same bug before about LTR.identifier.pl

[Z1997B]

Hi shujun ou,
Happy new year!
I have the same bug about LTR.identifier.pl(version 2.9.9), errors are listed below:

Invalid value for shared scalar at /public/home/zhangbo/mambaforge/envs/EDTA/share/LTR_retriever/bin/LTR.identifier.pl line 114, line 1199.
cp: cannot stat 'GCA_905340225.1_ilAbrTrip1.1_genomic.fa.mod.retriever.scn.adj': No such file or directory

Would you give me some advice to solve with it?

Best regards,
ZB

[oushujun]

Can you paste the command you used? Thanks!

shujun

[gorliver]

I have the exact same error.
My command is:

EDTA.pl --anno 1 --genome ./A626.fa --sensitive 1 --threads 50 --curatedlib ../database/rice6.9.5.liban

EDTA was install using conda.

The test run was successfully finished but there are two warnings Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. and Warning: No sequences were masked.

Here is the output(genome.fa.mod.EDTA.TE.fa.stat.all.sum) of the test run:

Confusion matrix of genome.fa.mod.EDTA.TE.fa.stat for the all category
        DNA/Mutator     DNA/PIF_Harbinger       DNA/Tc1_Mariner DNA/hAT DNA/unknown     LINE/unknown    LTR/Copia       LTR/Gypsy       SINE/unknown    nonDNA/helitron Inconsistent_rate
DNA/Mutator     8       0       0       0       0       0       0       0       0       0       0.0000
DNA/PIF_Harbinger       1       29      1       0       0       0       0       0       0       0       0.0645
DNA/Tc1_Mariner 0       0       38      0       0       0       0       0       0       0       0.0000
DNA/hAT 0       0       0       1       0       0       0       0       0       0       0.0000
DNA/unknown     0       0       0       0       1       0       0       0       0       0       0.0000
LINE/unknown    0       0       0       0       0       2       0       0       0       0       0.0000
LTR/Copia       0       0       0       0       0       0       1       0       0       0       0.0000
LTR/Gypsy       0       0       0       0       0       0       0       12      0       0       0.0000
SINE/unknown    0       0       0       0       0       0       0       0       1       0       0.0000
nonDNA/helitron 0       0       0       0       0       0       0       0       0       9       0.0000

[Z1997B]

Can you paste the command you used? Thanks!

shujun

HI shujun,

I have solved this problem. When you call EDTA, Chromosome ID must be rather than should be limited to 13 characters. What;s more, It is important to note that all the bases in the genome must be capitalized. 

Thanks for your reminding~