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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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conda activate EDTA？ #413

Open 8Purplegrapes opened 6 months ago

8Purplegrapes commented 6 months ago

Hi everyone，

Do I need to call EDTA's conda environment when running panEDTA? conda activate EDTA

Thanks very much

oushujun commented 6 months ago

Yes you do.

Thanks, Shujun

8Purplegrapes commented 6 months ago

hi oushujun， This is a previous pan EDTA analysis using the EDTA environment. The first genome analysis reported an error when it reached RepeatMasker. Is there any good solution?

2023-12-25 01:52:31,383 -INFO- writing classified protein domains in zs11.genome.cds.fasta.code.rexdb.cls.pep 2023-12-25 01:52:31,453 -INFO- Summary of classifications: Order Superfamily # of Sequences# of Clade Sequences # of Clades# of full Domains LTR Bel-Pao 26 0 0 0 LTR Copia 474 139 16 0 LTR Gypsy 821 535 17 0 LTR Retrovirus 14 0 0 0 LTR mixture 8 0 0 0 pararetrovirus unknown 25 0 0 0 DIRS unknown 40 0 0 0 Penelope unknown 14 0 0 0 LINE unknown 498 0 0 0 TIR EnSpm_CACTA 3 0 0 0 TIR MuDR_Mutator 7 0 0 0 TIR PIF_Harbinger 76 0 0 0 TIR hAT 22 0 0 0 Maverick unknown 327 0 0 0 mixture mixture 4 0 0 0 2023-12-25 01:52:31,455 -INFO- Pipeline done. 2023-12-25 01:52:31,456 -INFO- cleaning the temporary directory ./tmp Mon Dec 25 09:45:42 CST 2023 Homology-based annotation of TEs using ganganF73.genome.fa.mod.EDTA.TElib.fa from scratch.

**ERROR: RepeatMasker results not found in ganganF73.genome.fa.mod.out!

ERROR: Initial EDTA failed for ganganF73.genome.fa**

oushujun commented 5 months ago

Did you test EDTA on the small test file?

oushujun commented 5 months ago

any luck? @8Purplegrapes

8Purplegrapes commented 5 months ago

Thank you, I used "conda activate EDTA" and then ran panEDTA.sh, and then it ran successfully