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oushujun
Error in test and installation issue
Hello Dr Ou,
I am raising this issue, because I got an error while I was trying to run the test example.
The error I got is the following: Error: LTR_retriever is not found in the LTR_retriever path ./!
Most probably it is an installation issue and I tried to install EDTA with both conda ways, "Quick installation using conda (Linux64)" and "Other ways to install with conda".
With the first way I did not face any issues, while in the second one I got this:
Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with nexy repodata source. Collecting package metadata (current_repodata.json): done
And after that there is an infinite loading.
Do you have any ideas what is going wrong?
Thank you in advance.
Kind regards,
Elias Primetis
Hi Elias,
Please refer to other similar issues. for example #250.
Best, Shujun
Hi Dr Ou,
After a lot of my own research I managed to install EDTA, but when I try to run the test in order to understand how EDTA works I get the following errors:
########################################################
Extensive de-novo TE Annotator (EDTA) v2.0.1
Shujun Ou ([email protected])
########################################################
Wed 14 Sep 12:07:43 BST 2022 Dependency checking: All passed!
A custom library ../database/rice6.9.5.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 14 Sep 12:07:45 BST 2022 Obtain raw TE libraries using various structure-based programs: Wed 14 Sep 12:07:45 BST 2022 EDTA_raw: Check dependencies, prepare working directories.
Wed 14 Sep 12:07:46 BST 2022 Start to find LTR candidates.
Wed 14 Sep 12:07:46 BST 2022 Identify LTR retrotransposon candidates from scratch.
Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. Wed 14 Sep 12:08:11 BST 2022 Finish finding LTR candidates.
Wed 14 Sep 12:08:11 BST 2022 Start to find TIR candidates.
Wed 14 Sep 12:08:11 BST 2022 Identify TIR candidates from scratch.
Species: others dirname: missing operand Try 'dirname --help' for more information. Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /mnt/RAID/method/EDTA/util/rename_tirlearner.pl line 19. Warning: LOC list genome.fa.mod.TIR.ext30.list is empty.
Error: Error while loading sequenceCan't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3: No such file or directory. Warning: The TIR result file has 0 bp!
Wed 14 Sep 12:08:12 BST 2022 Start to find Helitron candidates.
Wed 14 Sep 12:08:12 BST 2022 Identify Helitron candidates from scratch.
Wed 14 Sep 12:08:36 BST 2022 Finish finding Helitron candidates.
Wed 14 Sep 12:08:36 BST 2022 Execution of EDTA_raw.pl is finished!
ERROR: Raw TIR results not found in genome.fa.mod.EDTA.raw/genome.fa.mod.TIR.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 have checked a lot of similar issues, but nothing worked.
Could you please help me with that?
Kind regards,
Elias
Hi Elias,
The error suggests the installation is still not good. Did you install EDTA on a standalone conda env or shared with other packages? You may try to reinstall in a brandnew env. Also, you may try mamba(https://anaconda.org/conda-forge/mamba) which can resolve environment much quicker than conda.
Best, Shujun
Hello Dr. Ou,
My issue is "ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found" in the TIR learner step. The quick installation using conda (Linux64) was OK. The test run could finish finding LTR candidates but failed in the step of "Identify TIR candidates from scratch" and proceeded to "Identify Helitron candidates" .
I checked the default gblic on CentOS 6.8, it's glibc2.12. However other glibc versions 2.14, 2.15, 2.17 were also installed. I tried to link glibc2.14 using export LD_LIBRARY_PATH or LD_PRELOAD but was not successful. I am not a root user of the system and changing the default gblic will cause more issues such as “core dumped”. Your suggestions will be greatly appreciated!
Best wishes,
Lingtong
Thu Feb 9 11:09:54 CST 2023 Dependency checking: All passed!
A custom library ../database/rice6.9.5.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 Feb 9 11:10:02 CST 2023 Obtain raw TE libraries using various structure-based programs: Thu Feb 9 11:10:02 CST 2023 EDTA_raw: Check dependencies, prepare working directories. Thu Feb 9 11:10:05 CST 2023 Start to find LTR candidates. Thu Feb 9 11:10:05 CST 2023 Identify LTR retrotransposon candidates from scratch. Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. Thu Feb 9 11:10:47 CST 2023 Finish finding LTR candidates.
Thu Feb 9 11:10:47 CST 2023 Start to find TIR candidates.
Thu Feb 9 11:10:47 CST 2023 Identify TIR candidates from scratch.
Species: others
Traceback (most recent call last):
File "/datapool/wangtai/liulingtong/anaconda3/envs/EDTA/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in
The install of TIR-Learner is incomplete. Try different ways to install in conda. Remove this one and install brand new.
Shujun
On Fri, Feb 10, 2023 at 3:58 AM 12oaks1 @.***> wrote:
Hello Dr. Ou,
My issue is "ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found" in the TIR learner step. The quick installation using conda (Linux64) was OK. The test run could finish finding LTR candidates but failed in the step of "Identify TIR candidates from scratch" and proceeded to "Identify Helitron candidates" .
I checked the default gblic on CentOS 6.8, it's glibc2.12. However other glibc versions 2.14, 2.15, 2.17 were also installed. I tried to link glibc2.14 using export LD_LIBRARY_PATH or LD_PRELOAD but was not successful. I am not a root user of the system and changing the default gblic will cause more issues such as “core dumped”. Your suggestions will be greatly appreciated!
Best wishes,
Lingtong
Thu Feb 9 11:09:54 CST 2023 Dependency checking: All passed!
A custom library ../database/rice6.9.5.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 Feb 9 11:10:02 CST 2023 Obtain raw TE libraries using various structure-based programs: Thu Feb 9 11:10:02 CST 2023 EDTA_raw: Check dependencies, prepare working directories. Thu Feb 9 11:10:05 CST 2023 Start to find LTR candidates. Thu Feb 9 11:10:05 CST 2023 Identify LTR retrotransposon candidates from scratch. Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. Thu Feb 9 11:10:47 CST 2023 Finish finding LTR candidates.
Thu Feb 9 11:10:47 CST 2023 Start to find TIR candidates.
Thu Feb 9 11:10:47 CST 2023 Identify TIR candidates from scratch.
Species: others Traceback (most recent call last): File "/datapool/wangtai/liulingtong/anaconda3/envs/EDTA/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in from tensorflow.python.pywrap_tensorflow_internal import * File "/datapool/wangtai/liulingtong/anaconda3/envs/EDTA/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in _pywrap_tensorflow_internal = swig_import_helper() File "/datapool/wangtai/liulingtong/anaconda3/envs/EDTA/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description) File "/datapool/wangtai/liulingtong/anaconda3/envs/EDTA/lib/python3.6/imp.py", line 243, in load_module return load_dynamic(name, filename, file) File "/datapool/wangtai/liulingtong/anaconda3/envs/EDTA/lib/python3.6/imp.py", line 343, in load_dynamic return _load(spec) ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /datapool/wangtai/liulingtong/anaconda3/envs/EDTA/lib/python3.6/lib-dynload/../../libssl.so.1.1)
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Hello Dr. Ou, when I try to run the test I get the following errors:
Tue Mar 21 10:05:56 CST 2023 EDTA_raw: Check dependencies, prepare working directories.
Tue Mar 21 10:06:01 CST 2023 Start to find LTR candidates.
Tue Mar 21 10:06:01 CST 2023 Identify LTR retrotransposon candidates from scratch.
Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty.
Tue Mar 21 10:07:33 CST 2023 Finish finding LTR candidates.
Tue Mar 21 10:07:34 CST 2023 Start to find TIR candidates.
Tue Mar 21 10:07:34 CST 2023 Identify TIR candidates from scratch.
Species: others
Tue Mar 21 10:08:23 CST 2023 Finish finding TIR candidates.
Tue Mar 21 10:08:23 CST 2023 Start to find Helitron candidates.
Tue Mar 21 10:08:23 CST 2023 Identify Helitron candidates from scratch.
Tue Mar 21 10:09:27 CST 2023 Finish finding Helitron candidates.
Tue Mar 21 10:09:27 CST 2023 Execution of EDTA_raw.pl is finished!
Died at /biodata/users/xiaogh/software/anaconda3/envs/EDTA/bin/BuildDatabase line 332.
cat: 'RM_*/consensi.fa': No such file or directory
Could you please help me with that?
Could you please paste the whole report and your command? Thanks!
Shujun
On Mon, Mar 20, 2023 at 10:34 PM sumoii @.***> wrote:
Hello Dr. Ou, when I try to run the test I get the following errors:
Tue Mar 21 10:05:56 CST 2023 EDTA_raw: Check dependencies, prepare working directories. Tue Mar 21 10:06:01 CST 2023 Start to find LTR candidates. Tue Mar 21 10:06:01 CST 2023 Identify LTR retrotransposon candidates from scratch. Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. Tue Mar 21 10:07:33 CST 2023 Finish finding LTR candidates. Tue Mar 21 10:07:34 CST 2023 Start to find TIR candidates. Tue Mar 21 10:07:34 CST 2023 Identify TIR candidates from scratch. Species: others Tue Mar 21 10:08:23 CST 2023 Finish finding TIR candidates. Tue Mar 21 10:08:23 CST 2023 Start to find Helitron candidates. Tue Mar 21 10:08:23 CST 2023 Identify Helitron candidates from scratch. Tue Mar 21 10:09:27 CST 2023 Finish finding Helitron candidates. Tue Mar 21 10:09:27 CST 2023 Execution of EDTA_raw.pl is finished! Died at /biodata/users/xiaogh/software/anaconda3/envs/EDTA/bin/BuildDatabase line 332. cat: 'RM_*/consensi.fa': No such file or directory
Could you please help me with that?
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Hi @oushujun ,
I'm an avid user of EDTA. I've recently installed version 2.1.3 with conda, and I've gotten the two issues reported by @sumoii
1.
Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty.
This may be considered solved after downgrading ltr_retriever from 2.9.4 (I believe) to 2.9.0. Is that correct?
2. This other issue I haven't been able to solve.
cat: 'RM_*/consensi.fa': No such file or directory
RepeatModeler is finished, but no consensi.fa files found.
Here is the command I ran:
perl $EDTA/EDTA.pl --genome $REF --step all --overwrite 0 --sensitive 1 --anno 1 --threads $CORES |& tee $REF.log_edta.txt
I ran it in an A. thaliana genome and this is the top of the output summary:
Repeat Classes
==============
Total Sequences: 126
Total Length: 143725422 bp
Class Count bpMasked %masked
===== ===== ======== =======
LTR -- -- --
Copia 1155 1386483 0.96%
Gypsy 87428 18654076 12.98%
unknown 2142 2868476 2.00%
TIR -- -- --
CACTA 1315 838089 0.58%
Mutator 3401 934735 0.65%
PIF_Harbinger 441 213671 0.15%
Tc1_Mariner 203 113080 0.08%
hAT 763 334602 0.23%
nonTIR -- -- --
helitron 12166 6716155 4.67%
---------------------------------
total interspersed 109014 32059367 22.31%
---------------------------------------------------------
Total 109014 32059367 22.31%
Thing is, I have ran EDTA v1.9.7 on this genome in the past, and this was the top of the result summary:
Repeat Classes
==============
Total Sequences: 126
Total Length: 143725422 bp
Class Count bpMasked %masked
===== ===== ======== =======
LTR -- -- --
Copia 1183 1387803 0.97%
Gypsy 87261 18679441 13.00%
unknown 2606 2916845 2.03%
TIR -- -- --
CACTA 1225 774288 0.54%
Mutator 3580 1095407 0.76%
PIF_Harbinger 463 246049 0.17%
Tc1_Mariner 205 114077 0.08%
hAT 791 369313 0.26%
nonLTR -- -- --
LINE_element 248 255290 0.18%
nonTIR -- -- --
helitron 11629 6503269 4.52%
repeat_region 12757 6810757 4.74%
---------------------------------
total interspersed 121948 39152539 27.24%
---------------------------------------------------------
Total 121948 39152539 27.24%
Thus, it seems I'm missing "nonLTR (LINE element)" and "repeat_region". I would very much appreciate your guidance with solving these issues, so I can run the latest EDTA version and move to the panEDTA step.
Kind regards,
Fernando
- Yes that's fine.
- You may want to check the EDTA.final/RM_* folder and see if RepeatModeler finished properly. If You run up to round-6 and still have 0 consensus, it worked on but just couldn't find repeats
On Fri, Jun 30, 2023 at 11:07 AM Fernando A. Rabanal < @.***> wrote:
Hi @oushujun https://github.com/oushujun ,
I'm an avid user of EDTA. I've recently installed version 2.1.3 with conda, and I've gotten the two issues reported by @sumoii https://github.com/sumoii
1. Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. This may be considered solved after downgrading ltr_retriever from 2.9.4 (I believe) to 2.9.0. Is that correct?
2. This other issue I haven't been able to solve.
cat: 'RM_*/consensi.fa': No such file or directory RepeatModeler is finished, but no consensi.fa files found.
Here is the command I ran: perl $EDTA/EDTA.pl --genome $REF --step all --overwrite 0 --sensitive 1 --anno 1 --threads $CORES |& tee $REF.log_edta.txt I ran it in an A. thaliana genome and this is the top of the output summary:
Repeat Classes
Total Sequences: 126 Total Length: 143725422 bp Class Count bpMasked %masked ===== ===== ======== ======= LTR -- -- -- Copia 1155 1386483 0.96% Gypsy 87428 18654076 12.98% unknown 2142 2868476 2.00% TIR -- -- -- CACTA 1315 838089 0.58% Mutator 3401 934735 0.65% PIF_Harbinger 441 213671 0.15% Tc1_Mariner 203 113080 0.08% hAT 763 334602 0.23% nonTIR -- -- -- helitron 12166 6716155 4.67% --------------------------------- total interspersed 109014 32059367 22.31%
Total 109014 32059367 22.31%
Thing is, I have ran EDTA v1.9.7 on this genome in the past, and this was the top of the result summary:
Repeat Classes
Total Sequences: 126 Total Length: 143725422 bp Class Count bpMasked %masked ===== ===== ======== ======= LTR -- -- -- Copia 1183 1387803 0.97% Gypsy 87261 18679441 13.00% unknown 2606 2916845 2.03% TIR -- -- -- CACTA 1225 774288 0.54% Mutator 3580 1095407 0.76% PIF_Harbinger 463 246049 0.17% Tc1_Mariner 205 114077 0.08% hAT 791 369313 0.26% nonLTR -- -- -- LINE_element 248 255290 0.18% nonTIR -- -- -- helitron 11629 6503269 4.52% repeat_region 12757 6810757 4.74% --------------------------------- total interspersed 121948 39152539 27.24%
Total 121948 39152539 27.24%
Thus, it seems I'm missing "nonLTR (LINE element)" and "repeat_region". I would very much appreciate your guidance with solving these issues, so I can run the latest EDTA version and move to the panEDTA step.
Kind regards,
Fernando
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Thank for the prompt response. EDTA.final/RM_* folder does not exist.
here the content of the directory ls -lt ANGE-B-10.fa.mod.EDTA.final/
-rw-r--r-- 1 frabanal ebio 613900 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.intact.gff3
-rw-r--r-- 1 frabanal ebio 5976124 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.intact.fa
-rw-r--r-- 1 frabanal ebio 56521 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.intact.fa.rename.list
-rw-r--r-- 1 frabanal ebio 2467 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.intact.fa.tbl
-rw-r--r-- 1 frabanal ebio 6087713 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.intact.fa.masked
-rw-r--r-- 1 frabanal ebio 680912 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.intact.fa.out
-rw-r--r-- 1 frabanal ebio 30563935 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.intact.fa.cat
-rw-r--r-- 1 frabanal ebio 2966550 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.TElib.fa
-rw-r--r-- 1 frabanal ebio 3227602 Jun 28 18:34 ANGE-B-10.fa.mod.EDTA.raw.fa
-rw-r--r-- 1 frabanal ebio 3227602 Jun 28 18:34 ANGE-B-10.fa.mod.LTR.TIR.Helitron.others.fa.stg2.clean
-rw-r--r-- 1 frabanal ebio 0 Jun 28 18:34 ANGE-B-10.fa.mod.RM.consensi.fa
-rw-r--r-- 1 frabanal ebio 555 Jun 28 18:34 ANGE-B-10.fa.mod.masked.njs
-rw-r--r-- 1 frabanal ebio 1752 Jun 28 18:34 ANGE-B-10.fa.mod.masked.translation
-rw-r--r-- 1 frabanal ebio 2474 Jun 28 18:34 ANGE-B-10.fa.mod.tbl
-rw-r--r-- 1 frabanal ebio 5096780 Jun 28 18:34 ANGE-B-10.fa.mod.out
lrwxrwxrwx 1 frabanal ebio 19 Jun 28 18:21 ANGE-B-10.fa.mod -> ../ANGE-B-10.fa.mod
-rw-r--r-- 1 frabanal ebio 5969968 Jun 28 18:21 ANGE-B-10.fa.mod.EDTA.intact.fa.raw
-rw-r--r-- 1 frabanal ebio 3227602 Jun 28 18:21 ANGE-B-10.fa.mod.LTR.TIR.Helitron.fa.stg1
I meant the Arabidopsis genome. If you don't have the RM_ folder, it suggests that you didn't run the annotation with the --sensitive 1 parameter.
Shujun
On Fri, Jun 30, 2023 at 4:56 PM Fernando A. Rabanal < @.***> wrote:
Thank for the prompt response. EDTA.final/RM_* folder does not exist. here the content of the directory ls -lt ANGE-B-10.fa.mod.EDTA.final/
-rw-r--r-- 1 frabanal ebio 613900 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.intact.gff3 -rw-r--r-- 1 frabanal ebio 5976124 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.intact.fa -rw-r--r-- 1 frabanal ebio 56521 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.intact.fa.rename.list -rw-r--r-- 1 frabanal ebio 2467 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.intact.fa.tbl -rw-r--r-- 1 frabanal ebio 6087713 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.intact.fa.masked -rw-r--r-- 1 frabanal ebio 680912 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.intact.fa.out -rw-r--r-- 1 frabanal ebio 30563935 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.intact.fa.cat -rw-r--r-- 1 frabanal ebio 2966550 Jun 28 18:35 ANGE-B-10.fa.mod.EDTA.TElib.fa -rw-r--r-- 1 frabanal ebio 3227602 Jun 28 18:34 ANGE-B-10.fa.mod.EDTA.raw.fa -rw-r--r-- 1 frabanal ebio 3227602 Jun 28 18:34 ANGE-B-10.fa.mod.LTR.TIR.Helitron.others.fa.stg2.clean -rw-r--r-- 1 frabanal ebio 0 Jun 28 18:34 ANGE-B-10.fa.mod.RM.consensi.fa -rw-r--r-- 1 frabanal ebio 555 Jun 28 18:34 ANGE-B-10.fa.mod.masked.njs -rw-r--r-- 1 frabanal ebio 1752 Jun 28 18:34 ANGE-B-10.fa.mod.masked.translation -rw-r--r-- 1 frabanal ebio 2474 Jun 28 18:34 ANGE-B-10.fa.mod.tbl -rw-r--r-- 1 frabanal ebio 5096780 Jun 28 18:34 ANGE-B-10.fa.mod.out lrwxrwxrwx 1 frabanal ebio 19 Jun 28 18:21 ANGE-B-10.fa.mod -> ../ANGE-B-10.fa.mod -rw-r--r-- 1 frabanal ebio 5969968 Jun 28 18:21 ANGE-B-10.fa.mod.EDTA.intact.fa.raw -rw-r--r-- 1 frabanal ebio 3227602 Jun 28 18:21 ANGE-B-10.fa.mod.LTR.TIR.Helitron.fa.stg1
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Indeed, that might be the problem: EDTA not detecting that I gave it the "--sensitive 1" parameter.
Below the command I used, same issue for another Arabidopsis genome, and an insect one: EDTA.final/RM_ folder does not exist.
perl $EDTA/EDTA.pl --genome $REF --step all --overwrite 0 --sensitive 1 --anno 1 --threads $CORES |& tee $REF.log_edta.txt
Is there something we can do about it?
Kind regards,
Fernando
Can you test whether RepeatModeler in the EDTA env can run normally abd generate results?
Shujun
On Sat, Jul 1, 2023 at 8:28 AM Fernando A. Rabanal @.***> wrote:
Indeed, that might be the problem: EDTA not detecting that I gave it the "--sensitive 1" parameter.
Below the command I used, same issue for another Arabidopsis genome, and an insect one: EDTA.final/RM_ folder does not exist.
perl $EDTA/EDTA.pl --genome $REF --step all --overwrite 0 --sensitive 1 --anno 1 --threads $CORES |& tee $REF.log_edta.txt
Is there something we can do about it?
Kind regards,
Fernando
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Hi again, Just tested it:
BuildDatabase -name ANGE-B-10 ANGE-B-10.fa
RepeatModeler -database ANGE-B-10 -threads 96 -LTRStruct >& run.out &
It worked well (RM_* was created, there are up to 5 round-* subdirs, and consensi.fa is there). So, I'm guessing "--sensitive 1" is not detected in the EDTA command.
Cheers
Hello @frabanal,
What version of EDTA are you using? Can you update EDTA and try again? Alternatively, you may extract the SINE/LINE sequences from the RepeatModeler result and give them to EDTA via --curatedlib.
Shujun
Hi @oushujun,
Just to update on my issue, which is not anymore. I re-install EDTA, this time with conda env create -f EDTA.yml (version 2.1.3), and everything worked out well: RepeatModeler works as expected.
Before I was installing version 2.1.0 through conda install -c bioconda edta. And that was giving me troubles.
Thanks and sorry for the confusion. Fernando