CrayonLinchan
commented
3 months ago I found some issues with my genome files!! I will fix it and try again!
Closed CrayonLinchan closed 3 months ago
CrayonLinchan
commented
3 months ago I found some issues with my genome files!! I will fix it and try again!
yanyew
commented
1 month ago I found some issues with my genome files!! I will fix it and try again!
What's the exact issue that cause this error?
Hi, thanks for the nice tools. 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). I am so confuded :(
Here is my code:
nohup EDTA/EDTA.pl --genome selected.fa --species others --sensitive 1 --step all --anno 1 -t 8 --u 7e-9 2> edta.log &And here is my EDTA.log file: nohup: ignoring input and appending output to 'nohup.out' Sat 09 Mar 2024 08:53:38 PM CST EDTA_raw: Check dependencies, prepare working directories.
Sat 09 Mar 2024 08:53:39 PM CST Start to find LTR candidates.
Sat 09 Mar 2024 08:53:39 PM CST Identify LTR retrotransposon candidates from scratch.
Sat 09 Mar 2024 09:24:37 PM CST Finish finding LTR candidates.
Sat 09 Mar 2024 09:24:37 PM CST Start to find SINE candidates.
Sat 09 Mar 2024 09:52:06 PM CST Finish finding SINE candidates.
Sat 09 Mar 2024 09:52:06 PM CST Start to find LINE candidates.
Sat 09 Mar 2024 09:52:06 PM CST Identify LINE retrotransposon candidates from scratch.
Sun 10 Mar 2024 01:54:53 AM CST Finish finding LINE candidates.
Sun 10 Mar 2024 01:54:53 AM CST Start to find TIR candidates.
Sun 10 Mar 2024 01:54:53 AM CST Identify TIR candidates from scratch.
Species: others Sun 10 Mar 2024 03:43:28 AM CST Finish finding TIR candidates.
Sun 10 Mar 2024 03:43:28 AM CST Start to find Helitron candidates.
Sun 10 Mar 2024 03:43:28 AM CST Identify Helitron candidates from scratch.
Sun 10 Mar 2024 04:24:48 AM CST Finish finding Helitron candidates.
Sun 10 Mar 2024 04:24:48 AM CST Execution of EDTA_raw.pl is finished!
Warning: No sequences were masked Sun 10 Mar 2024 04:30:12 AM CST Homology-based annotation of TEs using selected.fa.mod.EDTA.TElib.fa from scratch.
Use of uninitialized value $type in concatenation (.) or string at /EDTA/util/gff2bed.pl line 112, line 13922.
Use of uninitialized value $type in concatenation (.) or string at /EDTA/util/gff2bed.pl line 112, line 16127.
Use of uninitialized value $type in concatenation (.) or string at /EDTA/util/gff2bed.pl line 112, line 16612.
Use of uninitialized value $type in concatenation (.) or string at /EDTA/util/gff2bed.pl line 112, line 23942.
Use of uninitialized value $type in concatenation (.) or string at /EDTA/util/gff2bed.pl line 112, line 28139.
Use of uninitialized value $type in concatenation (.) or string at /EDTA/util/gff2bed.pl line 112, line 36110.
Use of uninitialized value $type in concatenation (.) or string at /EDTA/util/gff2bed.pl line 112, line 36974.
Use of uninitialized value $type in concatenation (.) or string at /EDTA/util/gff2bed.pl line 112, line 13999.
Use of uninitialized value $type in concatenation (.) or string at /EDTA/util/gff2bed.pl line 112, line 16192.
Use of uninitialized value $type in concatenation (.) or string at /EDTA/util/gff2bed.pl line 112, line 16681.
Use of uninitialized value $type in concatenation (.) or string at /EDTA/util/gff2bed.pl line 112, line 24052.
Use of uninitialized value $type in concatenation (.) or string at /EDTA/util/gff2bed.pl line 112, line 28349.
Use of uninitialized value $type in concatenation (.) or string at /EDTA/util/gff2bed.pl line 112, line 36329.
Use of uninitialized value $type in concatenation (.) or string at /EDTA/util/gff2bed.pl line 112, line 37176.
Use of uninitialized value $class in hash element at /EDTA/util/div_table2.pl line 80, <$fh> line 13502.
Use of uninitialized value $class in hash element at /EDTA/util/div_table2.pl line 81, <$fh> line 13502.
Use of uninitialized value $class in hash element at /EDTA/util/div_table2.pl line 80, <$fh> line 15655.
Use of uninitialized value $class in hash element at /EDTA/util/div_table2.pl line 81, <$fh> line 15655.
Use of uninitialized value $class in hash element at /EDTA/util/div_table2.pl line 80, <$fh> line 16134.
Use of uninitialized value $class in hash element at /EDTA/util/div_table2.pl line 81, <$fh> line 16134.
Use of uninitialized value $class in hash element at /EDTA/util/div_table2.pl line 80, <$fh> line 23140.
Use of uninitialized value $class in hash element at /EDTA/util/div_table2.pl line 81, <$fh> line 23140.
Use of uninitialized value $class in hash element at /EDTA/util/div_table2.pl line 80, <$fh> line 27207.
Use of uninitialized value $class in hash element at /EDTA/util/div_table2.pl line 81, <$fh> line 27207.
Use of uninitialized value $class in hash element at /EDTA/util/div_table2.pl line 80, <$fh> line 34902.
Use of uninitialized value $class in hash element at /EDTA/util/div_table2.pl line 81, <$fh> line 34902.
Use of uninitialized value $class in hash element at /EDTA/util/div_table2.pl line 80, <$fh> line 35739.
Use of uninitialized value $class in hash element at /EDTA/util/div_table2.pl line 81, <$fh> line 35739.
Use of uninitialized value in pattern match (m//) at /EDTA/util/call_seq_by_list.pl line 90.
Use of uninitialized value $chr_pre in hash element at /EDTA/util/call_seq_by_list.pl line 92.
Use of uninitialized value $pos in pattern match (m//) at /EDTA/util/call_seq_by_list.pl line 103.
Use of uninitialized value $pos in concatenation (.) or string at /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 selected.fa.mod.EDTA.TE.fa.stat!
And here is my nohup.out file:
#########################################################
Extensive de-novo TE Annotator (EDTA) v2.2.1
Shujun Ou (shujun.ou.1@gmail.com)
#########################################################
Parameters: --genome selected.fa --species others --sensitive 1 --step all --anno 1 -t 8 --u 7e-9
Sat 09 Mar 2024 08:53:34 PM CST Dependency checking: All passed!
Sat 09 Mar 2024 08:53:38 PM CST Obtain raw TE libraries using various structure-based programs: Sun 10 Mar 2024 04:24:48 AM CST Obtain raw TE libraries finished. All intact TEs found by EDTA: selected.fa.mod.EDTA.intact.raw.fa selected.fa.mod.EDTA.intact.raw.gff3
Sun 10 Mar 2024 04:24:48 AM CST Perform EDTA advance filtering for raw TE candidates and generate the stage 1 library:
Sun 10 Mar 2024 04:26:53 AM CST EDTA advance filtering finished.
Sun 10 Mar 2024 04:26:53 AM CST Perform EDTA final steps to generate a non-redundant comprehensive TE library.
Sun 10 Mar 2024 04:30:12 AM CST EDTA final stage finished! You may check out: The final EDTA TE library: selected.fa.mod.EDTA.TElib.fa Sun 10 Mar 2024 04:30:12 AM CST Perform post-EDTA analysis for whole-genome annotation:
Sun 10 Mar 2024 04:36:00 AM CST TE annotation using the EDTA library has finished! Check out: Whole-genome TE annotation (total TE: ): selected.fa.mod.EDTA.TEanno.gff3 Whole-genome TE annotation summary: selected.fa.mod.EDTA.TEanno.sum Whole-genome TE divergence plot: selected.fa.mod_divergence_plot.pdf Whole-genome TE density plot: selected.fa.mod.EDTA.TEanno.density_plots.pdf Low-threshold TE masking for MAKER gene annotation (masked: 14.49%): selected.fa.mod.MAKER.masked
Sun 10 Mar 2024 04:36:00 AM CST Evaluate the level of inconsistency for whole-genome TE annotation:
Looking forward to your kindly reply!! Have a nice day! :)