tallnuttrbgv
commented
1 month ago I have the same issue - conda yaml install. I have plenty of space on the disk. I did not get the masked output or full gffs. Only individual TE type gffs - I guess because TIR failed and it could not find the output to concatenate.
Genome is not large (0.9 Gbp). It also took 2.5 days to run with 24 cpus.. which seems slow.
perl /media/storage/bin/EDTA/EDTA.pl --genome themeda_scaf_norpts.fasta --species Maize --cds cds_from_genomic.fna --anno 1 --threads 24
Wed Jul 10 05:52:23 UTC 2024 EDTA_raw: Check dependencies, prepare working directories.
Wed Jul 10 05:52:25 UTC 2024 Start to find LTR candidates.
Wed Jul 10 05:52:25 UTC 2024 Identify LTR retrotransposon candidates from scratch.
Wed Jul 10 09:49:54 UTC 2024 Finish finding LTR candidates.
Wed Jul 10 09:49:54 UTC 2024 Start to find SINE candidates.
Wed Jul 10 11:11:10 UTC 2024 Finish finding SINE candidates.
Wed Jul 10 11:11:10 UTC 2024 Start to find LINE candidates.
Wed Jul 10 11:11:10 UTC 2024 Identify LINE retrotransposon candidates from scratch.
Use of uninitialized value in string ne at /media/storage/bin/EDTA/util/cleanup_misclas.pl line 61,
Fri Jul 12 04:53:54 UTC 2024 Start to find TIR candidates.
Fri Jul 12 04:53:54 UTC 2024 Identify TIR candidates from scratch.
Species: Maize
cannot write to stream: No space left on device
/media/storage/bin/miniforge3/envs/EDTA2/bin/gt tirvish: error: fopen(): cannot open file 'TIR-Learner-+-gt_index.prj': No such file or directory
Traceback (most recent call last):
File "/media/storage/bin/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 80, in
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 'themeda_scaf_norpts.fasta.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln': No such file or directory cp: cannot stat 'themeda_scaf_norpts.fasta.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list': No such file or directory cp: cannot stat 'themeda_scaf_norpts.fasta.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 /media/storage/bin/EDTA/util/output_by_list.pl line 39. Warning: The TIR result file has 0 bp!
Fri Jul 12 05:29:49 UTC 2024 Start to find Helitron candidates.
Fri Jul 12 05:29:50 UTC 2024 Identify Helitron candidates from scratch.
Fri Jul 12 13:06:11 UTC 2024 Finish finding Helitron candidates.
Fri Jul 12 13:06:11 UTC 2024 Execution of EDTA_raw.pl is finished!
ERROR: Raw TIR results not found in themeda_scaf_norpts.fasta.mod.EDTA.raw/themeda_scaf_norpts.fasta.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
Wildwiner
oushujun
Dear Dr. Ou,
Thanks for the EDTA software. I have installed EDTA via conda and the test run was fine. However with a plant genome, it got some errors about low disk space, perhaps at the stage of TIR:
#########################################################
Extensive de-novo TE Annotator (EDTA) v2.2.0
Shujun Ou (shujun.ou.1@gmail.com)
#########################################################
Parameters: --genome roth_hap1_split_rename.fa --step all --anno 1 -t 50 --sensitive 1
Thu Jul 11 02:56:55 PM EDT 2024 Dependency checking: All passed!
Thu Jul 11 03:23:51 PM EDT 2024 Obtain raw TE libraries using various structure-based programs: Thu Jul 11 03:23:51 PM EDT 2024 EDTA_raw: Check dependencies, prepare working directories.
Thu Jul 11 03:33:19 PM EDT 2024 Start to find LTR candidates.
Thu Jul 11 03:33:19 PM EDT 2024 Identify LTR retrotransposon candidates from scratch.
Sat Jul 13 04:24:03 AM EDT 2024 Finish finding LTR candidates.
Sat Jul 13 04:24:03 AM EDT 2024 Start to find SINE candidates.
Sat Jul 13 01:36:03 PM EDT 2024 Finish finding SINE candidates.
Sat Jul 13 01:36:03 PM EDT 2024 Start to find LINE candidates.
Sat Jul 13 01:36:03 PM EDT 2024 Identify LINE retrotransposon candidates from scratch.
Sun Jul 14 03:48:16 PM EDT 2024 Finish finding LINE candidates.
Sun Jul 14 03:48:16 PM EDT 2024 Start to find TIR candidates.
Sun Jul 14 03:48:16 PM EDT 2024 Identify TIR candidates from scratch.
Species: others cannot write to stream: No space left on device /ohta1/apps/miniconda3/envs/EDTA/bin/gt tirvish: error: fopen(): cannot open file 'TIR-Learner-+-gt_index.prj': No such file or directory Traceback (most recent call last): File "/apps/miniconda3/envs/EDTA/share/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 80, in
TIRLearner_instance = TIRLearner(genome_file, genome_name, species, TIR_length,
File "/apps/miniconda3/envs/EDTA/share/EDTA/bin/TIR-Learner3.0/bin/main.py", line 72, in init
self.execute()
File "/apps/miniconda3/envs/EDTA/share/EDTA/bin/TIR-Learner3.0/bin/main.py", line 110, in execute
self.execute_M4()
File "/apps/miniconda3/envs/EDTA/share/EDTA/bin/TIR-Learner3.0/bin/main.py", line 593, in execute_M4
self["TIRvish"] = run_TIRvish.execute(self)
File "/apps/miniconda3/envs/EDTA/share/EDTA/bin/TIR-Learner3.0/bin/run_TIRvish.py", line 76, in execute
return get_fasta_pieces_SeqIO(genome_file, df, cpu_cores, flag_verbose)
File "/apps/miniconda3/envs/EDTA/share/EDTA/bin/TIR-Learner3.0/bin/get_fasta_sequence.py", line 65, in get_fasta_pieces_SeqIO
return pd.concat(df_with_seq_list).sort_index()
File "/apps/miniconda3/envs/EDTA/lib/python3.8/site-packages/pandas/core/reshape/concat.py", line 372, in concat
op = _Concatenator(
File "/apps/miniconda3/envs/EDTA/lib/python3.8/site-packages/pandas/core/reshape/concat.py", line 452, in init
raise ValueError("All objects passed were None")
ValueError: All objects passed were None
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /apps/miniconda3/envs/EDTA/share/EDTA/util/rename_tirlearner.pl line 19.
Warning: LOC list roth_hap1_split_rename.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 'roth_hap1_split_rename.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln': No such file or directory cp: cannot stat 'roth_hap1_split_rename.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list': No such file or directory cp: cannot stat 'roth_hap1_split_rename.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 /apps/miniconda3/envs/EDTA/share/EDTA/util/output_by_list.pl line 39. Warning: The TIR result file has 0 bp!
Sun Jul 14 06:30:24 PM EDT 2024 Start to find Helitron candidates.
Sun Jul 14 06:30:24 PM EDT 2024 Identify Helitron candidates from scratch.
###########################################################
The disk space should be fine with 11TB free, and I couldn't figure out what else might the cause. Please help.
Thanks, yg