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EDTA ended with the final file '*.mod.EDTA.TEanno.sum' empty #219

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zhxh233 opened this issue Sep 8, 2021 · 14 comments
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EDTA ended with the final file '*.mod.EDTA.TEanno.sum' empty #219

zhxh233 opened this issue Sep 8, 2021 · 14 comments
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@zhxh233
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zhxh233 commented Sep 8, 2021 •
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Hi shujun!
I am using EDTA as several weeks ago (with --anno 1 --evaluate 1 --species others --step all --overwrite 0 --sensitive 1 --force 1
), but this time the script ended with *.mod.EDTA.TEanno.sum empty. I have tried to short the sequence name and the file name or without "--force 1" parameter, as you mentioned in other issues, but it didn't work.

  1. My EDTA version is v1.9.7
  2. The script output error information as
    a) Use of uninitialized value $type in concatenation (.) or string at (GFF file) (many lines of this one)
    b) Use of uninitialized value $chr_pre in hash element at /beegfs/store3/zhangxiaohang/software/EDTA-master/util/call_seq_by_list.pl line 90.
    c) Use of uninitialized value $pos in pattern match (m//) at /beegfs/store3/zhangxiaohang/software/EDTA-master/util/call_seq_by_list.pl line 100.
    d) Use of uninitialized value $pos in concatenation (.) or string at /beegfs/store3/zhangxiaohang/software/EDTA-master/util/call_seq_by_list.pl line 103.
    e) ERROR: Can not recognize this MSU position in the list!
    f) ERROR: TE annotation stats results not found in ${myfile}.mod.EDTA.TE.fa.stat!
  3. All other outputfiles look normal
    So, how can I fixed it? Or if I need the output_gff at least, should I use the *EDTA.intact.gff3 or *EDTA.TEanno.gff3 or another file in some folders or all these files may be with some mistakes?
    Thank you! : )
@hlkfoz
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hlkfoz commented Sep 9, 2021 •
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I have the similar error few day ago, the cause of empty '.mod.EDTA.TEanno.sum' file is the RepeatModeler step identifyied New TE classes that the "../util/gff2bed.pl" script program can't properly handled, and lead to New TE classes lines with incorrect formation in '.mod.EDTA.TEanno.bed' file, and finaly cause empty '*.mod.EDTA.TEanno.sum' file. you can try manully add New TE classes‘s matching regular expression type in "../util/gff2bed.pl" script, some like "$type = "DIRS" if $sequence_ontology =~ /DIRS/i" in line 51-60, and rerun EDTA with ".. --step anno --anno 1 --evaluate 1 --species others --step all --overwrite 0 --sensitive 1 --force 1".

@oushujun
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oushujun commented Sep 9, 2021

The latest version (v1.9.9) should have this issue resolved. - Shujun

@oushujun
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oushujun commented Sep 9, 2021 via email

@zhxh233
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zhxh233 commented Sep 9, 2021

I have the similar error few day ago, the cause of empty '.mod.EDTA.TEanno.sum' file is the RepeatModeler step identifyied New TE classes that the "../util/gff2bed.pl" script program can't properly handled, and lead to New TE classes lines with incorrect formation in '.mod.EDTA.TEanno.bed' file, and finaly cause empty '*.mod.EDTA.TEanno.sum' file. you can try manully add New TE classes‘s matching regular expression type in "../util/gff2bed.pl" script, some like "$type = "DIRS" if $sequence_ontology =~ /DIRS/i" in line 51-60, and rerun EDTA with ".. --step anno --anno 1 --evaluate 1 --species others --step all --overwrite 0 --sensitive 1 --force 1".

Thanks! I will try this one and shujun's advice after my program finish.

@zhxh233
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zhxh233 commented Sep 9, 2021

You may install the conda version, then clone the github to your server and you will get the latest versio. -Shujun
…
On Wed, Sep 8, 2021 at 11:13 PM hlkfoz @.***> wrote: The latest version (v1.9.9) should have this issue resolved. - Shujun Hi shujun! How can i download The latest version (v1.9.9) , I can't find The latest version (v1.9.9) in github.com, the lastest release is v1.9.6. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#219 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NF52RGRKAF3JWORWKTUBAYABANCNFSM5DVIMMLA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

Thank you, Shujun. I will try it later.

@zhxh233
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zhxh233 commented Sep 10, 2021 •
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You may install the conda version, then clone the github to your server and you will get the latest versio. -Shujun
…
On Wed, Sep 8, 2021 at 11:13 PM hlkfoz @.***> wrote: The latest version (v1.9.9) should have this issue resolved. - Shujun Hi shujun! How can i download The latest version (v1.9.9) , I can't find The latest version (v1.9.9) in github.com, the lastest release is v1.9.6. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#219 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NF52RGRKAF3JWORWKTUBAYABANCNFSM5DVIMMLA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

Hi Shujun, I have tried to re-annotation using EDTA v1.9.9, but that error is still here. I used the method @hlkfoz adviced, to modify "./util/gff2bed.pl" script like this, it seems everything goes well.
` 50 # determine $type for struc-homo TE annotation merging

51 $type = "Cent" if $sequence_ontology =~ /Cent/i;

52 $type = "knob" if $sequence_ontology =~ /knob/i;

53 $type = "LINE" if $sequence_ontology =~ /LINE|RIL/i;

54 $type = "SINE" if $sequence_ontology =~ /SINE|RIS/i;

55 $type = "nonLTR" if $sequence_ontology =~ /non_LTR/i;

56 $type = "rDNA" if $sequence_ontology =~ /rDNA/i;

57 $type = "satellite" if $sequence_ontology =~ /satellite/i;

58 $type = "low_complexity" if $sequence_ontology =~ /low_complexity/i;

59 $type = "telomere" if $sequence_ontology =~ /telomer/i;

60 $type = "subtelomere" if $sequence_ontology =~ /subtelomer/i;

61 $type = "Helitron" if $sequence_ontology =~ /Helitron|DHH/i;

62 $type = "Penelope" if $sequence_ontology =~ /Penelope|RPP/i;

63 $type = "repeat_region" if $sequence_ontology =~ /repeat_region/i;

**64 $type = "DIRS" if $sequence_ontology =~ /DIRS/i;

65 #line 64 is modified according to the reference solution**

66 $type = 'repeat_region' if $sequence_ontology =~ /Unknown/i; #suggested by Changfu Jia

67 $type = $1 if $sequence_ontology =~ /^(.)/./ and $1 !~ /DNA|MITE/i;`

@oushujun
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oushujun commented Sep 11, 2021 •
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@zhxh233 if you check the code of /util/gff2bed.pl on the current github (v1.9.9), it has the exact same code you posted above. I suscept you didn't use the latest version even you have downloaded it (i.e., you need to specify the path to your downloaded code). - Shujun

@hlkfoz
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hlkfoz commented Sep 12, 2021

@zhxh233 if you check the code of /util/gff2bed.pl on the current github (v1.9.9), it has the exact same code you posted above. I suscept you didn't use the latest version even you have downloaded it (i.e., you need to specify the path to your downloaded code). - Shujun
Hi Shujun, I have installed the current version (v1.9.9) follow your suggestion, and rerun the EDTA, but the same error also still remain, i post the test log below:

########################################################

Extensive de-novo TE Annotator (EDTA) v1.9.9
Shujun Ou (shujun.ou.1@gmail.com)

########################################################

2021年 09月 09日 星期四 12:26:11 CST Dependency checking:
All passed!

2021年 09月 09日 星期四 12:26:14 CST Obtain raw TE libraries using various structure-based programs:
2021年 09月 09日 星期四 12:26:14 CST EDTA_raw: Check dependencies, prepare working directories.

2021年 09月 09日 星期四 12:26:17 CST Start to find LTR candidates.

2021年 09月 09日 星期四 12:26:17 CST Identify LTR retrotransposon candidates from scratch.

2021年 09月 09日 星期四 12:32:25 CST Finish finding LTR candidates.

2021年 09月 09日 星期四 12:32:25 CST Start to find TIR candidates.

2021年 09月 09日 星期四 12:32:25 CST Identify TIR candidates from scratch.

Species: others
2021年 09月 09日 星期四 12:59:33 CST Finish finding TIR candidates.

2021年 09月 09日 星期四 12:59:33 CST Start to find Helitron candidates.

2021年 09月 09日 星期四 12:59:33 CST Identify Helitron candidates from scratch.

2021年 09月 09日 星期四 13:51:01 CST Finish finding Helitron candidates.

2021年 09月 09日 星期四 13:51:01 CST Execution of EDTA_raw.pl is finished!

2021年 09月 09日 星期四 13:51:01 CST Obtain raw TE libraries finished.
All intact TEs found by EDTA:
PhEs.test.fasta.mod.EDTA.intact.fa
PhEs.test.fasta.mod.EDTA.intact.gff3

2021年 09月 09日 星期四 13:51:01 CST Perform EDTA advance filtering for raw TE candidates and generate the stage 1 library:

2021年 09月 09日 星期四 13:54:24 CST EDTA advance filtering finished.

2021年 09月 09日 星期四 13:54:24 CST Perform EDTA final steps to generate a non-redundant comprehensive TE library:

			Use RepeatModeler to identify any remaining TEs that are missed by structure-based methods.

2021-09-09 18:40:15,186 -WARNING- Grid computing is not available because DRMAA not configured properly: Could not find drmaa library. Please specify its full path using the environment variable DRMAA_LIBRARY_PATH
2021-09-09 18:40:15,195 -INFO- VARS: {'sequence': 'PhEs.test.fasta.mod.RM.consensi.fa', 'hmm_database': 'rexdb', 'seq_type': 'nucl', 'prefix': 'PhEs.test.fasta.mod.RM.consensi.fa.rexdb', 'force_write_hmmscan': False, 'processors': 40, 'tmp_dir': './tmp', 'min_coverage': 20, 'max_evalue': 0.001, 'disable_pass2': False, 'pass2_rule': '80-80-80', 'no_library': False, 'no_reverse': False, 'no_cleanup': False, 'p2_identity': 80.0, 'p2_coverage': 80.0, 'p2_length': 80.0}
2021-09-09 18:40:15,195 -INFO- checking dependencies:
2021-09-09 18:40:15,212 -INFO- hmmer 3.3.1 OK
2021-09-09 18:40:15,308 -INFO- blastn 2.10.0+ OK
2021-09-09 18:40:15,309 -INFO- check database rexdb
2021-09-09 18:40:15,309 -INFO- db path: /home/biolinux/miniconda3/envs/EDTA/lib/python3.6/site-packages/TEsorter/database
2021-09-09 18:40:15,309 -INFO- db file: REXdb_protein_database_viridiplantae_v3.0_plus_metazoa_v3.hmm
2021-09-09 18:40:15,309 -INFO- REXdb_protein_database_viridiplantae_v3.0_plus_metazoa_v3.hmm OK
2021-09-09 18:40:15,310 -INFO- Start classifying pipeline
2021-09-09 18:40:15,346 -INFO- total 1713 sequences
2021-09-09 18:40:15,346 -INFO- translating PhEs.test.fasta.mod.RM.consensi.fa in six frames
/home/biolinux/miniconda3/envs/EDTA/lib/python3.6/site-packages/Bio/Seq.py:2338: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.
BiopythonWarning,
2021-09-09 18:40:16,417 -INFO- HMM scanning against /home/biolinux/miniconda3/envs/EDTA/lib/python3.6/site-packages/TEsorter/database/REXdb_protein_database_viridiplantae_v3.0_plus_metazoa_v3.hmm
2021-09-09 18:40:16,526 -INFO- Creating server instance (pp-1.6.4.4)
2021-09-09 18:40:16,526 -INFO- Running on Python 3.6.12 linux
2021-09-09 18:40:19,968 -INFO- pp local server started with 40 workers
2021-09-09 18:40:20,015 -INFO- Task 0 started
2021-09-09 18:40:20,016 -INFO- Task 1 started
2021-09-09 18:40:20,017 -INFO- Task 2 started
2021-09-09 18:40:20,017 -INFO- Task 3 started
2021-09-09 18:40:20,018 -INFO- Task 4 started
2021-09-09 18:40:20,019 -INFO- Task 5 started
2021-09-09 18:40:20,019 -INFO- Task 6 started
2021-09-09 18:40:20,019 -INFO- Task 7 started
2021-09-09 18:40:20,020 -INFO- Task 8 started
2021-09-09 18:40:20,021 -INFO- Task 9 started
2021-09-09 18:40:20,021 -INFO- Task 10 started
2021-09-09 18:40:20,023 -INFO- Task 11 started
2021-09-09 18:40:20,023 -INFO- Task 12 started
2021-09-09 18:40:20,024 -INFO- Task 13 started
2021-09-09 18:40:20,025 -INFO- Task 14 started
2021-09-09 18:40:20,026 -INFO- Task 15 started
2021-09-09 18:40:20,026 -INFO- Task 16 started
2021-09-09 18:40:20,027 -INFO- Task 17 started
2021-09-09 18:40:20,027 -INFO- Task 18 started
2021-09-09 18:40:20,028 -INFO- Task 19 started
2021-09-09 18:40:20,029 -INFO- Task 20 started
2021-09-09 18:40:20,030 -INFO- Task 21 started
2021-09-09 18:40:20,031 -INFO- Task 22 started
2021-09-09 18:40:20,032 -INFO- Task 23 started
2021-09-09 18:40:20,033 -INFO- Task 24 started
2021-09-09 18:40:20,034 -INFO- Task 25 started
2021-09-09 18:40:20,035 -INFO- Task 26 started
2021-09-09 18:40:20,035 -INFO- Task 27 started
2021-09-09 18:40:20,050 -INFO- Task 28 started
2021-09-09 18:40:20,052 -INFO- Task 29 started
2021-09-09 18:40:20,053 -INFO- Task 30 started
2021-09-09 18:40:20,054 -INFO- Task 31 started
2021-09-09 18:40:20,055 -INFO- Task 32 started
2021-09-09 18:40:20,056 -INFO- Task 33 started
2021-09-09 18:40:20,056 -INFO- Task 34 started
2021-09-09 18:40:20,057 -INFO- Task 35 started
2021-09-09 18:40:20,058 -INFO- Task 36 started
2021-09-09 18:40:20,058 -INFO- Task 37 started
2021-09-09 18:40:20,060 -INFO- Task 38 started
2021-09-09 18:40:20,060 -INFO- Task 39 started
2021-09-09 18:40:24,437 -INFO- generating gene anntations
2021-09-09 18:40:24,522 -INFO- 63 sequences classified by HMM
2021-09-09 18:40:24,522 -INFO- see protein domain sequences in PhEs.test.fasta.mod.RM.consensi.fa.rexdb.dom.faa and annotation gff3 file in PhEs.test.fasta.mod.RM.consensi.fa.rexdb.dom.gff3
2021-09-09 18:40:24,522 -INFO- classifying the unclassified sequences by searching against the classified ones
2021-09-09 18:40:24,571 -INFO- using the 80-80-80 rule
2021-09-09 18:40:24,571 -INFO- run CMD: makeblastdb -in ./tmp/pass1_classified.fa -dbtype nucl
2021-09-09 18:40:24,654 -INFO- run CMD: blastn -query ./tmp/pass1_unclassified.fa -db ./tmp/pass1_classified.fa -out ./tmp/pass1_unclassified.fa.blastout -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen qcovs qcovhsp sstrand' -num_threads 40
2021-09-09 18:40:25,133 -INFO- 19 sequences classified in pass 2
2021-09-09 18:40:25,134 -INFO- total 82 sequences classified.
2021-09-09 18:40:25,134 -INFO- see classified sequences in PhEs.test.fasta.mod.RM.consensi.fa.rexdb.cls.tsv
2021-09-09 18:40:25,134 -INFO- writing library for RepeatMasker in PhEs.test.fasta.mod.RM.consensi.fa.rexdb.cls.lib
2021-09-09 18:40:25,207 -INFO- writing classified protein domains in PhEs.test.fasta.mod.RM.consensi.fa.rexdb.cls.pep
2021-09-09 18:40:25,211 -INFO- Summary of classifications:
Order Superfamily # of Sequences# of Clade Sequences # of Clades# of full Domains
DIRS unknown 10 0 0 0
Penelope unknown 28 0 0 0
LINE unknown 44 0 0 0
2021-09-09 18:40:25,211 -INFO- Pipeline done.
2021-09-09 18:40:25,211 -INFO- cleaning the temporary directory ./tmp
Skipping the CDS cleaning step (--cds [File]) since no CDS file is provided or it's empty.

Penelope/NA not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
Penelope/NA not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
Penelope/NA not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
Penelope/NA not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
Penelope/NA not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
Penelope/NA not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
2021年 09月 09日 星期四 18:44:30 CST EDTA final stage finished! You may check out:
The final EDTA TE library: PhEs.test.fasta.mod.EDTA.TElib.fa
2021年 09月 09日 星期四 18:44:30 CST Perform post-EDTA analysis for whole-genome annotation:

2021年 09月 09日 星期四 18:44:30 CST Homology-based annotation of TEs using PhEs.test.fasta.mod.EDTA.TElib.fa from scratch.

Use of uninitialized value $type in concatenation (.) or string at /home/biolinux/miniconda3/envs/EDTA/share/EDTA/util/gff2bed.pl line 85, line 485.
Use of uninitialized value $type in concatenation (.) or string at /home/biolinux/miniconda3/envs/EDTA/share/EDTA/util/gff2bed.pl line 85, line 486.
Use of uninitialized value $type in concatenation (.) or string at /home/biolinux/miniconda3/envs/EDTA/share/EDTA/util/gff2bed.pl line 85, line 487.
Use of uninitialized value $type in concatenation (.) or string at /home/biolinux/miniconda3/envs/EDTA/share/EDTA/util/gff2bed.pl line 85, line 488.
Use of uninitialized value $type in concatenation (.) or string at /home/biolinux/miniconda3/envs/EDTA/share/EDTA/util/gff2bed.pl line 85, line 1350.
Use of uninitialized value $type in concatenation (.) or string at /home/biolinux/miniconda3/envs/EDTA/share/EDTA/util/gff2bed.pl line 85, line 1351.
Use of uninitialized value $type in concatenation (.) or string at /home/biolinux/miniconda3/envs/EDTA/share/EDTA/util/gff2bed.pl line 85, line 1352.
Use of uninitialized value $type in concatenation (.) or string at /home/biolinux/miniconda3/envs/EDTA/share/EDTA/util/gff2bed.pl line 85, line 1353.
... lots warning
Use of uninitialized value $type in concatenation (.) or string at /home/biolinux/miniconda3/envs/EDTA/share/EDTA/util/gff2bed.pl line 85, line 169567.
Use of uninitialized value $type in concatenation (.) or string at /home/biolinux/miniconda3/envs/EDTA/share/EDTA/util/gff2bed.pl line 85, line 170124.
2021年 09月 09日 星期四 18:59:13 CST TE annotation using the EDTA library has finished! Check out:
Whole-genome TE annotation (total TE: ): PhEs.test.fasta.mod.EDTA.TEanno.gff3
Whole-genome TE annotation summary: PhEs.test.fasta.mod.EDTA.TEanno.sum
Low-threshold TE masking for MAKER gene annotation (masked: 18.51%): PhEs.test.fasta.mod.MAKER.masked

2021年 09月 09日 星期四 18:59:14 CST Evaluate the level of inconsistency for whole-genome TE annotation (slow step):

Use of uninitialized value in pattern match (m//) at /home/biolinux/miniconda3/envs/EDTA/share/EDTA/util/call_seq_by_list.pl line 88.
Use of uninitialized value $chr_pre in hash element at /home/biolinux/miniconda3/envs/EDTA/share/EDTA/util/call_seq_by_list.pl line 90.
Use of uninitialized value $pos in pattern match (m//) at /home/biolinux/miniconda3/envs/EDTA/share/EDTA/util/call_seq_by_list.pl line 100.
Use of uninitialized value $pos in concatenation (.) or string at /home/biolinux/miniconda3/envs/EDTA/share/EDTA/util/call_seq_by_list.pl line 103.
ERROR: Can not recognize this MSU position in the list!
ERROR: TE annotation stats results not found in PhEs.test.fasta.mod.EDTA.TE.fa.stat!

I think the latest gff2bed.pl script still not handled "DIRS" type properly .

@zhxh233
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zhxh233 commented Sep 13, 2021

I downloaded another copy of the latest version from github on my Windows computer (which never installed or downloaded EDTA before) to check the code, in EDTA.pl, the version number is 1.9.9, while in gff2bed.pl, there is indeed no some code in the part "determine $type for struc-homo TE annotation merging" as @hlkfoz , like this:

`
# determine $type for struc-homo TE annotation merging
$type = "Cent" if $sequence_ontology =~ /Cent/i;
$type = "knob" if $sequence_ontology =~ /knob/i;
$type = "LINE" if $sequence_ontology =~ /LINE|RIL/i;
$type = "SINE" if $sequence_ontology =~ /SINE|RIS/i;
$type = "nonLTR" if $sequence_ontology =~ /non_LTR/i;
$type = "rDNA" if $sequence_ontology =~ /rDNA/i;
$type = "satellite" if $sequence_ontology =~ /satellite/i;
$type = "low_complexity" if $sequence_ontology =~ /low_complexity/i;
$type = "telomere" if $sequence_ontology =~ /telomer/i;
$type = "subtelomere" if $sequence_ontology =~ /subtelomer/i;
$type = "Helitron" if $sequence_ontology =~ /Helitron|DHH/i;
$type = "Penelope" if $sequence_ontology =~ /Penelope|RPP/i;
$type = "repeat_region" if $sequence_ontology =~ /repeat_region/i;
$type = 'repeat_region' if $sequence_ontology =~ /Unknown/i; #suggested by Changfu Jia
$type = $1 if $sequence_ontology =~ /^(.)/./ and $1 !~ /DNA|MITE/i;

`

the verision of gff2bed.pl is v0.3, 07/22/2020, so maybe there is still something wrong ?

@oushujun
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@zhxh233 Sorry for the delayed reply. What errors were you suggesting? Did you get results with the v1.9.9 conda version? - Shujun

@zhxh233
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zhxh233 commented Sep 26, 2021

@zhxh233 Sorry for the delayed reply. What errors were you suggesting? Did you get results with the v1.9.9 conda version? - Shujun

Thanks for reply. After I edited the EDTA.pl script as others' suggestion, the script can run normally. My last commented just said that I found the source code of EDTA.pl on github which version is 1.9.9, it still has no the code $type = "DIRS" if $sequence_ontology =~ /DIRS/i;, so before I edited, the program can't finished the annotation in some cases.

@oushujun
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Thanks for making that clear. I found the issue. The correct fix would be replacing line 43 with
if ($class =~ /(non_LTR|LINE|LINE_element|LINE_retrotransposon|SINE|SINE_element|SINE_retrotransposon|YR_retrotransposon|Penelope|Ngaro|DIRS|Viper)/i){

The fix will be updated in the next version. Thanks for helping to debug.

Best,
Shujun

@oushujun oushujun added the bug Something isn't working label Sep 28, 2021
@zhxh233
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zhxh233 commented Sep 29, 2021

Thank you for your great tools ! : ) I'll try this fix later.
Best,
Xiaohang

@oushujun oushujun mentioned this issue Oct 22, 2021
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oushujun added a commit that referenced this issue Nov 26, 2021
@oushujun
update TE SO and match the script. #219
538baa0
oushujun added a commit that referenced this issue Apr 21, 2023
@oushujun
add new TE categories to the TE_SO file to solve #151 #164 #178 #219
2d03828
@sahoo-rk sahoo-rk mentioned this issue Jul 28, 2023
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@surabhiranavat
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surabhiranavat commented Apr 11, 2024 •
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Hi Shujun,

Thank you for developing this excellent package.

I'm getting similar errors with EDTA v2.2.1 (--genome new_non_organelle_tgsgapclose_PAL046.fasta --sensitive 1 --anno 1 --threads 10)

unknown/NA not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
                                                                                                                                                                                                            
Use of uninitialized value $type in concatenation (.) or string at /srv/home/sran0007/EDTA/util/gff2bed.pl line 112, <GFF> line 82774. 

Use of uninitialized value $class in hash element at /srv/home/sran0007/EDTA/util/div_table2.pl line 80, <$fh> line 164570.

Evaluate the level of inconsistency for whole-genome TE annotation:

Use of uninitialized value in pattern match (m//) at /srv/home/sran0007/EDTA/util/call_seq_by_list.pl line 90.
Use of uninitialized value $chr_pre in hash element at /srv/home/sran0007/EDTA/util/call_seq_by_list.pl line 92.
Use of uninitialized value $pos in pattern match (m//) at /srv/home/sran0007/EDTA/util/call_seq_by_list.pl line 103.
Use of uninitialized value $pos in concatenation (.) or string at /srv/home/sran0007/EDTA/util/call_seq_by_list.pl line 106.
ERROR: Can not recognize this MSU position in the list!
ERROR: TE annotation stats results not found in new_non_organelle_tgsgapclose_PAL046.fasta.mod.EDTA.TE.fa.stat!

It did work successfully after I skipped --sensitive 1.

I cloned EDTA from github and installed the dependencies with mamba. The gff2bed.pl version is 0.6. Is there any fix for this?

Best wishes,
Surabhi

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@hlkfoz @oushujun @zhxh233 @surabhiranavat