oushujun
commented
1 month ago You installed the test branch for dependencies but used the master branch of the program - they do not match.
Run git checkout EDTA2 on your program folder should solve it
Shujun
On Thu, Sep 19, 2024 at 4:14 AM qfh20m20m @.***> wrote:
Hello， I installed it using the method you recommended：
mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython cd-hit coreutils genericrepeatfinder genometools-genometools glob2 tir-learner ltr_finder_parallel ltr_retriever mdust multiprocess muscle openjdk perl perl-text-soundex r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr tesorter samtools bedtools LTR_HARVEST_parallel HelitronScanner -y The following error occurred while running the test data：
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 > test.log Fri Sep 13 19:54:56 HKT 2024 EDTA_raw: Check dependencies, prepare working directories. Fri Sep 13 19:54:58 HKT 2024 Start to find LTR candidates. Fri Sep 13 19:54:58 HKT 2024 Identify LTR retrotransposon candidates from scratch. Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty.
Fri Sep 13 19:55:25 HKT 2024 Finish finding LTR candidates. Fri Sep 13 19:55:25 HKT 2024 Start to find SINE candidates. Fri Sep 13 19:56:20 HKT 2024 Warning: The SINE result file has 0 bp! Fri Sep 13 19:56:20 HKT 2024 Start to find LINE candidates. Fri Sep 13 19:56:20 HKT 2024 Identify LINE retrotransposon candidates from scratch. Fri Sep 13 19:58:07 HKT 2024 Warning: The LINE result file has 0 bp! Fri Sep 13 19:58:07 HKT 2024 Start to find TIR candidates. Fri Sep 13 19:58:07 HKT 2024 Identify TIR candidates from scratch. Species: others Traceback (most recent call last): File "/nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 14, in
from bin.main import TIRLearner File "/nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/TIR-Learner3.0/bin/main.py", line 22, in from prog_const import * File "/nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/TIR-Learner3.0/bin/prog_const.py", line 29, in import tensorflow as tf ModuleNotFoundError: No module named 'tensorflow' Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /nfs_fs/nfs1/pengxiaochang/software/EDTA/util/rename_tirlearner.pl line 19. Warning: LOC list genome.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 @.***) 10/11/2019 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 /nfs_fs/nfs1/pengxiaochang/software/EDTA/util/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
When I run my data, I can predict the LTR, but the TIR prediction still gives an error：
perl /nfs_fs/nfs1/pengxiaochang/software/EDTA/EDTA.pl --genome Hedychium_hic.post.FINAL.fa --species others --overwrite 1 --sensitive 1 --anno 1 --threads 20 > test.log Fri Sep 13 20:06:24 HKT 2024 EDTA_raw: Check dependencies, prepare working directories. Fri Sep 13 20:06:41 HKT 2024 Start to find LTR candidates. Fri Sep 13 20:06:41 HKT 2024 Identify LTR retrotransposon candidates from scratch. Fri Sep 13 22:03:32 HKT 2024 Finish finding LTR candidates. Fri Sep 13 22:03:32 HKT 2024 Start to find SINE candidates. Sat Sep 14 00:44:59 HKT 2024 Finish finding SINE candidates. Sat Sep 14 00:44:59 HKT 2024 Start to find LINE candidates. Sat Sep 14 00:44:59 HKT 2024 Identify LINE retrotransposon candidates from scratch. Sun Sep 15 03:14:29 HKT 2024 Finish finding LINE candidates. Sun Sep 15 03:14:29 HKT 2024 Start to find TIR candidates. Sun Sep 15 03:14:29 HKT 2024 Identify TIR candidates from scratch. Species: others Traceback (most recent call last): File "/nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 14, in
from bin.main import TIRLearner File "/nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/TIR-Learner3.0/bin/main.py", line 22, in from prog_const import * File "/nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/TIR-Learner3.0/bin/prog_const.py", line 29, in import tensorflow as tf ModuleNotFoundError: No module named 'tensorflow' Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /nfs_fs/nfs1/pengxiaochang/software/EDTA/util/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 @.***) 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/util/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 check
Hope to get your help, thanks!
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Hello， I installed it using the method you recommended：
Fri Sep 13 19:55:25 HKT 2024 Finish finding LTR candidates. Fri Sep 13 19:55:25 HKT 2024 Start to find SINE candidates. Fri Sep 13 19:56:20 HKT 2024 Warning: The SINE result file has 0 bp! Fri Sep 13 19:56:20 HKT 2024 Start to find LINE candidates. Fri Sep 13 19:56:20 HKT 2024 Identify LINE retrotransposon candidates from scratch. Fri Sep 13 19:58:07 HKT 2024 Warning: The LINE result file has 0 bp! Fri Sep 13 19:58:07 HKT 2024 Start to find TIR candidates. Fri Sep 13 19:58:07 HKT 2024 Identify TIR candidates from scratch. Species: others Traceback (most recent call last): File "/nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 14, in
from bin.main import TIRLearner
File "/nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/TIR-Learner3.0/bin/main.py", line 22, in
from prog_const import *
File "/nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/TIR-Learner3.0/bin/prog_const.py", line 29, in
import tensorflow as tf
ModuleNotFoundError: No module named 'tensorflow'
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /nfs_fs/nfs1/pengxiaochang/software/EDTA/util/rename_tirlearner.pl line 19.
Warning: LOC list genome.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 '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 /nfs_fs/nfs1/pengxiaochang/software/EDTA/util/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
perl /nfs_fs/nfs1/pengxiaochang/software/EDTA/EDTA.pl --genome Hedychium_hic.post.FINAL.fa --species others --overwrite 1 --sensitive 1 --anno 1 --threads 20 > test.log Fri Sep 13 20:06:24 HKT 2024 EDTA_raw: Check dependencies, prepare working directories. Fri Sep 13 20:06:41 HKT 2024 Start to find LTR candidates. Fri Sep 13 20:06:41 HKT 2024 Identify LTR retrotransposon candidates from scratch. Fri Sep 13 22:03:32 HKT 2024 Finish finding LTR candidates. Fri Sep 13 22:03:32 HKT 2024 Start to find SINE candidates. Sat Sep 14 00:44:59 HKT 2024 Finish finding SINE candidates. Sat Sep 14 00:44:59 HKT 2024 Start to find LINE candidates. Sat Sep 14 00:44:59 HKT 2024 Identify LINE retrotransposon candidates from scratch. Sun Sep 15 03:14:29 HKT 2024 Finish finding LINE candidates. Sun Sep 15 03:14:29 HKT 2024 Start to find TIR candidates. Sun Sep 15 03:14:29 HKT 2024 Identify TIR candidates from scratch. Species: others Traceback (most recent call last): File "/nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 14, in
from bin.main import TIRLearner
File "/nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/TIR-Learner3.0/bin/main.py", line 22, in
from prog_const import *
File "/nfs_fs/nfs1/pengxiaochang/software/EDTA/bin/TIR-Learner3.0/bin/prog_const.py", line 29, in
import tensorflow as tf
ModuleNotFoundError: No module named 'tensorflow'
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /nfs_fs/nfs1/pengxiaochang/software/EDTA/util/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/util/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 check