PanEDTA Line Detection about edta

[oushujun]

Hi Scott,

Thank you for reporting this! Can you please update EDTA to 2.2.0 and test panEDTA again? There are many big changes to the new version for improved SINE/LINE annotations.

Thanks,
Shujun

[oushujun]

Any luck?

Shujun

[sjteresi]

My apologies for the delayed response Shujun, I will update EDTA this weekend or early next week and follow-up

[sjteresi]

Hi Shujun,

I am actually having additional trouble with EDTA 2.2.0 now that I have updated. I am having a lot of error getting conda to resolve dependencies when installing, so I elected to use singularity. That installation worked, but now when I run the genomes I get 0 LINE result files and the TIR detection fails, but does not crash. Here is a sample output:

Mon Apr 15 15:59:43 EDT 2024    Start to find LINE candidates.

Mon Apr 15 15:59:43 EDT 2024    Identify LINE retrotransposon candidates from scratch.

Tue Apr 16 07:25:21 EDT 2024    Warning: The LINE result file has 0 bp! 

Tue Apr 16 07:25:21 EDT 2024    Start to find TIR candidates.

Tue Apr 16 07:25:21 EDT 2024    Identify TIR candidates from scratch.

Species: others
find: ./TIR-Learner-+-TIRvish.gff3: No such file or directory
Traceback (most recent call last):
  File "/mnt/ufs18/rs-004/edgerpat_lab/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 80, in <module>
    TIRLearner_instance = TIRLearner(genome_file, genome_name, species, TIR_length,

The test that you included in your README works mostly... The dependencies check out, but I get a similar set of warnings:

Tue Apr 16 12:02:56 EDT 2024	Start to find LTR candidates.

Tue Apr 16 12:02:56 EDT 2024	Identify LTR retrotransposon candidates from scratch.

Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty.
Tue Apr 16 12:03:25 EDT 2024	Finish finding LTR candidates.

Tue Apr 16 12:03:25 EDT 2024	Start to find SINE candidates.

Tue Apr 16 12:04:07 EDT 2024	Warning: The SINE result file has 0 bp!

Tue Apr 16 12:04:07 EDT 2024	Start to find LINE candidates.

Tue Apr 16 12:04:07 EDT 2024	Identify LINE retrotransposon candidates from scratch.

Tue Apr 16 12:05:15 EDT 2024	Warning: The LINE result file has 0 bp!

Tue Apr 16 12:05:15 EDT 2024	Start to find TIR candidates.

Tue Apr 16 12:05:15 EDT 2024	Identify TIR candidates from scratch.

Species: others
Traceback (most recent call last):
  File "/mnt/ufs18/rs-004/edgerpat_lab/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 80, in <module>
    TIRLearner_instance = TIRLearner(genome_file, genome_name, species, TIR_length,
  File "/mnt/ufs18/rs-004/edgerpat_lab/EDTA/bin/TIR-Learner3.0/bin/main.py", line 81, in __init__
    self.execute()
  File "/mnt/ufs18/rs-004/edgerpat_lab/EDTA/bin/TIR-Learner3.0/bin/main.py", line 121, in execute
    self.execute_M4()
  File "/mnt/ufs18/rs-004/edgerpat_lab/EDTA/bin/TIR-Learner3.0/bin/main.py", line 672, in execute_M4
    self["base"] = CNN_predict.execute(self)
  File "/mnt/ufs18/rs-004/edgerpat_lab/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line 114, in execute
    df = predict(df, TIRLearner_instance.genome_file_path,
  File "/mnt/ufs18/rs-004/edgerpat_lab/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line 62, in predict
    model = load_model(path_to_model)
  File "/usr/local/lib/python3.10/site-packages/keras/src/saving/saving_api.py", line 262, in load_model
    return legacy_sm_saving_lib.load_model(
  File "/usr/local/lib/python3.10/site-packages/keras/src/utils/traceback_utils.py", line 70, in error_handler
    raise e.with_traceback(filtered_tb) from None
  File "/usr/local/lib/python3.10/site-packages/tensorflow/python/framework/function_def_to_graph.py", line 278, in function_def_to_graph_def
    input_shape = input_shape.as_proto()
AttributeError: as_proto
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /mnt/ufs18/rs-004/edgerpat_lab/EDTA/util/rename_tirlearner.pl line 19.
Warning: LOC list genome.fa.mod.TIR.ext30.list is empty.

Error: Error while loading sequence
Filter sequence based on TEsorter classifications. Unclassified sequences will also be output to the clean file.
	Usage: perl cleanup_misclas.pl sequence.fa.rexdb.cls.tsv
	Author: Shujun Ou ([email protected]) 10/11/2019
	
mv: cannot stat 'genome.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln': No such file or directory
cp: cannot stat 'genome.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list': No such file or directory
cp: cannot stat 'genome.fa.mod.TIR.intact.raw.fa.anno.list': No such file or directory
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3: No such file or directory.
Warning: The TIR result file has 0 bp!

Tue Apr 16 12:05:31 EDT 2024	Start to find Helitron candidates.

Tue Apr 16 12:05:31 EDT 2024	Identify Helitron candidates from scratch.

[sjteresi]

Currently re-trying with a fresh Anaconda installation and conda environment.

[oushujun]

The yml file should be helpful for conda installation. I don’t think the singularity version is working at the moment Shujun

…

On Tue, Apr 16, 2024 at 3:36 PM Scott Teresi ***@***.***> wrote: Currently re-trying with a fresh Anaconda installation and conda environment. — Reply to this email directly, view it on GitHub <#424 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NDXPHCEGJVCJ6UNAWLY5V4UFAVCNFSM6AAAAABCRVERVWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJZG44TOMJTGQ> . You are receiving this because you commented.Message ID: ***@***.***>

[sjteresi]

Hi Shujun,

I got the latest version of EDTA to complete the system test, still running it on my genomes. I will report back. I had to install bedtools and samtools on top of the conda environment for this latest upgrade. I did not see those being specified in the yml file, and I was having trouble making the basic install work. Perhaps I am wrong and messed up the install, or maybe they were pre-loaded on your computing cluster system so they were missed. Either way, I hope this helps!