Hello Dr. Ou,
Sorry in advance, I know this is a lot of text. I tried installing and running EDTA, but I haven't been able to run it properly. I have tried running the test script using both conda and apptainer, and also tried using apptainer to run on my data which seems to have failed to complete. I tried to test and document the output of each run below. Ultimately it seems EDTA is not working properly with either conda or apptainer, but not sure whether this is something on my end or the program/testing file itself.
Installed EDTA through conda using these commands
conda create -n edta_v2.3.0
conda activate edta_v2.3.0
mamba install -c conda-forge -c bioconda edta
git clone https://github.com/oushujun/EDTA.git
on slurm I allocated 10gb of memory and 10 cores in an interactive session, then activated the conda environment and ran the test script 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 on the file located at ./edta/test which produced this output:
#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.3.1 #####
##### 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
Thu Jun 25 11:19:22 PM UTC 2026 Dependency checking:
All passed!
Thu Jun 25 11:19:27 PM UTC 2026 Cleaning and normalizing sequence IDs...
Encoded 1 sequences with 3-char codes (prefix '_J' + 1 base-62 digits, longest clean ID: 25, id_len_max: 16, longest scaffold: 1000000 bp)
Sequence IDs encoded. Mapping file: genome.fa.mod.seqid.map
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.
Thu Jun 25 11:19:27 PM UTC 2026 Obtain raw TE libraries using various structure-based programs:
Thu Jun 25 11:19:27 PM UTC 2026 EDTA_raw: Check dependencies, prepare working directories.
Thu Jun 25 11:19:31 PM UTC 2026 Start to find LTR candidates.
Thu Jun 25 11:19:31 PM UTC 2026 Identify LTR retrotransposon candidates from scratch.
Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty.
Thu Jun 25 11:20:06 PM UTC 2026 Finish finding LTR candidates.
Thu Jun 25 11:20:06 PM UTC 2026 Start to find SINE candidates.
Thu Jun 25 11:21:04 PM UTC 2026 Warning: The SINE result file has 0 bp!
Thu Jun 25 11:21:04 PM UTC 2026 Start to find LINE candidates.
Thu Jun 25 11:21:04 PM UTC 2026 Identify LINE retrotransposon candidates from scratch.
Thu Jun 25 11:22:12 PM UTC 2026 Warning: The LINE result file has 0 bp!
Thu Jun 25 11:22:12 PM UTC 2026 Start to find TIR candidates.
Thu Jun 25 11:22:12 PM UTC 2026 Identify TIR candidates from scratch.
Species: others
Thu Jun 25 11:22:43 PM UTC 2026 Finish finding TIR candidates.
Thu Jun 25 11:22:43 PM UTC 2026 Start to find Helitron candidates.
Thu Jun 25 11:22:43 PM UTC 2026 Identify Helitron candidates from scratch.
Thu Jun 25 11:23:16 PM UTC 2026 Finish finding Helitron candidates.
Thu Jun 25 11:23:16 PM UTC 2026 Execution of EDTA_raw.pl is finished!
Thu Jun 25 11:23:16 PM UTC 2026 Obtain raw TE libraries finished.
All intact TEs found by EDTA:
genome.fa.mod.EDTA.intact.raw.fa
genome.fa.mod.EDTA.intact.raw.gff3
Thu Jun 25 11:23:16 PM UTC 2026 Perform EDTA advance filtering for raw TE candidates and generate the stage 1 library:
Warning: No sequences were masked
Thu Jun 25 11:23:47 PM UTC 2026 EDTA advance filtering finished.
Thu Jun 25 11:23:47 PM UTC 2026 Perform EDTA final steps to generate a non-redundant comprehensive TE library.
Filter RepeatModeler results that are ignored in the raw step.
Thu Jun 25 11:23:53 PM UTC 2026 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.
Thu Jun 25 11:24:08 PM UTC 2026 Combine the high-quality TE library rice7.0.0.liban with the EDTA library:
Thu Jun 25 11:24:20 PM UTC 2026 EDTA final stage finished! You may check out:
The final EDTA TE library: genome.fa.mod.EDTA.TElib.fa
Family names of intact TEs have been updated by rice7.0.0.liban: genome.fa.mod.EDTA.intact.gff3
Comparing to the provided library, EDTA found these novel TEs: genome.fa.mod.EDTA.TElib.novel.fa
The provided library has been incorporated into the final library: genome.fa.mod.EDTA.TElib.fa
Thu Jun 25 11:24:41 PM UTC 2026 Perform post-EDTA analysis for whole-genome annotation:
Thu Jun 25 11:24:41 PM UTC 2026 Homology-based annotation of TEs using genome.fa.mod.EDTA.TElib.fa from scratch.
Thu Jun 25 11:24:59 PM UTC 2026 TE annotation using the EDTA library has finished! Check out:
Whole-genome TE annotation (total TE: 35.61%): genome.fa.mod.EDTA.TEanno.gff3 genome.fa.mod.EDTA.TEanno.gtf
Whole-genome TE annotation summary: genome.fa.mod.EDTA.TEanno.sum
Whole-genome TE divergence plot: genome.fa.mod_divergence_plot.pdf
Whole-genome TE density plot: genome.fa.mod.EDTA.TEanno.density_plots.pdf
Low-threshold TE masking for MAKER gene annotation (masked: 17.58%): genome.fa.mod.MAKER.masked
Thu Jun 25 11:25:01 PM UTC 2026 Evaluate the level of inconsistency for whole-genome TE annotation:
Thu Jun 25 11:25:11 PM UTC 2026 Evaluation of TE annotation finished! Check out these files:
(each contains unfiltered + divergence-titrated reports at <=40%, <=30%, <=20%, <=10%, <=5%)
Overall: genome.fa.mod.EDTA.TE.fa.stat.all.sum
Nested: genome.fa.mod.EDTA.TE.fa.stat.nested.sum
Non-nested: genome.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
When looking at the output I noticed there seemed to be errors such as Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. and messages about SINE's and LINE's not being found. To see if I would get the same errors I installed the newest singularity image with singularity pull EDTA.sif docker://quay.io/biocontainers/edta:2.3.0--hdfd78af_0, cloned the repo into a different directory to prevent previous conda test run from interacting/interfering with this apptainer test run, and allocated a 10gb + 10 cpu interactive compute node with slurm. Running with the same test command produced this output:
#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.3.1 #####
##### 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
Thu Jun 25 22:54:48 UTC 2026 Dependency checking:
All passed!
Thu Jun 25 22:54:53 UTC 2026 Cleaning and normalizing sequence IDs...
Encoded 1 sequences with 3-char codes (prefix '_J' + 1 base-62 digits, longest clean ID: 25, id_len_max: 16, longest scaffold: 1000000 bp)
Sequence IDs encoded. Mapping file: genome.fa.mod.seqid.map
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.
Thu Jun 25 22:54:53 UTC 2026 Obtain raw TE libraries using various structure-based programs:
Thu Jun 25 22:54:53 UTC 2026 EDTA_raw: Check dependencies, prepare working directories.
Thu Jun 25 22:55:23 UTC 2026 Start to find LTR candidates.
Thu Jun 25 22:55:23 UTC 2026 Identify LTR retrotransposon candidates from scratch.
Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty.
Thu Jun 25 22:56:01 UTC 2026 Finish finding LTR candidates.
Thu Jun 25 22:56:01 UTC 2026 Start to find SINE candidates.
Thu Jun 25 22:56:49 UTC 2026 Warning: The SINE result file has 0 bp!
Thu Jun 25 22:56:49 UTC 2026 Start to find LINE candidates.
Thu Jun 25 22:56:49 UTC 2026 Identify LINE retrotransposon candidates from scratch.
Thu Jun 25 22:58:03 UTC 2026 Warning: The LINE result file has 0 bp!
Thu Jun 25 22:58:03 UTC 2026 Start to find TIR candidates.
Thu Jun 25 22:58:03 UTC 2026 Identify TIR candidates from scratch.
Species: others
usage: TIR-Learner [-h] [-v] -f GENOME_FILE [-n GENOME_NAME] -s SPECIES
[-l LENGTH] [-t PROCESSOR] [-m MODE] [-w WORKING_DIR]
[-o OUTPUT_DIR] [-c [CHECKPOINT_DIR]] [--verbose] [-d]
[--grf_path GRF_PATH] [--gt_path GT_PATH]
[-a ADDITIONAL_ARGS]
TIR-Learner: error: unrecognized arguments: -p 10
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /scratch/workspace/matthew_sharon_student_uml_edu-summer/temp/bin/rename_tirlearner.pl line 19.
Warning: LOC list genome.fa.mod.TIR.ext30.list is empty.
Error: Could not load sequence. Empty file or bad format.
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 /scratch/workspace/matthew_sharon_student_uml_edu-summer/temp/bin/output_by_list.pl line 39.
Error: TIR results not found!
ERROR: Raw TIR results not found in genome.fa.mod.EDTA.raw/genome.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 check
I believe this basically errors out and doesn't finish running.
Just to see if using an interactive session in slurm was causing errors, I ran EDTA within this slurm script:
#!/bin/bash -l
#SBATCH --job-name=edta
#SBATCH --nodes=1
#SBATCH --cpus-per-task=10
#SBATCH --mem=10G
#SBATCH --time=00:10:00
#SBATCH --output=edta_%j.out
#SBATCH --error=edta_%j.err
# ==============================================================================
module load apptainer/latest
# ==============================================================================
BASE_DIR="/scratch/workspace/matthew_sharon_student_uml_edu-summer/"
SIF_IMAGE="${BASE_DIR}/EDTA.sif"
# ==============================================================================
apptainer exec "${SIF_IMAGE}" 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
which produced these .out and .err files:
cat edta_61172160.out
#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.3.1 #####
##### 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
Thu Jun 25 23:30:55 UTC 2026 Dependency checking:
All passed!
Thu Jun 25 23:31:00 UTC 2026 Cleaning and normalizing sequence IDs...
Sequence IDs encoded. Mapping file: genome.fa.mod.seqid.map
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.
Thu Jun 25 23:31:00 UTC 2026 Obtain raw TE libraries using various structure-based programs:
cat edta_61172160.err
Loading apptainer version latest
Encoded 1 sequences with 3-char codes (prefix '_J' + 1 base-62 digits, longest clean ID: 25, id_len_max: 16, longest scaffold: 1000000 bp)
Thu Jun 25 23:31:00 UTC 2026 EDTA_raw: Check dependencies, prepare working directories.
Thu Jun 25 23:31:24 UTC 2026 Start to find LTR candidates.
Thu Jun 25 23:31:24 UTC 2026 Identify LTR retrotransposon candidates from scratch.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/LTR_retriever/bin/LTR.identifier.pl line 174.
Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty.
Thu Jun 25 23:31:55 UTC 2026 Finish finding LTR candidates.
Thu Jun 25 23:31:55 UTC 2026 Start to find SINE candidates.
Thu Jun 25 23:32:40 UTC 2026 Warning: The SINE result file has 0 bp!
Thu Jun 25 23:32:40 UTC 2026 Start to find LINE candidates.
Thu Jun 25 23:32:40 UTC 2026 Identify LINE retrotransposon candidates from scratch.
Thu Jun 25 23:33:49 UTC 2026 Warning: The LINE result file has 0 bp!
Thu Jun 25 23:33:49 UTC 2026 Start to find TIR candidates.
Thu Jun 25 23:33:49 UTC 2026 Identify TIR candidates from scratch.
Species: others
usage: TIR-Learner [-h] [-v] -f GENOME_FILE [-n GENOME_NAME] -s SPECIES
[-l LENGTH] [-t PROCESSOR] [-m MODE] [-w WORKING_DIR]
[-o OUTPUT_DIR] [-c [CHECKPOINT_DIR]] [--verbose] [-d]
[--grf_path GRF_PATH] [--gt_path GT_PATH]
[-a ADDITIONAL_ARGS]
TIR-Learner: error: unrecognized arguments: -p 10
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /scratch/workspace/matthew_sharon_student_uml_edu-summer/test/edta_apptainer/bin/rename_tirlearner.pl line 19.
Warning: LOC list genome.fa.mod.TIR.ext30.list is empty.
Error: Could not load sequence. Empty file or bad format.
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 /scratch/workspace/matthew_sharon_student_uml_edu-summer/test/edta_apptainer/bin/output_by_list.pl line 39.
Error: TIR results not found!
ERROR: Raw TIR results not found in genome.fa.mod.EDTA.raw/genome.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 check
which differ from the interactive run.
And finally when running EDTA through the apptainer container with this slurm script:
#!/bin/bash -l
#SBATCH --job-name=edta
#SBATCH --nodes=1
#SBATCH --cpus-per-task=20
#SBATCH --mem=200G
#SBATCH --time=7-00:00:00
#SBATCH --output=edta_%j.out
#SBATCH --error=edta_%j.err
# ==============================================================================
module load apptainer/latest
# ==============================================================================
BASE_DIR="/scratch/workspace/matthew_sharon_student_uml_edu-summer/edta/EDTA/EDTA.pl"
GENOME="${BASE_DIR}/sb_files/GCF_964276395.1_fGasAcu3.hap1.1_genomic.shortnames.fna"
CDS="${BASE_DIR}/sb_files/GCF_964276395.1_fGasAcu3.hap1.1.CDS.fna"
CURATEDLIB="${BASE_DIR}/sb_files/Gasterosteus_aculeatus_transposon_library.fa"
SIF_IMAGE="${BASE_DIR}/EDTA.sif"
# ==============================================================================
apptainer exec "${SIF_IMAGE}" perl EDTA.pl \
--genome "${GENOME}" \
--cds "${CDS}" \
--curatedlib "${CURATEDLIB}" \
--sensitive 1 \
--anno 1 \
--evaluate 1 \
--threads "${SLURM_CPUS_PER_TASK}"
I get this output:
cat edta_61048317.out
#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.3.1 #####
##### Shujun Ou (shujun.ou.1@gmail.com) #####
#########################################################
Parameters: --genome /scratch/workspace/matthew_sharon_student_uml_edu-summer/edta/EDTA/EDTA.pl/sb_files/GCF_964276395.1_fGasAcu3.hap1.1_genomic.shortnames.fna --cds /scratch/workspace/matthew_sharon_student_uml_edu-summer/edta/EDTA/EDTA.pl/sb_files/GCF_964276395.1_fGasAcu3.hap1.1.CDS.fna --curatedlib /scratch/workspace/matthew_sharon_student_uml_edu-summer/edta/EDTA/EDTA.pl/sb_files/Gasterosteus_aculeatus_transposon_library.fa --sensitive 1 --anno 1 --evaluate 1 --threads 20
Tue Jun 23 03:48:06 UTC 2026 Dependency checking:
All passed!
Tue Jun 23 03:48:11 UTC 2026 Existing normalized genome GCF_964276395.1_fGasAcu3.hap1.1_genomic.shortnames.fna.mod found (no encoding needed).
A custom library /scratch/workspace/matthew_sharon_student_uml_edu-summer/edta/EDTA/EDTA.pl/sb_files/Gasterosteus_aculeatus_transposon_library.fa is provided via --curatedlib. Please make sure this is a manually curated library but not machine generated.
A CDS file /scratch/workspace/matthew_sharon_student_uml_edu-summer/edta/EDTA/EDTA.pl/sb_files/GCF_964276395.1_fGasAcu3.hap1.1.CDS.fna is provided via --cds. Please make sure this is the DNA sequence of coding regions only.
Tue Jun 23 03:48:11 UTC 2026 Obtain raw TE libraries using various structure-based programs:
cat edta_61048317.err
Loading apptainer version latest
Tue Jun 23 03:48:11 UTC 2026 EDTA_raw: Check dependencies, prepare working directories.
Tue Jun 23 03:48:31 UTC 2026 Start to find LTR candidates.
Tue Jun 23 03:48:31 UTC 2026 Identify LTR retrotransposon candidates from scratch.
Tue Jun 23 04:39:48 UTC 2026 Finish finding LTR candidates.
Tue Jun 23 04:39:48 UTC 2026 Start to find SINE candidates.
Tue Jun 23 05:32:59 UTC 2026 Finish finding SINE candidates.
Tue Jun 23 05:32:59 UTC 2026 Start to find LINE candidates.
Tue Jun 23 05:32:59 UTC 2026 Identify LINE retrotransposon candidates from scratch.
Wed Jun 24 13:37:00 UTC 2026 Finish finding LINE candidates.
Wed Jun 24 13:37:00 UTC 2026 Start to find TIR candidates.
Wed Jun 24 13:37:00 UTC 2026 Identify TIR candidates from scratch.
Species: others
usage: TIR-Learner [-h] [-v] -f GENOME_FILE [-n GENOME_NAME] -s SPECIES
[-l LENGTH] [-t PROCESSOR] [-m MODE] [-w WORKING_DIR]
[-o OUTPUT_DIR] [-c [CHECKPOINT_DIR]] [--verbose] [-d]
[--grf_path GRF_PATH] [--gt_path GT_PATH]
[-a ADDITIONAL_ARGS]
TIR-Learner: error: unrecognized arguments: -p 20
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /scratch/workspace/matthew_sharon_student_uml_edu-summer/edta/EDTA/EDTA.pl/bin/rename_tirlearner.pl line 19.
Warning: LOC list GCF_964276395.1_fGasAcu3.hap1.1_genomic.shortnames.fna.mod.TIR.ext30.list is empty.
Error: Could not load sequence. Empty file or bad format.
mv: cannot stat 'GCF_964276395.1_fGasAcu3.hap1.1_genomic.shortnames.fna.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln': No such file or directory
cp: cannot stat 'GCF_964276395.1_fGasAcu3.hap1.1_genomic.shortnames.fna.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list': No such file or directory
cp: cannot stat 'GCF_964276395.1_fGasAcu3.hap1.1_genomic.shortnames.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 /scratch/workspace/matthew_sharon_student_uml_edu-summer/edta/EDTA/EDTA.pl/bin/output_by_list.pl line 39.
Error: TIR results not found!
ERROR: Raw TIR results not found in GCF_964276395.1_fGasAcu3.hap1.1_genomic.shortnames.fna.mod.EDTA.raw/GCF_964276395.1_fGasAcu3.hap1.1_genomic.shortnames.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
Ideally the test conditions would produce the same output between both conda and apptainer but it seems like there is a different error/output for each type of run, so I don't know if the apptainer run on my data failed due to an issue with my data (such as sequence headers being too long) or if I don't have EDTA set up properly. If some of these errors are expected (ie. no SINE's or LINE's detected) it would be good to run EDTA with a consistent seed and post the proper results for that seed to validate that it's producing the correct output.
Hello Dr. Ou,
Sorry in advance, I know this is a lot of text. I tried installing and running EDTA, but I haven't been able to run it properly. I have tried running the test script using both conda and apptainer, and also tried using apptainer to run on my data which seems to have failed to complete. I tried to test and document the output of each run below. Ultimately it seems EDTA is not working properly with either conda or apptainer, but not sure whether this is something on my end or the program/testing file itself.
Installed EDTA through conda using these commands
on slurm I allocated 10gb of memory and 10 cores in an interactive session, then activated the conda environment and ran the test script
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 10on the file located at./edta/testwhich produced this output:When looking at the output I noticed there seemed to be errors such as
Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty.and messages about SINE's and LINE's not being found. To see if I would get the same errors I installed the newest singularity image withsingularity pull EDTA.sif docker://quay.io/biocontainers/edta:2.3.0--hdfd78af_0, cloned the repo into a different directory to prevent previous conda test run from interacting/interfering with this apptainer test run, and allocated a 10gb + 10 cpu interactive compute node with slurm. Running with the same test command produced this output:I believe this basically errors out and doesn't finish running.
Just to see if using an interactive session in slurm was causing errors, I ran EDTA within this slurm script:
which produced these .out and .err files:
which differ from the interactive run.
And finally when running EDTA through the apptainer container with this slurm script:
I get this output:
Ideally the test conditions would produce the same output between both conda and apptainer but it seems like there is a different error/output for each type of run, so I don't know if the apptainer run on my data failed due to an issue with my data (such as sequence headers being too long) or if I don't have EDTA set up properly. If some of these errors are expected (ie. no SINE's or LINE's detected) it would be good to run EDTA with a consistent seed and post the proper results for that seed to validate that it's producing the correct output.