Error in helitron identification step

[lancelot-bio]

Hi, I encountered this error when testing:
`#########################################################

Extensive de-novo TE Annotator (EDTA) v2.2.2

Shujun Ou ([email protected])

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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

Wed Mar 5 17:00:24 CST 2025 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.

Wed Mar 5 17:00:25 CST 2025 Obtain raw TE libraries using various structure-based programs:
Wed Mar 5 17:00:25 CST 2025 EDTA_raw: Check dependencies, prepare working directories.

Wed Mar 5 17:00:30 CST 2025 Start to find LTR candidates.

Wed Mar 5 17:00:30 CST 2025 Identify LTR retrotransposon candidates from scratch.

Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty.
Wed Mar 5 17:01:18 CST 2025 Finish finding LTR candidates.

Wed Mar 5 17:01:18 CST 2025 Start to find SINE candidates.

Wed Mar 5 17:02:10 CST 2025 Warning: The SINE result file has 0 bp!

Wed Mar 5 17:02:10 CST 2025 Start to find LINE candidates.

Wed Mar 5 17:02:10 CST 2025 Identify LINE retrotransposon candidates from scratch.

Wed Mar 5 17:03:31 CST 2025 Warning: The LINE result file has 0 bp!

Wed Mar 5 17:03:31 CST 2025 Start to find TIR candidates.

Wed Mar 5 17:03:31 CST 2025 Identify TIR candidates from scratch.

Species: others
Wed Mar 5 17:05:04 CST 2025 Finish finding TIR candidates.

Wed Mar 5 17:05:04 CST 2025 Start to find Helitron candidates.

Wed Mar 5 17:05:04 CST 2025 Identify Helitron candidates from scratch.

bash: java: command not found
bash: java: command not found
bash: java: command not found
bash: java: command not found
bash: java: command not found
bash: java: command not found
bash: java: command not found
bash: java: command not found
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 /share/org/01_Tools/EDTA/bin/output_by_list.pl line 37.

Error: Error while loading sequencemv: 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`

I have reinstalled EDTA in different ways, but the error still bothers me. Could you give me some suggestions?
Thanks