test data about edta HOT 6 CLOSED

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 — Reply to this email directly, view it on GitHub <#468>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NFS53NTI7HDWL56LMLZFAOWDAVCNFSM6AAAAABISH77AKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGMZDOMJRGQYTKNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>