error in Identify TIR candidates #516
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Hi! I also have a similar issue Thank you for your help! |
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TIR-Learner did not installed correctly, please reinstall EDTA following
other similar issues.
Shujun
…On Mon, Nov 4, 2024 at 1:35 PM Lourdes ***@***.***> wrote:
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
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
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 "", 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
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 ***@***.***) 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 check`
Thank you for your help!
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Any luck? |
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hello Shujun, It seems that LTR FINDER parallel is not working correctly. When I reinstall EDTA2.2.2 using the method in #497, the following error occurs Do you have any ideas on the problem I'm having？ |
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Please reinstall and try again. The bug has fixed. #526 |
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hello |
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@qfh20m20m I could not reproduce your error with v2.2.2. It should continue with a warning for both SINE and LINE searching if no candidates were found. |
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Hello Shujun, I would greatly appreciate any guidance or suggestions you could provide to resolve this problem. Thank you for your time and support. I look forward to hearing from you. Best regards, |
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Seems like TIR-Learner is overutilizing server CPUs. @lutianyu2001 |
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hello Prof. Ou, |
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Hello Shujun, I hope this message finds you well. Thank you for your hard work and dedication over the past period. A few days ago, after TIR-learn and EDTA_raw.pl were updated, I ran EDTA-v2.2.2 again. Now, I‘m able to obtain the result successfully. Once again, thank you for your help. Best regards, |
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@lyysxb @qfh20m20m @lourdesalo can you please reinstall EDTA2 and test if your problem goes away? Shujun |
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This issue should be fixed. If not, please try with the updated yml file to install. I am closing this issue for now. Please reopen if you still have the problem. Thanks! Shujun |
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Hi Prof. Ou,
My EDTA was wrong in the TIR prediction, and the running log is as follows:
Best wish,
Peng
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