Closed 8Purplegrapes closed 3 months ago
Yes you do.
Thanks, Shujun
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**
Did you test EDTA on the small test file?
any luck? @8Purplegrapes
Thank you, I used "conda activate EDTA" and then ran panEDTA.sh, and then it ran successfully
Hi everyone,
Do I need to call EDTA's conda environment when running panEDTA? conda activate EDTA
Thanks very much