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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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TEanno.sum file empty #123

Closed rimjhimroy closed 4 years ago

rimjhimroy commented 4 years ago

Hi @oushujun,

I am running EDTA as follows: EDTA.pl --step all --curatedlib ../Brassicaceae_repbase_all_march2019.fa --sensitive 1 --evaluate 1 --anno 1 --threads 10 --genome athchr1.fasta

I am testing the pipeline with Arabidopsis chromosome 1. I am getting this error at the end of the EDTA pipeline,

Tue Oct  6 22:04:39 CEST 2020   Evaluate the level of inconsistency for whole-genome TE annotation (slow step):

Use of uninitialized value in pattern match (m//) at /data/users/rchoudhury/programs/EDTA1.9/EDTA/util/call_seq_by_list.pl line 88.
Use of uninitialized value $chr_pre in hash element at /data/users/rchoudhury/programs/EDTA1.9/EDTA/util/call_seq_by_list.pl line 90.
Use of uninitialized value $pos in pattern match (m//) at /data/users/rchoudhury/programs/EDTA1.9/EDTA/util/call_seq_by_list.pl line 100.
Use of uninitialized value $pos in concatenation (.) or string at /data/users/rchoudhury/programs/EDTA1.9/EDTA/util/call_seq_by_list.pl line 103.
ERROR: Can not recognize this MSU position in the list!
ERROR: TE annotation stats results not found in athchr1.fasta.mod.EDTA.TE.fa.stat!

I have attached the full error report here EDTA.txt

Many thanks for your help.

Rimjhim

oushujun commented 4 years ago

Hi Rimjhim,

It's likely that the curated library you provided Brassicaceae_repbase_all_march2019.fa does not have classification info in it.

v1.9.3 should have fixed this error: Use of uninitialized value $type in concatenation (.) or string at /data/users/rchoudhury/programs/EDTA1.9/EDTA/util/gff2bed.pl line 82, <GFF> line 6331.

Please update and try again.

Best, Shujun

sanyalab commented 4 years ago

Hi Shujun,

I am facing the same issue. The summary file is empty. I am running v1.9.0 via conda. I do not see v1.9.3. Should I install it separately?

Thanks Abhijit

rimjhimroy commented 4 years ago

Hi Shujun,

Thanks for your swift response. Indeed, updating to v1.9.3 + a library with classification information in RepeatMasker format solved the issue.

Many Thanks, Rimjhim

oushujun commented 4 years ago

Hi @sanyalab, you may install v1.9.0 using conda, then git clone v1.9.3 and run EDTA from the cloned path using the conda env. - Shujun

Min84-dl commented 1 year ago

Hi, @oushujun

I ran EDTA with v2.1.3, and I met the same issue that 'TEanno.sum file is empty'.

My commond: EDTA.pl --genome genome.fa --cds cds.fa --species others --step all --sensitive 1 --anno 1 --overwrite 0

Error: Use of uninitialized value $type in concatenation (.) or string at /home/wangmin/software/EDTA/util/gff2bed.pl line 110, line 5320. Use of uninitialized value $type in concatenation (.) or string at /home/wangmin/software/EDTA/util/gff2bed.pl line 110, line 7173. ...

Can you help me?

Thanks Min

oushujun commented 1 year ago

Hi Min,

I tested on v2.1.3 and v2.0.1 on my end and they are working fine. One trivial thing, you need to specify the path to the EDTA v2.1.3 script otherwise it will use the conda version available in $ENV. The latest conda version is v2.1.0.

If the error persists, you may want to reinstall EDTA in an isolated conda env and test again.

Best, Shujun