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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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LTR_retriever": No such file or directory at /home/ubuntu/deru/EDTA/EDTA_raw.pl line 307. #389

Closed karthickbrlab closed 7 months ago

karthickbrlab commented 9 months ago

KINDLY LOOK INTO THIS ISSUE.

Thursday 21 September 2023 11:23:36 AM IST Dependency checking: All passed!

Thursday 21 September 2023 11:23:58 AM IST Obtain raw TE libraries using various structure-based programs: Thursday 21 September 2023 11:23:58 AM IST EDTA_raw: Check dependencies, prepare working directories.

Thursday 21 September 2023 11:24:01 AM IST Start to find LTR candidates.

Thursday 21 September 2023 11:24:01 AM IST Identify LTR retrotransposon candidates from scratch.

Can't exec "./LTR_retriever": No such file or directory at /home/ubuntu/EDTA/EDTA_raw.pl line 307. awk: fatal: cannot open file `out3_JBAT.FINAL.fa.mod.pass.list' for reading: No such file or directory Warning: LOC list - is empty.

perl rename_LTR_skim.pl target_sequence.fa LTR_retriever.defalse

sh: 1: ./mdust: not found

Error: Error while loading sequence perl filter_gff3.pl file.gff3 file.list > new.gff3

Thursday 21 September 2023 02:53:48 PM IST Warning: The LTR result file has 0 bp!

Thursday 21 September 2023 02:53:48 PM IST Start to find TIR candidates.

Thursday 21 September 2023 02:53:48 PM IST 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 /home/ubuntu/EDTA/util/rename_tirlearner.pl line 19. Warning: LOC list out3_JBAT.FINAL.fa.mod.TIR.ext30.list is empty. sh: 1: ./mdust: not found

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!

Thursday 21 September 2023 02:54:08 PM IST Start to find Helitron candidates.

Thursday 21 September 2023 02:54:08 PM IST Identify Helitron candidates from scratch.

sh: 1: ./mdust: not found

Error: Error while loading sequence perl make_bed_with_intact.pl EDTA.intact.fa > EDTA.intact.bed

Thursday 21 September 2023 10:14:40 PM IST Warning: The Helitron result file has 0 bp!

Thursday 21 September 2023 10:14:40 PM IST Execution of EDTA_raw.pl is finished!

ERROR: Raw LTR results not found in out3_JBAT.FINAL.fa.mod.EDTA.raw/out3_JBAT.FINAL.fa.mod.LTR.raw.fa If you believe the program is working properly, this may be caused by the lack of intact LTRs in your genome. Consider to use the --force 1 parameter to overwrite this check

oushujun commented 9 months ago

Your installation is not proper. Please reinstall and test with the test file.

Shujun

karthickbrlab commented 9 months ago

i tried to install EDTA using conda EDTA.yml

conda env create -f EDTA.yml Collecting package metadata (repodata.json): done Solving environment: \ Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. Examining conflict for cairo xorg-libx11 pthread-stubs libxcb: : 229it [23Examining conflict for libev libcurl libnghttp2: : 230it [23:47, 1.24it/sExamining conflict for edta scikit-learn: : 231it [23:47, 1.24it/s] Examining conflict for threadpoolctl edta scikit-learn: : 232it [23:47, 1Examining conflict for edta joblib scikit-learn: : 233it [23:48, 1.24it/sExamining conflict for edta joblib scikit-learn: : 234it [23:48, 2.28it/sExamining conflict for edta biopython tesorter: : 234it [23:49, 2.28it/s]Examining conflict for perl-xml-parser perl-xml-simple perl-xml-sax-expat:Examining conflict for perl-compress-raw-bzip2 perl-io-compress perl-archiExamining conflict for edta genometools-genometools repeatmodeler: : 237itExamining conflict for edta repeatmodeler tesorter: : 238it [23:50, 1.86iExamining conflict for edta repeatmodeler tesorter: : 239it [23:50, 2.41iExamining conflict for rmblast tesorter edta repeatmasker gnutls repeatmodExamining conflict for edta repeatmasker tesorter: : 240it [23:51, 2.41itExamining conflict for edta repeatmasker tesorter: : 241it [23:51, 2.00itExamining conflict for edta drmaa tesorter: : 241it [23:53, 2.00it/s] Examining conflict for rmblast tesorter edta nettle repeatmasker gnutls reExamining conflict for rmblast tesorter edta nettle repeatmasker gnutls reExamining conflict for edta regex: : 245it [24:00, 1.41s/it] Examining conflict for perl-business-isbn-data perl-business-isbn perl-uriExamining conflict for perl-business-isbn-data perl-business-isbn perl-uriExamining conflict for edta genericrepeatfinder: : 248it [24:01, 1.06s/itExamining conflict for edta repeatmodeler ltr_retriever genericrepeatfindeExamining conflict for cd-hit edta ltr_retriever repeatmodeler genericrepeExamining conflict for cd-hit edta ltr_retriever repeatmodeler genericrepeExamining conflict for edta mafft repeatmodeler: : 251it [24:03, 1.35it/sExamining conflict for edta mafft repeatmodeler: : 252it [24:03, 1.23it/sExamining conflict for wheel python pip: : 252it [24:05, 1.23it/s] Examining conflict for edta ltr_retriever repeatmodeler: : 253it [24:05, Examining conflict for edta repeatmasker ltr_retriever repeatmodeler: : 25Examining conflict for edta repeatmasker ltr_retriever repeatmodeler: : 25Examining conflict for ltr_retriever perl-text-soundex edta repeatmasker rExamining conflict for ltr_retriever perl-text-soundex edta repeatmasker rExamining conflict for ltr_retriever rmblast edta repeatmasker repeatmodelExamining conflict for scipy numpy: : 257it [24:08, 1.20it/s] Examining conflict for edta perl-gd libgd openjdk: : 260it [24:10, 1.13itExamining conflict for edta perl-gd libgd openjdk: : 261it [24:10, 1.32itExamining conflict for muscle edta: : 261it [24:12, 1.32it/s] Examining conflict for edta repeatmodeler recon: : 262it [24:12, 1.17it/sExamining conflict for edta glob2: : 263it [24:13, 1.17it/s] failed

oushujun commented 8 months ago

Hi,

Sorry for the delayed response. You need to add two channels -c bioconda -c conda-forge. Previously it was not required but somehow you need to specify these now.

Best, Shujun

karthickbrlab commented 7 months ago

Hi Shujun

Can you please explain how to add those channels. I have tried using conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge conda config --set channel_priority strict

Im getting Warning: 'bioconda' already in 'channels' list, moving to the top Warning: 'conda-forge' already in 'channels' list, moving to the top

oushujun commented 7 months ago

Adding these channels should allow you to install EDTA. If not, you can manually specify these channels using -c while installing EDTA.

Shujun

On Thu, Nov 9, 2023 at 11:57 PM kbsivakumar @.***> wrote:

Hi Shujun

Can you please explain how to add those channels. I have tried using conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge conda config --set channel_priority strict

Im getting Warning: 'bioconda' already in 'channels' list, moving to the top Warning: 'conda-forge' already in 'channels' list, moving to the top

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/389#issuecomment-1805087424, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NCZ3GBOVOOMHNSDMQLYDWXZ7AVCNFSM6AAAAAA5DAVUWGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBVGA4DONBSGQ . You are receiving this because you commented.Message ID: @.***>

karthickbrlab commented 7 months ago

Dear shujun.

Issue was with conda channel priority. I changed it to flexible and now it is working well. Im closing this thread.

Thank you for your support.