lourdesalo
commented
3 weeks ago Hi! I also have a similar issue
Parameters: --genome /mnt/home/lopezj38/ref_genome/GCF_000001735.4_TAIR10.1_genomic.fna --cds /mnt/home/lopezj38/ref_genome/GCF_000001735.4_TAIR10.1_TAIR_cds_from_genomic.fna --curatedlib /mnt/home/lopezj38/ref_genome/athrep.updated.nonredun.fasta --exclude /mnt/home/lopezj38/ref_genome/plasmid.bed --overwrite 1 --sensitive 1 --anno 1 --evaluate 1 --u 1.5e-8 --threads 28
Tue Oct 29 02:03:54 PM EDT 2024 Dependency checking:
All passed!
A custom library /mnt/home/lopezj38/ref_genome/athrep.updated.nonredun.fasta is provided via --curatedlib. Please make sure this is a manually curated library but not machine generated.
A CDS file /mnt/home/lopezj38/ref_genome/GCF_000001735.4_TAIR10.1_TAIR_cds_from_genomic.fna is provided via --cds. Please make sure this is the DNA sequence of coding regions only.
A BED file is provided via --exclude. Regions specified by this file will be excluded from TE annotation and masking.
Tue Oct 29 02:03:58 PM EDT 2024 Obtain raw TE libraries using various structure-based programs:
Tue Oct 29 02:03:58 PM EDT 2024 EDTA_raw: Check dependencies, prepare working directories.
Tue Oct 29 02:04:42 PM EDT 2024 Start to find LTR candidates.
Tue Oct 29 02:04:42 PM EDT 2024 Identify LTR retrotransposon candidates from scratch.
Tue Oct 29 02:12:08 PM EDT 2024 Finish finding LTR candidates.
Tue Oct 29 02:12:08 PM EDT 2024 Start to find SINE candidates.
Tue Oct 29 02:29:54 PM EDT 2024 Finish finding SINE candidates.
Tue Oct 29 02:29:54 PM EDT 2024 Start to find LINE candidates.
Tue Oct 29 02:29:54 PM EDT 2024 Identify LINE retrotransposon candidates from scratch.
Tue Oct 29 06:58:16 PM EDT 2024 Finish finding LINE candidates.
Tue Oct 29 06:58:16 PM EDT 2024 Start to find TIR candidates.
Tue Oct 29 06:58:16 PM EDT 2024 Identify TIR candidates from scratch.
Species: others
Traceback (most recent call last):
File "/mnt/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/lib/python3.9/site-packages/swifter/swifter.py", line 419, in apply
tmp_df = func(sample, *args, **kwds)
File "/mnt/gs21/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/get_fasta_sequence.py", line 23, in <lambda>
df["end"] = df.swifter.progress_bar(flag_verbose).apply(lambda x: min(x["end"], fasta_len_dict[x["seqid"]]), axis=1)
TypeError: unhashable type: 'Series'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/mnt/gs21/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/share/TIR-Learner3/TIR-Learner.py", line 95, in <module>
TIRLearner_instance = TIRLearner(genome_file, genome_name, species, TIR_length,
File "/mnt/gs21/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/main.py", line 91, in __init__
self.execute()
File "/mnt/gs21/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/main.py", line 131, in execute
self.execute_M4()
File "/mnt/gs21/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/main.py", line 632, in execute_M4
self["base"] = get_fasta_sequence.execute(self)
File "/mnt/gs21/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/get_fasta_sequence.py", line 67, in execute
df = get_start_end(TIRLearner_instance.genome_file_path, TIRLearner_instance["base"],
File "/mnt/gs21/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/get_fasta_sequence.py", line 23, in get_start_end
df["end"] = df.swifter.progress_bar(flag_verbose).apply(lambda x: min(x["end"], fasta_len_dict[x["seqid"]]), axis=1)
File "/mnt/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/lib/python3.9/site-packages/swifter/swifter.py", line 428, in apply
timed = timeit.timeit(wrapped, number=N_REPEATS)
File "/mnt/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/lib/python3.9/timeit.py", line 233, in timeit
return Timer(stmt, setup, timer, globals).timeit(number)
File "/mnt/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/lib/python3.9/timeit.py", line 177, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "/mnt/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/lib/python3.9/site-packages/swifter/swifter.py", line 337, in wrapped
self._obj.iloc[self._SAMPLE_INDEX].apply(
File "/mnt/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/lib/python3.9/site-packages/pandas/core/frame.py", line 10374, in apply
return op.apply().__finalize__(self, method="apply")
File "/mnt/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/lib/python3.9/site-packages/pandas/core/apply.py", line 916, in apply
return self.apply_standard()
File "/mnt/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/lib/python3.9/site-packages/pandas/core/apply.py", line 1063, in apply_standard
results, res_index = self.apply_series_generator()
File "/mnt/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/lib/python3.9/site-packages/pandas/core/apply.py", line 1081, in apply_series_generator
results[i] = self.func(v, *self.args, **self.kwargs)
File "/mnt/gs21/scratch/lopezj38/bin/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/get_fasta_sequence.py", line 23, in <lambda>
df["end"] = df.swifter.progress_bar(flag_verbose).apply(lambda x: min(x["end"], fasta_len_dict[x["seqid"]]), axis=1)
KeyError: 'NC_003070.9_split_1of7'
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /mnt/gs21/scratch/lopezj38/TE_annotation/EDTA/bin/rename_tirlearner.pl line 19.
Warning: LOC list GCF_000001735.4_TAIR10.1_genomic.fna.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 'GCF_000001735.4_TAIR10.1_genomic.fna.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln': No such file or directory
cp: cannot stat 'GCF_000001735.4_TAIR10.1_genomic.fna.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list': No such file or directory
cp: cannot stat 'GCF_000001735.4_TAIR10.1_genomic.fna.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 /mnt/gs21/scratch/lopezj38/TE_annotation/EDTA/bin/output_by_list.pl line 39.
Error: TIR results not found!
ERROR: Raw TIR results not found in GCF_000001735.4_TAIR10.1_genomic.fna.mod.EDTA.raw/GCF_000001735.4_TAIR10.1_genomic.fna.mod.TIR.intact.raw.fa
If you believe the program is working properly, this may be caused by the lack of intact TIRs in your genome. Consider to use the --force 1 parameter to overwrite this checkThank you for your help!
oushujun
Hi Prof. Ou,
My EDTA was wrong in the TIR prediction, and the running log is as follows:
Best wish, Peng