error in Identify TIR candidates
Closed this issue · 13 comments
qfh20m20m commented
Hi Prof. Ou,
My EDTA was wrong in the TIR prediction, and the running log is as follows:
#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.2.2 #####
##### Shujun Ou (shujun.ou.1@gmail.com) #####
#########################################################
Parameters: --genome ../2nd/Hedychium_hic.post.FINAL.fa --species others --step all -t 50 --sensitive 1
Wed Oct 30 17:29:20 HKT 2024 Dependency checking:
All passed!
Wed Oct 30 17:29:54 HKT 2024 Obtain raw TE libraries using various structure-based programs:
Wed Oct 30 17:29:54 HKT 2024 EDTA_raw: Check dependencies, prepare working directories.
Wed Oct 30 17:31:24 HKT 2024 Start to find LTR candidates.
Wed Oct 30 17:31:24 HKT 2024 Identify LTR retrotransposon candidates from scratch.
Wed Oct 30 19:00:00 HKT 2024 Finish finding LTR candidates.
Wed Oct 30 19:00:00 HKT 2024 Start to find SINE candidates.
Wed Oct 30 21:01:07 HKT 2024 Finish finding SINE candidates.
Wed Oct 30 21:01:07 HKT 2024 Start to find LINE candidates.
Wed Oct 30 21:01:07 HKT 2024 Identify LINE retrotransposon candidates from scratch.
Thu Oct 31 23:48:25 HKT 2024 Finish finding LINE candidates.
Thu Oct 31 23:48:25 HKT 2024 Start to find TIR candidates.
Thu Oct 31 23:48:25 HKT 2024 Identify TIR candidates from scratch.
Species: others
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multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/lib/python3.12/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/lib/python3.12/multiprocessing/pool.py", line 51, in starmapstar
return list(itertools.starmap(args[0], args[1]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/run_GRF.py", line 36, in GRF_mp
GRF(genome_file_name, genome_name, cpu_cores, TIR_length, GRF_path)
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/run_GRF.py", line 29, in GRF
subprocess.Popen(grf + shell_filter, shell=True).wait()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/lib/python3.12/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/lib/python3.12/subprocess.py", line 1885, in _execute_child
self.pid = _fork_exec(
^^^^^^^^^^^
BlockingIOError: [Errno 11] Resource temporarily unavailable
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/nfs_fs/nfs1/pengxiaochang/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 "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/main.py", line 91, in __init__
self.execute()
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/main.py", line 131, in execute
self.execute_M4()
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/main.py", line 598, in execute_M4
self["GRF"] = run_GRF.execute(self)
^^^^^^^^^^^^^^^^^^^^^
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/run_GRF.py", line 182, in execute
return run_GRF_py_para(genome_file, genome_name, TIR_length, cpu_cores, para_mode, flag_debug, GRF_path,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/run_GRF.py", line 82, in run_GRF_py_para
pool.starmap(GRF_mp, mp_args_list)
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/lib/python3.12/multiprocessing/pool.py", line 375, in starmap
return self._map_async(func, iterable, starmapstar, chunksize).get()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/lib/python3.12/multiprocessing/pool.py", line 774, in get
raise self._value
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/lib/python3.12/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/lib/python3.12/multiprocessing/pool.py", line 51, in starmapstar
return list(itertools.starmap(args[0], args[1]))
^^^^^^^^^^^^^^^^^
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/run_GRF.py", line 36, in GRF_mp
GRF(genome_file_name, genome_name, cpu_cores, TIR_length, GRF_path)
^^^^^^^^^^^^^^^^^
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/share/TIR-Learner3/bin/run_GRF.py", line 29, in GRF
subprocess.Popen(grf + shell_filter, shell=True).wait()
^^^^^^^^^^^^^^^^^
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/lib/python3.12/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
^^^^^^^^^^^^^^^
File "/nfs_fs/nfs1/pengxiaochang/miniforge3/envs/EDTA2.2/lib/python3.12/subprocess.py", line 1885, in _execute_child
self.pid = _fork_exec(
^^^^^^^
BlockingIOError: [Errno 11] Resource temporarily unavailable
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/rename_tirlearner.pl line 19.
Warning: LOC list Hedychium_hic.post.FINAL.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 'Hedychium_hic.post.FINAL.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln': No such file or directory
cp: cannot stat 'Hedychium_hic.post.FINAL.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list': No such file or directory
cp: cannot stat 'Hedychium_hic.post.FINAL.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 /nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/output_by_list.pl line 39.
Error: TIR results not found!
ERROR: Raw TIR results not found in Hedychium_hic.post.FINAL.fa.mod.EDTA.raw/Hedychium_hic.post.FINAL.fa.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 checkBest wish,
Peng
lourdesalo commented
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 check
Thank you for your help!
oushujun commented
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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oushujun commented
Any luck?
qfh20m20m commented
hello Shujun,
I tried to reinstall EDTA, but something else went wrong. When I install EDTA2.2.2 using conda and singulariity, The same error occured with both installations.
singularity exec ~/sigsif/EDTA.sif EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice7.0.0.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --evaluate 1 --threads 10 > EDTA.test
Fri Dec 13 21:35:49 HKT 2024 EDTA_raw: Check dependencies, prepare working directories.
Fri Dec 13 21:36:23 HKT 2024 Start to find LTR candidates.
Fri Dec 13 21:36:24 HKT 2024 Identify LTR retrotransposon candidates from scratch.
Can't open perl script "/usr/local/share/EDTA/bin/LTR_FINDER_parallel/LTR_FINDER_parallel": No such file or directory
Invalid value for shared scalar at /usr/local/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 sequenceThe sequence file for genome.fa.mod.LTR.intact.fa.ori.dusted.cln.rexdb.cls.tsv is not found in the same folder!
You may specify the sequence file with perl cleanup_misclas.pl TEsorter.cls.tsv sequence.fa
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
perl filter_gff3.pl file.gff3 file.list > new.gff3
Fri Dec 13 21:36:42 HKT 2024 Warning: The LTR result file has 0 bp!
Fri Dec 13 21:36:42 HKT 2024 Start to find SINE candidates.
Fri Dec 13 21:37:38 HKT 2024 Warning: The SINE result file has 0 bp!
Fri Dec 13 21:37:38 HKT 2024 Start to find LINE candidates.
Fri Dec 13 21:37:38 HKT 2024 Identify LINE retrotransposon candidates from scratch.
Fri Dec 13 21:38:59 HKT 2024 Warning: The LINE result file has 0 bp!
Fri Dec 13 21:38:59 HKT 2024 Start to find TIR candidates.
Fri Dec 13 21:38:59 HKT 2024 Identify TIR candidates from scratch.
Species: others
Fri Dec 13 21:39:54 HKT 2024 Finish finding TIR candidates.
Fri Dec 13 21:39:54 HKT 2024 Start to find Helitron candidates.
Fri Dec 13 21:39:54 HKT 2024 Identify Helitron candidates from scratch.
Fri Dec 13 21:40:42 HKT 2024 Finish finding Helitron candidates.
Fri Dec 13 21:40:42 HKT 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
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
perl ../EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice7.0.0.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --threads 10
#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.2.2 #####
##### Shujun Ou (shujun.ou.1@gmail.com) #####
#########################################################
Parameters: --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice7.0.0.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --threads 10
Fri Dec 13 21:24:49 HKT 2024 Dependency checking:
All passed!
A custom library ../database/rice7.0.0.liban is provided via --curatedlib. Please make sure this is a manually curated library but not machine generated.
A CDS file genome.cds.fa 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.
Fri Dec 13 21:24:53 HKT 2024 Obtain raw TE libraries using various structure-based programs:
Fri Dec 13 21:24:53 HKT 2024 EDTA_raw: Check dependencies, prepare working directories.
Fri Dec 13 21:25:07 HKT 2024 Start to find LTR candidates.
Fri Dec 13 21:25:07 HKT 2024 Identify LTR retrotransposon candidates from scratch.
Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty.
Fri Dec 13 21:25:46 HKT 2024 Finish finding LTR candidates.
Fri Dec 13 21:25:46 HKT 2024 Start to find SINE candidates.
Fri Dec 13 21:26:40 HKT 2024 Warning: The SINE result file has 0 bp!
Fri Dec 13 21:26:40 HKT 2024 Start to find LINE candidates.
Fri Dec 13 21:26:40 HKT 2024 Identify LINE retrotransposon candidates from scratch.
Fri Dec 13 21:26:42 HKT 2024 Warning: The LINE result file has 0 bp!
Fri Dec 13 21:26:42 HKT 2024 Start to find TIR candidates.
Fri Dec 13 21:26:42 HKT 2024 Identify TIR candidates from scratch.
Species: others
Fri Dec 13 21:27:37 HKT 2024 Finish finding TIR candidates.
Fri Dec 13 21:27:37 HKT 2024 Start to find Helitron candidates.
Fri Dec 13 21:27:37 HKT 2024 Identify Helitron candidates from scratch.
Error: dl failure on line 894
Error: failed /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.412.b08-1.el7_9.x86_64/jre/lib/amd64/server/libjvm.so, because /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /lib64/libstdc++.so.6)
Error: dl failure on line 894
Error: failed /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.412.b08-1.el7_9.x86_64/jre/lib/amd64/server/libjvm.so, because /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /lib64/libstdc++.so.6)
Error: dl failure on line 894
Error: failed /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.412.b08-1.el7_9.x86_64/jre/lib/amd64/server/libjvm.so, because /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /lib64/libstdc++.so.6)
Error: dl failure on line 894
Error: failed /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.412.b08-1.el7_9.x86_64/jre/lib/amd64/server/libjvm.so, because /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /lib64/libstdc++.so.6)
Error: dl failure on line 894
Error: failed /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.412.b08-1.el7_9.x86_64/jre/lib/amd64/server/libjvm.so, because /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /lib64/libstdc++.so.6)
Error: dl failure on line 894
Error: failed /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.412.b08-1.el7_9.x86_64/jre/lib/amd64/server/libjvm.so, because /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /lib64/libstdc++.so.6)
Error: dl failure on line 894
Error: failed /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.412.b08-1.el7_9.x86_64/jre/lib/amd64/server/libjvm.so, because /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /lib64/libstdc++.so.6)
Error: dl failure on line 894
Error: failed /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.412.b08-1.el7_9.x86_64/jre/lib/amd64/server/libjvm.so, because /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /lib64/libstdc++.so.6)
HelitronScanner result files for the genome.fa.mod is not found!
Filter HelitronScanner fasta candidates
perl format_helitronscanner_out.pl -genome genome.fa [options]
-sitefilter [0|1] 1 will filter out candidate without AT or TT target site (default); 0 will not.
-minscore [int] Candidates with head and tail quality scores add up less than this will be discarded. Default: 12
-keepshorter [0|1] 1 will keep the shorter possible when multi 5' end presents (default); 0 will not; 2 will keep all possible 5' ends.
-extlen [int] Length of flanking sequence for blast and output. Default: 30 (bp)
-extout [0|1] Output original sequence (0, default) or extended (1) sequence.
-h|-help Display this help messege and exit.
HelitronScanner result files for the genome.fa.mod is not found!
Filter HelitronScanner fasta candidates
perl format_helitronscanner_out.pl -genome genome.fa [options]
-sitefilter [0|1] 1 will filter out candidate without AT or TT target site (default); 0 will not.
-minscore [int] Candidates with head and tail quality scores add up less than this will be discarded. Default: 12
-keepshorter [0|1] 1 will keep the shorter possible when multi 5' end presents (default); 0 will not; 2 will keep all possible 5' ends.
-extlen [int] Length of flanking sequence for blast and output. Default: 30 (bp)
-extout [0|1] Output original sequence (0, default) or extended (1) sequence.
-h|-help Display this help messege and exit.
The query file genome.fa.mod.HelitronScanner.filtered.ext.fa is not found!
Filter HelitronScanner fasta candidates
perl flanking_filter.pl -genome genome.fa -query candidate.fa [options]
-genome [file] The multifasta file that used to generate the -query
-query [file] The candidate TE sequence to be filtered by this script
-extlen [int] The length of extended flanking sequence in -query. Default: 30 (bp)
-tgt_out [int] Output taget site with [int] length on each terminal. Default: 15 (bp)
-miniden [int] Minimum identity for flanking sequence alignment. Default: 80 (%)
-mincov [float] Minimum coverage for flanking sequence alignment that counts as full match. Default: 0.8
-maxct [int] Maximum allowed copy number for flanking sequence for a true element. Default: 1.
-blastplus [path] Path to the blastn program. Defalut: read from $ENV
-t|-threads [int] Number of threads to run this program. Default: 4
-h|-help Display this help messege and exit.
ERROR: No such file or directory at /nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/output_by_list.pl line 37.
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.HelitronScanner.filtered.fa.pass.fa.dusted.cln.cln': No such file or directory
cp: cannot stat 'genome.fa.mod.HelitronScanner.filtered.fa.pass.fa.dusted.cln.cln.list': No such file or directory
cp: cannot stat 'genome.fa.mod.Helitron.intact.raw.fa.anno.list': No such file or directory
perl make_bed_with_intact.pl EDTA.intact.fa > EDTA.intact.bed
Error: Helitron results not found!
ERROR: Raw Helitron results not found in genome.fa.mod.EDTA.raw/genome.fa.mod.Helitron.intact.raw.fa
If you believe the program is working properly, this may be caused by the lack of intact Helitrons in your genome. Consider to use the --force 1 parameter to overwrite this check
Do you have any ideas on the problem I'm having？
@oushujun
qfh20m20m commented
hello
I reinstalled EDTA .2.2 using conda, but still got an error. Now the error code is as follows：
EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice7.0.0.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --evaluate 1 --threads 10 > EDTA.test
Tue Dec 17 10:59:24 HKT 2024 EDTA_raw: Check dependencies, prepare working directories.
Tue Dec 17 11:01:00 HKT 2024 Start to find LTR candidates.
Tue Dec 17 11:01:00 HKT 2024 Identify LTR retrotransposon candidates from scratch.
Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty.
Tue Dec 17 11:01:58 HKT 2024 Finish finding LTR candidates.
Tue Dec 17 11:01:58 HKT 2024 Start to find SINE candidates.
cp: cannot stat 'genome.fa.mod.SINE.raw.fa': No such file or directory
Error: SINE results not found!
ERROR: Raw SINE results not found in genome.fa.mod.EDTA.raw/genome.fa.mod.SINE.raw.fa
If you believe the program is working properly, this may be caused by the lack of SINEs in your genome.
oushujun commented
@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.
Xuuuurj commented
Hello Shujun,
When using EDTA_2.2.2, I also encountered the error, libgomp: Thread creation failed: Resource temporarily unavailable. I tried reinstalling EDTA_2.2.2 using Conda, but the error still occurred. Below are the error messages and the details of my Conda environment.
#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.2.2 #####
##### Shujun Ou (shujun.ou.1@gmail.com) #####
#########################################################
Parameters: --genome NIP.fa --cds NIP.cds.fa --species rice --sensitive 1 --anno 1 --step all --overwrite 1 --evaluate 1 -u 1.3e-8 --threads 50
Sun Dec 22 15:42:35 CST 2024 Dependency checking:
All passed!
A CDS file NIP.cds.fa is provided via --cds. Please make sure this is the DNA sequence of coding regions only.
Sun Dec 22 15:42:47 CST 2024 Obtain raw TE libraries using various structure-based programs:
Sun Dec 22 15:42:47 CST 2024 EDTA_raw: Check dependencies, prepare working directories.
Sun Dec 22 15:43:06 CST 2024 Start to find LTR candidates.
Sun Dec 22 15:43:06 CST 2024 Identify LTR retrotransposon candidates from scratch.
Wed Dec 25 07:20:09 CST 2024 Finish finding LTR candidates.
Wed Dec 25 07:20:09 CST 2024 Start to find SINE candidates.
Wed Dec 25 07:48:45 CST 2024 Finish finding SINE candidates.
Wed Dec 25 07:48:45 CST 2024 Start to find LINE candidates.
Wed Dec 25 07:48:45 CST 2024 Identify LINE retrotransposon candidates from scratch.
Thu Dec 26 03:53:00 CST 2024 Finish finding LINE candidates.
Thu Dec 26 03:53:00 CST 2024 Start to find TIR candidates.
Thu Dec 26 03:53:00 CST 2024 Identify TIR candidates from scratch.
Species: Rice
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
/bin/sh: fork: retry: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
/bin/sh: fork: retry: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
/bin/sh: fork: retry: No child processes
/bin/sh: fork: retry: No child processes
libgomp: /bin/sh: fork: retry: No child processes
Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp:
libgomp: Thread creation failed: Resource temporarily unavailable
Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
/bin/sh: fork: retry: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
/bin/sh: fork: retry: No child processes
/bin/sh: fork: retry: No child processes
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: /bin/sh: fork: retry: Resource temporarily unavailable
Thread creation failed: Resource temporarily unavailable
/bin/sh: fork: retry: No child processes
/bin/sh: fork: retry: No child processes
/bin/sh: fork: retry: No child processes
/bin/sh: fork: retry: No child processes
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
/bin/sh: fork: retry: No child processes
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
/bin/sh: fork: retry: No child processes
/bin/sh: fork: retry: No child processes
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
/bin/sh: fork: retry: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
/bin/sh: fork: retry: No child processes
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
/bin/sh: fork: retry: No child processes
libgomp: Thread creation failed: Resource temporarily unavailable
/bin/sh: fork: retry: No child processes
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
failed to execute command /data/home/xurongjing/miniconda3/envs/edta_zxy/bin/grf-filter 10 2147483647 10 5000 TIR-Learner_GRFmite/candidate.fasta TIR-Learner_GRFmite/candidate.fasta.filterd
can't open file: TIR-Learner_GRFmite/candidate.fasta
can't open file: TIR-Learner_GRFmite/candidate.fasta
can't open file: TIR-Learner_GRFmite/candidate.fasta
$conda list
# packages in environment at /data/home/xurongjing/miniconda3/envs/edta_zxy:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
absl-py 2.1.0 pyhd8ed1ab_1 conda-forge
alsa-lib 1.2.13 hb9d3cd8_0 conda-forge
annosine2 2.0.7 pyh7e72e81_1 bioconda
aws-c-auth 0.8.0 hb921021_15 conda-forge
aws-c-cal 0.8.1 h1a47875_3 conda-forge
aws-c-common 0.10.6 hb9d3cd8_0 conda-forge
aws-c-compression 0.3.0 h4e1184b_5 conda-forge
aws-c-event-stream 0.5.0 h7959bf6_11 conda-forge
aws-c-http 0.9.2 hefd7a92_4 conda-forge
aws-c-io 0.15.3 h831e299_5 conda-forge
aws-c-mqtt 0.11.0 h11f4f37_12 conda-forge
aws-c-s3 0.7.7 hf454442_0 conda-forge
aws-c-sdkutils 0.2.1 h4e1184b_4 conda-forge
aws-checksums 0.2.2 h4e1184b_4 conda-forge
aws-crt-cpp 0.29.7 hd92328a_7 conda-forge
aws-sdk-cpp 1.11.458 hc430e4a_4 conda-forge
azure-core-cpp 1.14.0 h5cfcd09_0 conda-forge
azure-identity-cpp 1.10.0 h113e628_0 conda-forge
azure-storage-blobs-cpp 12.13.0 h3cf044e_1 conda-forge
azure-storage-common-cpp 12.8.0 h736e048_1 conda-forge
azure-storage-files-datalake-cpp 12.12.0 ha633028_1 conda-forge
bedtools 2.31.1 h13024bc_3 bioconda
binutils_impl_linux-64 2.43 h4bf12b8_2 conda-forge
biopython 1.84 py312h9a8786e_0 conda-forge
bokeh 3.6.2 pyhd8ed1ab_1 conda-forge
brotli 1.1.0 hb9d3cd8_2 conda-forge
brotli-bin 1.1.0 hb9d3cd8_2 conda-forge
brotli-python 1.1.0 py312h2ec8cdc_2 conda-forge
bwidget 1.10.1 ha770c72_0 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.4 hb9d3cd8_0 conda-forge
ca-certificates 2024.12.14 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.18.2 h3394656_1 conda-forge
cd-hit 4.8.1 h5ca1c30_12 bioconda
cffi 1.17.1 py312h06ac9bb_0 conda-forge
click 8.1.7 unix_pyh707e725_1 conda-forge
cloudpickle 3.1.0 pyhd8ed1ab_1 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
contourpy 1.3.1 py312h68727a3_0 conda-forge
coreutils 9.5 hd590300_0 conda-forge
cpython 3.12.8 py312hd8ed1ab_1 conda-forge
curl 8.11.1 h332b0f4_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
cytoolz 1.0.1 py312h66e93f0_0 conda-forge
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namex 0.0.8 pyhd8ed1ab_1 conda-forge
ncbi-vdb 3.1.1 h9948957_3 bioconda
ncurses 6.5 he02047a_1 conda-forge
networkx 3.4.2 pyh267e887_2 conda-forge
nodejs 22.6.0 hc19f0b3_1 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
nseg 1.0.1 h7b50bb2_6 bioconda
numpy 2.2.0 py312h7e784f5_0 conda-forge
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openssl 3.4.0 hb9d3cd8_0 conda-forge
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orc 2.0.3 h97ab989_1 conda-forge
packaging 24.2 pyhd8ed1ab_2 conda-forge
pandas 2.2.3 py312hf9745cd_1 conda-forge
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perl 5.26.2 h36c2ea0_1008 conda-forge
perl-app-cpanminus 1.7044 pl526_1 bioconda
perl-archive-tar 2.32 pl526_0 bioconda
perl-carp 1.38 pl526_3 bioconda
perl-common-sense 3.74 pl526_2 bioconda
perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda
perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda
perl-constant 1.33 pl526_1 bioconda
perl-exporter 5.72 pl526_1 bioconda
perl-exporter-tiny 1.002001 pl526_0 bioconda
perl-extutils-makemaker 7.36 pl526_1 bioconda
perl-file-path 2.16 pl526_0 bioconda
perl-file-temp 0.2304 pl526_2 bioconda
perl-file-which 1.23 pl526_0 bioconda
perl-gd 2.56 pl526h470a237_8 bioconda
perl-io-compress 2.087 pl526he1b5a44_0 bioconda
perl-io-zlib 1.10 pl526_2 bioconda
perl-json 4.02 pl526_0 bioconda
perl-json-xs 2.34 pl526h6bb024c_3 bioconda
perl-list-moreutils 0.428 pl526_1 bioconda
perl-list-moreutils-xs 0.428 pl526_0 bioconda
perl-parent 0.236 pl526_1 bioconda
perl-pathtools 3.75 pl526h14c3975_1 bioconda
perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda
perl-text-soundex 3.05 pl526_1000 conda-forge
perl-types-serialiser 1.0 pl526_2 bioconda
perl-xsloader 0.24 pl526_0 bioconda
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pip 24.3.1 pyh8b19718_2 conda-forge
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pp 1.6.4.4 py_0 bioconda
psutil 6.1.0 py312h66e93f0_0 conda-forge
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pyarrow 18.1.0 py312h7900ff3_0 conda-forge
pyarrow-core 18.1.0 py312h01725c0_0_cpu conda-forge
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python 3.12.8 h9e4cc4f_1_cpython conda-forge
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python-isal 1.7.1 py312h66e93f0_0 conda-forge
python-tzdata 2024.2 pyhd8ed1ab_1 conda-forge
python-zlib-ng 0.5.1 py312h27ca174_0 conda-forge
python_abi 3.12 5_cp312 conda-forge
pytorch 2.5.1 cpu_generic_py312h3cb2d7b_6 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py312h66e93f0_1 conda-forge
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r-lattice 0.22_6 r44hb1dbf0f_1 conda-forge
r-lifecycle 1.0.4 r44hc72bb7e_1 conda-forge
r-magrittr 2.0.3 r44hb1dbf0f_3 conda-forge
r-mass 7.3_60.0.1 r44hb1dbf0f_1 conda-forge
r-matrix 1.6_5 r44he966344_1 conda-forge
r-mgcv 1.9_1 r44h0d28552_1 conda-forge
r-munsell 0.5.1 r44hc72bb7e_1 conda-forge
r-nlme 3.1_165 r44hbcb9c34_1 conda-forge
r-pillar 1.10.0 r44hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r44hc72bb7e_4 conda-forge
r-purrr 1.0.2 r44hdb488b9_1 conda-forge
r-r6 2.5.1 r44hc72bb7e_3 conda-forge
r-rcolorbrewer 1.1_3 r44h785f33e_3 conda-forge
r-rlang 1.1.4 r44ha18555a_1 conda-forge
r-rprojroot 2.0.4 r44hc72bb7e_1 conda-forge
r-scales 1.3.0 r44hc72bb7e_1 conda-forge
r-stringi 1.8.4 r44h33cde33_3 conda-forge
r-stringr 1.5.1 r44h785f33e_1 conda-forge
r-tibble 3.2.1 r44hdb488b9_3 conda-forge
r-tidyr 1.3.1 r44h0d4f4ea_1 conda-forge
r-tidyselect 1.2.1 r44hc72bb7e_1 conda-forge
r-utf8 1.2.4 r44hb1dbf0f_1 conda-forge
r-vctrs 0.6.5 r44h0d4f4ea_1 conda-forge
r-viridislite 0.4.2 r44hc72bb7e_2 conda-forge
r-withr 3.0.2 r44hc72bb7e_0 conda-forge
re2 2024.07.02 h77b4e00_1 conda-forge
readline 8.2 h8228510_1 conda-forge
recon 1.08 h031d066_7 bioconda
regex 2024.11.6 py312h66e93f0_0 conda-forge
repeatmasker 4.1.2.p1 pl5262hdfd78af_0 bioconda
repeatmodeler 2.0.1 pl526_0 bioconda
repeatscout 1.0.7 h7b50bb2_1 bioconda
rich 13.9.4 pyhd8ed1ab_1 conda-forge
rmblast 2.14.1 h91eb8de_1 bioconda
s2n 1.5.10 hb5b8611_0 conda-forge
samtools 1.6 h5fe306e_11 bioconda
scikit-learn 1.6.0 py312h7a48858_0 conda-forge
scipy 1.14.1 py312h62794b6_2 conda-forge
sed 4.8 he412f7d_0 conda-forge
seqtk 1.4 h577a1d6_3 bioconda
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six 1.17.0 pyhd8ed1ab_0 conda-forge
sleef 3.7 h1b44611_2 conda-forge
snappy 1.2.1 h8bd8927_1 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
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sympy 1.13.3 pyh2585a3b_104 conda-forge
sysroot_linux-64 2.17 h4a8ded7_18 conda-forge
tblib 3.0.0 pyhd8ed1ab_1 conda-forge
tesorter 1.4.7 pyhdfd78af_1 bioconda
threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge
tir-learner 3.0.3 hdfd78af_1 bioconda
tk 8.6.13 noxft_h4845f30_101 conda-forge
tktable 2.10 h8bc8fbc_6 conda-forge
toolz 1.0.0 pyhd8ed1ab_1 conda-forge
tornado 6.4.2 py312h66e93f0_0 conda-forge
tqdm 4.67.1 pyhd8ed1ab_0 conda-forge
trf 4.09.1 h7b50bb2_7 bioconda
typing-extensions 4.12.2 hd8ed1ab_1 conda-forge
typing_extensions 4.12.2 pyha770c72_1 conda-forge
tzdata 2024b hc8b5060_0 conda-forge
unicodedata2 15.1.0 py312h66e93f0_1 conda-forge
urllib3 2.2.3 pyhd8ed1ab_1 conda-forge
wget 1.21.4 hda4d442_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xopen 2.0.2 pyh707e725_2 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.5 he73a12e_0 conda-forge
xorg-libx11 1.8.10 h4f16b4b_1 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxfixes 6.0.1 hb9d3cd8_0 conda-forge
xorg-libxi 1.8.2 hb9d3cd8_0 conda-forge
xorg-libxrandr 1.5.4 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
xorg-libxtst 1.2.5 hb9d3cd8_3 conda-forge
xyzservices 2024.9.0 pyhd8ed1ab_1 conda-forge
xz 5.6.3 hbcc6ac9_1 conda-forge
xz-gpl-tools 5.6.3 hbcc6ac9_1 conda-forge
xz-tools 5.6.3 hb9d3cd8_1 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zict 3.0.0 pyhd8ed1ab_1 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zlib-ng 2.2.2 h5888daf_0 conda-forge
zstandard 0.23.0 py312hef9b889_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
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,
Rongjing
oushujun commented
Seems like TIR-Learner is overutilizing server CPUs. @lutianyu2001
lyysxb commented
hello Prof. Ou,
I'm encountering an error while running both EDTA and EDTA2 on the Rice.
Xuuuurj commented
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.
#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.2.2 #####
##### Shujun Ou (shujun.ou.1@gmail.com) #####
#########################################################
Parameters: --genome AUS.fa --cds AUS.cds.fa --species others --sensitive 1 --anno 1 --step all --overwrite 1 --evaluate 1 -u 1.3e-8 --threads 50
Fri Jan 10 17:05:03 CST 2025 Dependency checking:
All passed!
A CDS file AUS.cds.fa is provided via --cds. Please make sure this is the DNA sequence of coding regions only.
Fri Jan 10 17:05:17 CST 2025 Obtain raw TE libraries using various structure-based programs:
Fri Jan 10 17:05:17 CST 2025 EDTA_raw: Check dependencies, prepare working directories.
Fri Jan 10 17:05:47 CST 2025 Start to find LTR candidates.
Fri Jan 10 17:05:47 CST 2025 Identify LTR retrotransposon candidates from scratch.
Wed Jan 15 11:38:08 CST 2025 Finish finding LTR candidates.
Wed Jan 15 11:38:08 CST 2025 Start to find SINE candidates.
Wed Jan 15 12:21:43 CST 2025 Finish finding SINE candidates.
Wed Jan 15 12:21:43 CST 2025 Start to find LINE candidates.
Wed Jan 15 12:21:43 CST 2025 Identify LINE retrotransposon candidates from scratch.
Thu Jan 16 06:02:22 CST 2025 Finish finding LINE candidates.
Thu Jan 16 06:02:22 CST 2025 Start to find TIR candidates.
Thu Jan 16 06:02:22 CST 2025 Identify TIR candidates from scratch.
Species: others
Thu Jan 16 18:50:36 CST 2025 Finish finding TIR candidates.
Thu Jan 16 18:50:36 CST 2025 Start to find Helitron candidates.
Thu Jan 16 18:50:36 CST 2025 Identify Helitron candidates from scratch.
Fri Jan 17 03:43:46 CST 2025 Finish finding Helitron candidates.
Fri Jan 17 03:43:46 CST 2025 Execution of EDTA_raw.pl is finished!
Fri Jan 17 03:43:47 CST 2025 Obtain raw TE libraries finished.
All intact TEs found by EDTA:
AUS.fa.mod.EDTA.intact.raw.fa
AUS.fa.mod.EDTA.intact.raw.gff3
Fri Jan 17 03:43:47 CST 2025 Perform EDTA advance filtering for raw TE candidates and generate the stage 1 library:
Sun Jan 19 02:38:31 CST 2025 EDTA advance filtering finished.
Sun Jan 19 02:38:31 CST 2025 Perform EDTA final steps to generate a non-redundant comprehensive TE library.
Filter RepeatModeler results that are ignored in the raw step.
Sun Jan 19 02:42:09 CST 2025 Clean up TE-related sequences in the CDS file with TEsorter.
Remove CDS-related sequences in the EDTA library.
Remove CDS-related sequences in intact TEs.
Sun Jan 19 16:29:22 CST 2025 EDTA final stage finished! You may check out:
The final EDTA TE library: AUS.fa.mod.EDTA.TElib.fa
Sun Jan 19 16:29:22 CST 2025 Perform post-EDTA analysis for whole-genome annotation:
Sun Jan 19 16:29:22 CST 2025 Homology-based annotation of TEs using AUS.fa.mod.EDTA.TElib.fa from scratch.
Sun Jan 19 18:07:56 CST 2025 TE annotation using the EDTA library has finished! Check out:
Whole-genome TE annotation (total TE: 68.76%): AUS.fa.mod.EDTA.TEanno.gff3
Whole-genome TE annotation summary: AUS.fa.mod.EDTA.TEanno.sum
Whole-genome TE divergence plot: AUS.fa.mod_divergence_plot.pdf
Whole-genome TE density plot: AUS.fa.mod.EDTA.TEanno.density_plots.pdf
Low-threshold TE masking for MAKER gene annotation (masked: 39.01%): AUS.fa.mod.MAKER.masked
Sun Jan 19 18:07:59 CST 2025 Evaluate the level of inconsistency for whole-genome TE annotation:
Sun Jan 19 18:36:11 CST 2025 Evaluation of TE annotation finished! Check out these files:
Overall: AUS.fa.mod.EDTA.TE.fa.stat.all.sum
Nested: AUS.fa.mod.EDTA.TE.fa.stat.nested.sum
Non-nested: AUS.fa.mod.EDTA.TE.fa.stat.redun.sum
If you want to learn more about the formatting and information of these files, please visit:
https://github.com/oushujun/EDTA/wiki/Making-sense-of-EDTA-usage-and-outputs---Q&A
Once again, thank you for your help.
Best regards,
Rongjing
oushujun commented
@lyysxb @qfh20m20m @lourdesalo can you please reinstall EDTA2 and test if your problem goes away?
Shujun
oushujun commented
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