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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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GO Enrichment failed in F. COMPARE #458

Closed vcastroagudin closed 3 years ago

vcastroagudin commented 4 years ago

Hello,

I run funannotate compare and came up with no results in the GO enrichment tab. I found this message in the log file; " GO terms not found in go.obo " and the go-enrichment file is empty but the go_term file has the files with the data.

Any idea how can I solve this problem?

Thanks in advance.

Vanina

nextgenusfs commented 4 years ago

GO terms are pulled from InterProScan results -- did every genome have interpro/GO annotations? And you have installed go.obo I assume? Does this happen in funannotate test -t compare?

$ funannotate database

Funannotate Databases currently installed:

  Database          Type        Version      Date         Num_Records   Md5checksum                     
  pfam              hmmer3      33.1         2020-04            18259   228db640818af54066a1c23404a3ba38
  gene2product      text        1.62         2020-05-18         33289   04026bbca965378b2d7682c141a839f7
  interpro          xml         80.0         2020-06-18         37471   f8969fc149009016774ba1a71525152b
  dbCAN             hmmer3      8.0          2019-08-08           641   04696dfba1c3bb82ff9b72cfbb3e4a65
  busco_outgroups   outgroups   1.0          2020-06-22             7   6795b1d4545850a4226829c7ae8ef058
  merops            diamond     12.0         2017-10-04          5009   a6dd76907896708f3ca5335f58560356
  mibig             diamond     1.4          2020-06-22         31023   118f2c11edde36c81bdea030a0228492
  uniprot           diamond     2020_03      2020-06-17        562755   a4c8f55dab78451be23a3820fa2aed0d
  go                text        2020-06-01   2020-06-01         47358   e5a9693191fea3019ce5f00dd1da4ae2
  repeats           diamond     1.0          2020-06-22         11950   4e8cafc3eea47ec7ba505bb1e3465d21

To update a database type:
    funannotate setup -i DBNAME -d /usr/local/share/funannotate --force

To see install BUSCO outgroups type:
    funannotate database --show-outgroups

To see BUSCO tree type:
    funannotate database --show-buscos
vcastroagudin commented 4 years ago

I did run Interproscan with the genomes, not sure about the go.obo file. WHat does it do?

On Mon, Jul 27, 2020 at 12:31 PM Jon Palmer notifications@github.com wrote:

GO terms are pulled from InterProScan results -- did every genome have interpro/GO annotations? And you have installed go.obo I assume?

$ funannotate database

Funannotate Databases currently installed:

Database Type Version Date Num_Records Md5checksum pfam hmmer3 33.1 2020-04 18259 228db640818af54066a1c23404a3ba38 gene2product text 1.62 2020-05-18 33289 04026bbca965378b2d7682c141a839f7 interpro xml 80.0 2020-06-18 37471 f8969fc149009016774ba1a71525152b dbCAN hmmer3 8.0 2019-08-08 641 04696dfba1c3bb82ff9b72cfbb3e4a65 busco_outgroups outgroups 1.0 2020-06-22 7 6795b1d4545850a4226829c7ae8ef058 merops diamond 12.0 2017-10-04 5009 a6dd76907896708f3ca5335f58560356 mibig diamond 1.4 2020-06-22 31023 118f2c11edde36c81bdea030a0228492 uniprot diamond 2020_03 2020-06-17 562755 a4c8f55dab78451be23a3820fa2aed0d go text 2020-06-01 2020-06-01 47358 e5a9693191fea3019ce5f00dd1da4ae2 repeats diamond 1.0 2020-06-22 11950 4e8cafc3eea47ec7ba505bb1e3465d21

To update a database type: funannotate setup -i DBNAME -d /usr/local/share/funannotate --force

To see install BUSCO outgroups type: funannotate database --show-outgroups

To see BUSCO tree type: funannotate database --show-buscos

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/nextgenusfs/funannotate/issues/458#issuecomment-664502668, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALNO35RQXI4OJNPRWFHAXTTR5WTXJANCNFSM4PI3HGQA .

-- Vanina L. Castroagudín, PhD

Postdoctoral Researcher

Mycology & Nematology Genetic Diversity & Biology Laboratory

USDA - ARS

10300 Baltimore Avenue, Bldg 10A, Room 227

Beltsville, MD 20705

Cell: (479) 313-3780

Vanina.Castroagudin@usda.gov vanina.castroagudin@usda.gov

v.castroagudin@gmail.com v.castroagudin@gmail.com

vcastroagudin commented 4 years ago

To do the comparison I only have to provide the gbk files, right? not the entire annotate_results folder? How do I check the InterPro scan info needed for the GO enrichment is included in them?

On Mon, Jul 27, 2020 at 12:31 PM Jon Palmer notifications@github.com wrote:

GO terms are pulled from InterProScan results -- did every genome have interpro/GO annotations? And you have installed go.obo I assume?

$ funannotate database

Funannotate Databases currently installed:

Database Type Version Date Num_Records Md5checksum pfam hmmer3 33.1 2020-04 18259 228db640818af54066a1c23404a3ba38 gene2product text 1.62 2020-05-18 33289 04026bbca965378b2d7682c141a839f7 interpro xml 80.0 2020-06-18 37471 f8969fc149009016774ba1a71525152b dbCAN hmmer3 8.0 2019-08-08 641 04696dfba1c3bb82ff9b72cfbb3e4a65 busco_outgroups outgroups 1.0 2020-06-22 7 6795b1d4545850a4226829c7ae8ef058 merops diamond 12.0 2017-10-04 5009 a6dd76907896708f3ca5335f58560356 mibig diamond 1.4 2020-06-22 31023 118f2c11edde36c81bdea030a0228492 uniprot diamond 2020_03 2020-06-17 562755 a4c8f55dab78451be23a3820fa2aed0d go text 2020-06-01 2020-06-01 47358 e5a9693191fea3019ce5f00dd1da4ae2 repeats diamond 1.0 2020-06-22 11950 4e8cafc3eea47ec7ba505bb1e3465d21

To update a database type: funannotate setup -i DBNAME -d /usr/local/share/funannotate --force

To see install BUSCO outgroups type: funannotate database --show-outgroups

To see BUSCO tree type: funannotate database --show-buscos

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/nextgenusfs/funannotate/issues/458#issuecomment-664502668, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALNO35RQXI4OJNPRWFHAXTTR5WTXJANCNFSM4PI3HGQA .

-- Vanina L. Castroagudín, PhD

Postdoctoral Researcher

Mycology & Nematology Genetic Diversity & Biology Laboratory

USDA - ARS

10300 Baltimore Avenue, Bldg 10A, Room 227

Beltsville, MD 20705

Cell: (479) 313-3780

Vanina.Castroagudin@usda.gov vanina.castroagudin@usda.gov

v.castroagudin@gmail.com v.castroagudin@gmail.com

nextgenusfs commented 4 years ago

The go.obo file should have been installed with funannotate setup -- it is just the ontology association file needed to run the enrichment analysis. I'm making a few updates to the logging that I'll push here in a few minutes to master and you can try that. Yes, the GO terms should be incorporated into the GBK files output by funannotate annotate.

vcastroagudin commented 4 years ago

Thanks

On Mon, Jul 27, 2020 at 1:03 PM Jon Palmer notifications@github.com wrote:

The go.obo file should have been installed with funannotate setup -- it is just the ontology association file needed to run the enrichment analysis. I'm making a few updates to the logging that I'll push here in a few minutes to master and you can try that. Yes, the GO terms should be incorporated into the GBK files output by funannotate annotate.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/nextgenusfs/funannotate/issues/458#issuecomment-664519345, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALNO35WVSKOIQFQYRKLSFMTR5WXN5ANCNFSM4PI3HGQA .

-- Vanina L. Castroagudín, PhD

Postdoctoral Researcher

Mycology & Nematology Genetic Diversity & Biology Laboratory

USDA - ARS

10300 Baltimore Avenue, Bldg 10A, Room 227

Beltsville, MD 20705

Cell: (479) 313-3780

Vanina.Castroagudin@usda.gov vanina.castroagudin@usda.gov

v.castroagudin@gmail.com v.castroagudin@gmail.com

nextgenusfs commented 4 years ago

Okay, you can install updated from master and try to re-run -- there will be a log file in the compare output folder (go_enrichment subfolder). 

python -m pip install git+https://github.com/nextgenusfs/funannotate.git
vcastroagudin commented 4 years ago

Thanks a lot!

On Mon, Jul 27, 2020 at 1:07 PM Jon Palmer notifications@github.com wrote:

Okay, you can install updated from master and try to re-run -- there will be a log file in the compare output folder (go_enrichment subfolder).

python -m pip install git+https://github.com/nextgenusfs/funannotate.git

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/nextgenusfs/funannotate/issues/458#issuecomment-664521691, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALNO35WZXUWZFPC65NCS54DR5WX6RANCNFSM4PI3HGQA .

-- Vanina L. Castroagudín, PhD

Postdoctoral Researcher

Mycology & Nematology Genetic Diversity & Biology Laboratory

USDA - ARS

10300 Baltimore Avenue, Bldg 10A, Room 227

Beltsville, MD 20705

Cell: (479) 313-3780

Vanina.Castroagudin@usda.gov vanina.castroagudin@usda.gov

v.castroagudin@gmail.com v.castroagudin@gmail.com