTGGCTCGTATTTTTTGATGTCAAAATTATACGAGTAAAAGAATTGTGTTAATTCTATGGGACAATAGTCCCACATCGACAACAAAAAGGAAGTTTTCAAGTTTAAATATGCCAAGGCACGTACAAGACATCGTGACTTAGATCATGTCCTCCCTCCCATGCCTCATGTTATGCTTGCTACCTATCGTTGTTCCCTCACTACCTCAATCTTGTTGTTGTTGACTTTTCCACCCCCTGCCTGCCTGTTGACACCCCCACCTTGTGGTTATTGCTATTGACTGCCCCATGTTGCGTTATCTATCTCGTATTGCATGCCACCCTGTCTACTGTCTGCCTCATGTCCCACACTGCTCTTGTCCACCTTCCACCTCATGTCCCACTGCCTTGTCACTGACTTGTCTCGCCATGTCATCCACACTAATATTAACCATTTAAGGGGACAAAACTAAAGTTGCAACAACCAAATTTTTGACATGTTCAACAAAATTGCCAAATGGTTTTGACAAAATATTGTTCAAAATTACCCAATTACAAAATTGATGAAAATTCTTATAATTATTTTTGCACATAATTGACACAAATTTGCGATAAAATTTCTGACAATAATTCTTGTAACCATTTTTACAAAACTTTTGTCAACTTTTATGCTGCCCAATTTTGATGACGACTTTTAGCAACTTTTGTCAATTTTTTCACGATGGTTTTTGTGACGATTTTCAACAAAATTAGTGATAACCTCCAACAATGACTACACAAATGGCCATCGATGGAATATCTCATGATCCCAATATACTTTCATCGATTAATCTCACCACCCTTAGTCAAATTACTTTCATGCATGCATATAAAAATCAGTGCCAGGATATCATCAATTACATCTCTGGGTTAGATGAATCATTTCTCATAAGTTGCTTTGTCAATGGATTAAAGGATGAGATTAGGAAGGAGGTGGAAATATTCAATCCTTGCACCCTAATGCAGACCTTTGGATTAGCTTTATTAGCTAAAGATAAACTCAATGTTCAACGTCGATTAGGAAAACCACCTATGGGGAAATCACAAACCACTTACACCATCCCCAAACCTAACCAAACTTTACCAATTTAATTTCTTAGATTTAAGGAGAAGAAGGAACGATGAGTGAAATATCTTTGCGATACTTGTGATGAGAAATTTGGAACCCACCATAAATGCGCTACACAAACATTGTATTTATTGAAGGTAGTTGATCCTTGTCAATCCATAAAGGGTGAATATGAGGAAGATGAGCAAGAAATAACTGAAACACCTAATCAAATCTATGGAGACAATGATATTGAGGTGCAAGAAGTAACCAAAGCACCTAATCAAAAAAATAAATGCAATAAGGTTGATGTGCAATAAGTGATCGATTTCCCAGGAAAATATAAGGTAGACATAGAAGACGTGACCAATGAAGGCTACACATACACTCTAAAAATACTACCCATAAGTTCATCACAAATAGTGAGTTCTCACCACATGGTAAAACCTATCTAAAAATAAGGTAGAAAGTTGACTGCACACTTAATTTTTGTTGACTCTCTCAGGGAACAACCAAAAGATGTGGGAGTGTTACCACCATTTTTGATGCATCCTTCCAAAGTGTTTGAGGAGTCCCAAGGGTTACCCCCCCATCATCATCACGATCCTACTATTCTTCCTGGAAACCCCCCACTAATGCTTTGATCCTCAAGATATCCCTACCTCCAAAAAAGTGATATTAAACTTGTGCAAATACTACTTGGAAAGCACCTCATCAAT ") -db data/omendivi/TREES_2020/TE_WN_v3/merge/TElib.list.panTE.raw.iter8 -word_size 7 -evalue 1e-5 -dust no -outfmt "6 qseqid sseqid pident length mismatch gapopen...

oliviamr

The percent of LINE is way below my expectation

4

Hi, @oushujun Thanks for developing EDTA. I am studying fall armyworm which is a lepidopteran pest. before using EDTA(1.9.8) to annotate assembly,i tried some methods to annotate this assembly. 1....

BonesAQ

Use of uninitialized value $lLTR_start ($rLTR_end, $chr)

4

Hi shujun, Thanks for your excellent work in developing `EDTA` as an Extensive _de-novo_ TE Annotator for the research community. I am using `EDTA` to annotate interspersed repeat in a...

kingforest93

with TIR/Sola2 TE_Sorter chokes?

8

Hi Shujun, Thank you for EDTA it is a nice tool. I have run EDTA on a large genome split in chunks. One of the chunk ran EDTA_raw.pl without an...

oliviamr

ERROR while running edta: TE annotation stats results not found

19

Hi, after 20 hours, my run crushed when I ran: `EDTA.pl --genome ../hbf.fa --sensitive 1 --anno 1 --evaluate 1 --threads 32 --force 1 --overwrite 0 &>edta.log` and before crushed, edta...

zx-morningstar