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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

Closed 8Purplegrapes closed 3 months ago

8Purplegrapes commented 10 months ago

Hi everyone，

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

Thanks very much

oushujun commented 10 months ago

Yes you do.

Thanks, Shujun

8Purplegrapes commented 10 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 10 months ago

Did you test EDTA on the small test file?

oushujun commented 9 months ago

any luck? @8Purplegrapes

8Purplegrapes commented 9 months ago

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