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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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ERROR: TE annotation stats results not found in B.purpurea.fasta.mod.EDTA.TE.fa.stat! #457

Open Qikiiso opened 6 months ago

Qikiiso commented 6 months ago

Hi Shujun,

Thank you very much for providing EDTA to the world.I have installed the latest EDTA v2.2.1 using conda and run the test file successfully. However, when I ran my own data, I encountered the following error message and obtain TEanno.sum file with 0k (but I have gff3 file for TE annotation).

Here is my code: nohup EDTA.pl --genome B.purpurea.fasta --cds Bauhinia.variegata.CDS.fa --species others --step all --sensitive 1 --anno 1 --evaluate 1 -t 32 --rmout ./moder/repeatmasker/purpurea.upper.fasta.out

And here is my EDTA.log file: Use of uninitialized value in pattern match (m//) at /disk1/xsq/xsq/softwares/EDTA/util/call_seq_by_list.pl line 90. Use of uninitialized value $chr_pre in hash element at /disk1/xsq/xsq/softwares/EDTA/util/call_seq_by_list.pl line 92. Use of uninitialized value $pos in pattern match (m//) at /disk1/xsq/xsq/softwares/EDTA/util/call_seq_by_list.pl line 103. Use of uninitialized value $pos in concatenation (.) or string at /disk1/xsq/xsq/softwares/EDTA/util/call_seq_by_list.pl line 106. ERROR: Can not recognize this MSU position in the list! ERROR: TE annotation stats results not found in B.purpurea.fasta.mod.EDTA.TE.fa.stat!

wang-zewen commented 6 months ago

Hello, I also encountered the same problem. The reason is that there is no attribute for $type when $class=snRNA in gff2bel.pl, resulting in subsequent errors related to bed files.

FayeFang17 commented 3 months ago

Hey, I just updated EDTA to add missing types. You may try the EDTA2 branch version if you like!

emilpaulitz commented 3 months ago

I had the same issue but am mainly interested in the genome.fa.mod.EDTA.MAKER.masked file. Is this file okay to use after the error was encountered? Its size is in the expected range.

Sidenote: I also tried the EDTA2 branch, but always got the error "Error: LTR_FINDER_parallel not installed!". ltr_finder is installed with version 1.07 in the conda environment. I tried different conda environments installed by either the yml or by specifying all the packages and more. Then, because of previous errors and respective solutions I found in these issues, I call 

export PATH="${conda_env}/bin:$PATH"  # fix SINE error
export PYTHONNOUSERSITE=True  # fix (possible) TIR error
perl github_repo/EDTA.pl --genome ... --cds ... --overwrite 1 --sensitive 1 --threads 16

The same error does not occur with the master branch version of EDTA.