EDTA
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test data
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, <ANNO> 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 ([email protected]) 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 .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 ([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. 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