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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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test data #468

Open wwenc opened 3 weeks ago

wwenc commented 3 weeks ago

When I run the test data, I meet some error. The log is following:

Fri May 31 15:04:06 CST 2024 EDTA_raw: Check dependencies, prepare working directories.

Fri May 31 15:04:07 CST 2024 Start to find LTR candidates.

Fri May 31 15:04:07 CST 2024 Identify LTR retrotransposon candidates from scratch.

Invalid value for shared scalar at /home/wuwenchao/software/anaconda/envs/EDTA/share/LTR_retriever/bin/LTR.identifier.pl line 114, line 11. cp: cannot stat 'genome.fa.mod.retriever.scn.adj': No such file or directory awk: fatal: cannot open file `genome.fa.mod.pass.list' for reading: No such file or directory Warning: LOC 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 (shujun.ou.1@gmail.com) 10/11/2019

mv: cannot stat 'genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln': No such file or directory mv: cannot stat 'genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln.list': No such file or directory cp: cannot stat 'genome.fa.mod.LTR.intact.raw.fa.anno.list': No such file or directory ERROR: No such file or directory at /home/wuwenchao/software/EDTA/util/output_by_list.pl line 39.

    perl filter_gff3.pl file.gff3 file.list > new.gff3

Fri May 31 15:04:10 CST 2024 Warning: The LTR result file has 0 bp!

Fri May 31 15:04:10 CST 2024 Start to find SINE candidates.

Fri May 31 15:04:26 CST 2024 Warning: The SINE result file has 0 bp!

Fri May 31 15:04:26 CST 2024 Start to find LINE candidates.

Fri May 31 15:04:26 CST 2024 Identify LINE retrotransposon candidates from scratch.

Fri May 31 15:04:56 CST 2024 Warning: The LINE result file has 0 bp!

Fri May 31 15:04:56 CST 2024 Start to find TIR candidates.

Fri May 31 15:04:56 CST 2024 Identify TIR candidates from scratch.

Species: others Traceback (most recent call last): File "/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 80, in TIRLearner_instance = TIRLearner(genome_file, genome_name, species, TIR_length, File "/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/bin/main.py", line 81, in init self.execute() File "/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/bin/main.py", line 121, in execute self.execute_M4() File "/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/bin/main.py", line 672, in execute_M4 self["base"] = CNN_predict.execute(self) File "/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line 114, in execute df = predict(df, TIRLearner_instance.genome_file_path, File "/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line 62, in predict model = load_model(path_to_model) File "/home/wuwenchao/software/anaconda/envs/EDTA/lib/python3.10/site-packages/keras/src/saving/saving_api.py", line 193, in load_model raise ValueError( ValueError: File format not supported: filepath=/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/cnn0912_tf_savedmodel. Keras 3 only supports V3 .keras files and legacy H5 format files (.h5 extension). Note that the legacy SavedModel format is not supported by load_model() in Keras 3. In order to reload a TensorFlow SavedModel as an inference-only layer in Keras 3, use keras.layers.TFSMLayer(/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/cnn0912_tf_savedmodel, call_endpoint='serving_default') (note that your call_endpoint might have a different name). Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /home/wuwenchao/software/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 (shujun.ou.1@gmail.com) 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. ERROR: No such file or directory at /home/wuwenchao/software/EDTA/util/output_by_list.pl line 39. Warning: The TIR result file has 0 bp!

Fri May 31 15:05:06 CST 2024 Start to find Helitron candidates.

Fri May 31 15:05:06 CST 2024 Identify Helitron candidates from scratch.

Fri May 31 15:05:20 CST 2024 Finish finding Helitron candidates.

Fri May 31 15:05:20 CST 2024 Execution of EDTA_raw.pl is finished!

ERROR: Raw LTR results not found in genome.fa.mod.EDTA.raw/genome.fa.mod.LTR.raw.fa and genome.fa.mod.EDTA.raw/genome.fa.mod.LTR.intact.raw.fa If you believe the program is working properly, this may be caused by the lack of intact LTRs in your genome. Consider to use the --force 1 parameter to overwrite this check

oushujun commented 3 weeks ago

Please reinstall EDTA.

Shujun

On Fri, May 31, 2024 at 3:08 PM wwenc @.***> wrote:

When I run the test data, I meet some error. The log is following:

Fri May 31 15:04:06 CST 2024 EDTA_raw: Check dependencies, prepare working directories.

Fri May 31 15:04:07 CST 2024 Start to find LTR candidates.

Fri May 31 15:04:07 CST 2024 Identify LTR retrotransposon candidates from scratch.

Invalid value for shared scalar at /home/wuwenchao/software/anaconda/envs/EDTA/share/LTR_retriever/bin/ LTR.identifier.pl line 114, line 11. cp: cannot stat 'genome.fa.mod.retriever.scn.adj': No such file or directory awk: fatal: cannot open file `genome.fa.mod.pass.list' for reading: No such file or directory Warning: LOC 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 @.***) 10/11/2019

mv: cannot stat 'genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln': No such file or directory mv: cannot stat 'genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln.list': No such file or directory cp: cannot stat 'genome.fa.mod.LTR.intact.raw.fa.anno.list': No such file or directory ERROR: No such file or directory at /home/wuwenchao/software/EDTA/util/ output_by_list.pl line 39.

perl filter_gff3.pl file.gff3 file.list > new.gff3

Fri May 31 15:04:10 CST 2024 Warning: The LTR result file has 0 bp!

Fri May 31 15:04:10 CST 2024 Start to find SINE candidates.

Fri May 31 15:04:26 CST 2024 Warning: The SINE result file has 0 bp!

Fri May 31 15:04:26 CST 2024 Start to find LINE candidates.

Fri May 31 15:04:26 CST 2024 Identify LINE retrotransposon candidates from scratch.

Fri May 31 15:04:56 CST 2024 Warning: The LINE result file has 0 bp!

Fri May 31 15:04:56 CST 2024 Start to find TIR candidates.

Fri May 31 15:04:56 CST 2024 Identify TIR candidates from scratch.

Species: others Traceback (most recent call last): File "/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 80, in TIRLearner_instance = TIRLearner(genome_file, genome_name, species, TIR_length, File "/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/bin/main.py", line 81, in init self.execute() File "/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/bin/main.py", line 121, in execute self.execute_M4() File "/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/bin/main.py", line 672, in execute_M4 self["base"] = CNN_predict.execute(self) File "/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line 114, in execute df = predict(df, TIRLearner_instance.genome_file_path, File "/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line 62, in predict model = load_model(path_to_model) File "/home/wuwenchao/software/anaconda/envs/EDTA/lib/python3.10/site-packages/keras/src/saving/saving_api.py", line 193, in load_model raise ValueError( ValueError: File format not supported: filepath=/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/cnn0912_tf_savedmodel. Keras 3 only supports V3 .keras files and legacy H5 format files (.h5 extension). Note that the legacy SavedModel format is not supported by load_model() in Keras 3. In order to reload a TensorFlow SavedModel as an inference-only layer in Keras 3, use keras.layers.TFSMLayer(/home/wuwenchao/software/EDTA/bin/TIR-Learner3.0/cnn0912_tf_savedmodel, call_endpoint='serving_default') (note that your call_endpoint might have a different name). Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /home/wuwenchao/software/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 @.***) 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. ERROR: No such file or directory at /home/wuwenchao/software/EDTA/util/ output_by_list.pl line 39. Warning: The TIR result file has 0 bp!

Fri May 31 15:05:06 CST 2024 Start to find Helitron candidates.

Fri May 31 15:05:06 CST 2024 Identify Helitron candidates from scratch.

Fri May 31 15:05:20 CST 2024 Finish finding Helitron candidates.

Fri May 31 15:05:20 CST 2024 Execution of EDTA_raw.pl is finished!

ERROR: Raw LTR results not found in genome.fa.mod.EDTA.raw/genome.fa.mod.LTR.raw.fa and genome.fa.mod.EDTA.raw/genome.fa.mod.LTR.intact.raw.fa If you believe the program is working properly, this may be caused by the lack of intact LTRs in your genome. Consider to use the --force 1 parameter to overwrite this check

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wwenc commented 3 weeks ago

ok, I will try again

jsoghigian commented 3 weeks ago

I have what appears to be the same identical error messages as here on the test dataset using the example command, installed via mamba today. How should I reinstall EDTA to avoid this error?

bioteksampath commented 3 weeks ago

hi... Is there any updates, i'm facing same error using test data. Invalid value for shared scalar at /anaconda/envs/EDTA/share/LTR_retriever/bin/LTR.identifier.pl line 114, line 11.

Marh32 commented 1 week ago

This may be caused by the incorrect version of LTR_Retriever. When I install edta with mamba, LTR_Retriever in 2.9.4 will be installed by default.Maybe you can update the retriever version to 2.9.9 or use yml to reinstall it to try it out.

Yorks0n commented 1 week ago

Encountered same problem, solved it by reinstall it with yml. git clone https://github.com/oushujun/EDTA.git and then mamba env create -f EDTA_2.2.x.yml Use mamba activate EDTA2, remove genome.fa.mod.EDTA.raw in the ./test folder, and then run the test again.