stats file is null - Githubissues

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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stats file is null #377

Closed HaoWenhy closed 5 months ago

HaoWenhy commented 10 months ago

Hello, after my EDTA annotation, there is no sum stats file, I follow the question #169 to process and distribute to get the bed, out and stats file, and then use buildSummary.pl to build the sum stats file, I don't know why, my stats file is still null, and there is no other error, I hope you can answer, thank you very much!

oushujun commented 10 months ago

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

Shujun

HaoWenhy commented 10 months ago

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 commented 10 months ago

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 commented 10 months ago

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

xujialupaoli commented 10 months ago

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 commented 8 months ago

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 commented 5 months ago

@xujialupaoli any luck?

oushujun commented 5 months ago

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