stats file is null about edta

[oushujun]

Do you have a non-empty TEanno.gff3 file? Any errors during the run?

Shujun

[HaoWenhy]

Yes, the TEanno.gff3 files all have data, I have run a total of three genomes and all of them came up with no sum file and after going to fix it according to problem #169, none of them worked. There are two errors reported throughout the EDTA run:
ERROR: Can not recognize this MSU position in the list!
ERROR: TE annotation stats results not found in finall.fasta.mod.EDTA.TE.fa.stat!
I'm looking forward to your advice.

[HaoWenhy]

For the EDTA annotations for all three genes, the error reported is the same, no stats file for any of them. However I went through gff2bed.pl, Convert bed to RepeatMasker .out, count_base.pl, buildSummary.pl, to generate TEanno.bed, TEanno.out, $genome.stats, and TEanno.sum respectively . Finally TEanno.sum is an empty file. I'm not sure what's wrong with it, please advise!

[oushujun]

I don't know how to debug without error messages. Can you give a small example to reproduce your issue?

[xujialupaoli]

Hi shujun!
I have the similar error, and my TEanno.gff3 files all have data.
I am using EDTA (perl /home/jialu/jialusoftware/EDTA-master/EDTA.pl --genome /home/work/jialu/Mt/Drive/new_res/MtrunR108.changed.fasta --cds /home/work/jialu/Mt/Drive/new_res/MtrunR108.changed.cdsNEW.fa --exclude /home/work/jialu/Mt/Drive/new_res/MtrunR108
), but this time the script ended with
ERROR: Can not recognize this MSU position in the list!
ERROR: TE annotation stats results not found in MtrunR108.changed.fasta.mod.EDTA.TE.fa.stat!

I'm not sure what's wrong with it, please advise!

My EDTA version is v2.1.3

Thank you! : )

[oushujun]

Hello @xujialupaoli,

Sorry for the delayed response. Have you solved this issue? Looks like the program had issues before it finished the annotation.

Shujun

[oushujun]

@xujialupaoli any luck?

[oushujun]

Closing due to no response. Please reopen if the issue remains. You may also want to try the v2.2.0 update.