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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 2 months ago

Qikiiso commented 2 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 2 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.