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eggnogdb / eggnog-mapper

Fast genome-wide functional annotation through orthology assignment
http://eggnog-mapper.embl.de
GNU Affero General Public License v3.0
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error DATABASE and Diamond #218

Closed vcastroagudin closed 4 years ago

vcastroagudin commented 4 years ago

Hello,

I am trying to run EggNOg V1 and got the following error message. I would appreciate any help for fixing it.

emapper-1.0.3

./emapper.py -i Calonectria_pseudonaviculata_CBS139707.proteins.fa --output CT1_EggNog -m diamond

/home/vanina/conda/envs/funannotate/bin/diamond blastp -d /home/vanina/eggnog-mapper/data/eggnog_proteins.dmnd -q /home/vanina/eggnog-mapper/Calonectria_pseudonaviculata_CBS139707.proteins.fa --more-sensitive --threads 2 -e 0.001000 -o /home/vanina/eggnog-mapper/emappertmp_dmdn_DinVKD/ac5d30a0222d4b4c9e5258c507378d08 --top 3 Error: Database was built with a different version of Diamond and is incompatible. Traceback (most recent call last): File "emapper.py", line 1001, in main(args) File "emapper.py", line 216, in main dump_diamond_matches(args.input, seed_orthologs_file, args) File "emapper.py", line 353, in dump_diamond_matches raise e subprocess.CalledProcessError: Command '/home/vanina/conda/envs/funannotate/bin/diamond blastp -d /home/vanina/eggnog-mapper/data/eggnog_proteins.dmnd -q /home/vanina/eggnog-mapper/Calonectria_pseudonaviculata_CBS139707.proteins.fa --more-sensitive --threads 2 -e 0.001000 -o /home/vanina/eggnog-mapper/emappertmp_dmdn_DinVKD/ac5d30a0222d4b4c9e5258c507378d08 --top 3' returned non-zero exit status 1

Thanks,

Vanina

Cantalapiedra commented 4 years ago

Hi Vanina,

is there any reason why you are running version 1.0.3 using "-m diamond"? If not at all, I would encourage you to install version 2.0.1 in conda instead.

Besides that, it seems that the diamond version you are using is not compatible with the diamond database used by eggnog-mapper:

"Error: Database was built with a different version of Diamond and is incompatible."

You could try to install another version of diamond with conda and try the next command until it works.

'/home/vanina/conda/envs/funannotate/bin/diamond blastp -d /home/vanina/eggnog-mapper/data/eggnog_proteins.dmnd -q /home/vanina/eggnog-mapper/Calonectria_pseudonaviculata_CBS139707.proteins.fa --more-sensitive --threads 2 -e 0.001000 -o /home/vanina/eggnog-mapper/emappertmp_dmdn_DinVKD/ac5d30a0222d4b4c9e5258c507378d08 --top 3

I still would recommend you to migrate to version 2.0.1 if using eggnog-mapper from conda.

Thank you.

Best, Carlos

vcastroagudin commented 4 years ago

Hi Carlos,

i can use EggNOg version 2.0.1 because the output format is not compatible with FUNNOTATE and I can not parse them into my genome. I know FUNANNOTATE programmer has contacted the people who wrote EGGNOG but they never fixed the output format. Unfortunately, I have no other option.

Vanina

Cantalapiedra commented 4 years ago

Hi Vanina,

I see. Then, you could try to check the diamond version included with eggnog-mapper 1.0.3, and try to install such diamond version (or closer as possible) into conda. To test which diamond version is installed with 1.0.3 version maybe you can clone such version from this repository, and run bin/diamond --version.

Another option is that you use eggnog-mapper outside conda, downloading the corresponding release from this repository, and then use the output for downstream analyses. Not sure if this is compatible with using FUNNOTATE or not.

Best, Carlos

vcastroagudin commented 4 years ago

Carlos,

do you know which is the difference in the format between the output of the EggNog V1 and V2. Can I transform one into the other with a text editor?

Thanks,

Vanina

On Mon, Jul 13, 2020 at 4:21 PM Carlos P Cantalapiedra < notifications@github.com> wrote:

Hi Vanina,

I see. Then, you could try to check the diamond version included with eggnog-mapper 1.0.3, and try to install such diamond version (or closer as possible) into conda. To test which diamond version is installed with 1.0.3 version maybe you can clone such version from this repository, and run bin/diamond --version.

Another option is that you use eggnog-mapper outside conda, downloading the corresponding release from this repository, and then use the output for downstream analyses. Not sure if this is compatible with using FUNNOTATE or not.

Best, Carlos

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/eggnogdb/eggnog-mapper/issues/218#issuecomment-657770944, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALNO35V76K4OCXYBPV227L3R3NUDDANCNFSM4OYWRUWQ .

-- 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

Cantalapiedra commented 4 years ago

Hi Vanina,

fields in v1:

query_name: query sequence name seed_eggNOG_ortholog: best protein match in eggNOG seed_ortholog_evalue: best protein match (e-value) seed_ortholog_score: best protein match (bit-score) predicted_gene_name: Predicted gene name for query sequences GO_terms: Comma delimited list of predicted Gene Ontology terms KEGG_KO: Comma delimited list of predicted KEGG KOs BiGG_Reactions: Comma delimited list of predicted BiGG metabolic reactions Annotation_tax_scope: The taxonomic scope used to annotate this query sequence Matching_OGs: Comma delimited list of matching eggNOG Orthologous Groups best_OG|evalue|score: Best matching Orthologous Groups (only in HMM mode) COG functional categories: COG functional category inferred from best matching OG eggNOG_HMM_model_annotation: eggNOG functional description inferred from best matching OG

fields in v2:

  1. query_name
  2. seed eggNOG ortholog
  3. seed ortholog evalue
  4. seed ortholog score
  5. Predicted taxonomic group
  6. Predicted protein name
  7. Gene Ontology terms
  8. EC number
  9. KEGG_ko
  10. KEGG_Pathway
  11. KEGG_Module
  12. KEGG_Reaction
  13. KEGG_rclass
  14. BRITE
  15. KEGG_TC
  16. CAZy
  17. BiGG Reaction
  18. tax_scope: eggNOG taxonomic level used for annotation
  19. eggNOG OGs
  20. bestOG (deprecated, use smallest from eggnog OGs)
  21. COG Functional Category
  22. eggNOG free text description

I hope that helps.

Carlos

vcastroagudin commented 4 years ago

Muchisimas gracias Carlos!

On Tue, Jul 14, 2020 at 2:58 AM Carlos P Cantalapiedra < notifications@github.com> wrote:

Hi Vanina,

fields in v1:

query_name: query sequence name seed_eggNOG_ortholog: best protein match in eggNOG seed_ortholog_evalue: best protein match (e-value) seed_ortholog_score: best protein match (bit-score) predicted_gene_name: Predicted gene name for query sequences GO_terms: Comma delimited list of predicted Gene Ontology terms KEGG_KO: Comma delimited list of predicted KEGG KOs BiGG_Reactions: Comma delimited list of predicted BiGG metabolic reactions Annotation_tax_scope: The taxonomic scope used to annotate this query sequence Matching_OGs: Comma delimited list of matching eggNOG Orthologous Groups best_OG|evalue|score: Best matching Orthologous Groups (only in HMM mode) COG functional categories: COG functional category inferred from best matching OG eggNOG_HMM_model_annotation: eggNOG functional description inferred from best matching OG

fields in v2:

  1. query_name
  2. seed eggNOG ortholog
  3. seed ortholog evalue
  4. seed ortholog score
  5. Predicted taxonomic group
  6. Predicted protein name
  7. Gene Ontology terms
  8. EC number
  9. KEGG_ko
  10. KEGG_Pathway
  11. KEGG_Module
  12. KEGG_Reaction
  13. KEGG_rclass
  14. BRITE
  15. KEGG_TC
  16. CAZy
  17. BiGG Reaction
  18. tax_scope: eggNOG taxonomic level used for annotation
  19. eggNOG OGs
  20. bestOG (deprecated, use smallest from eggnog OGs)
  21. COG Functional Category
  22. eggNOG free text description

I hope that helps.

Carlos

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/eggnogdb/eggnog-mapper/issues/218#issuecomment-658006564, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALNO35RM5ISJWFSEDYHD3FLR3P6ZPANCNFSM4OYWRUWQ .

-- 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

Cantalapiedra commented 4 years ago

De nada Vanina :)

Should we close the issue or do we wait just in case you have further questions / problems with this?

vcastroagudin commented 4 years ago

Si, Carlos no hay ningun problema. Tu ayuda ha sido muy valiosa. Infinitamente agradecida.

Vanina

On Tue, Jul 14, 2020 at 4:48 PM Carlos P Cantalapiedra < notifications@github.com> wrote:

De nada Vanina :)

Should we close the issue or do we wait just in case you have further questions / problems with this?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/eggnogdb/eggnog-mapper/issues/218#issuecomment-658405302, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALNO35WCLCL7H42IRRQRHDTR3TAA3ANCNFSM4OYWRUWQ .

-- 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

Cantalapiedra commented 4 years ago

Feliz de leer eso. Si tienes algún problema o duda más no dudes en reabrir este issue o en crear uno nuevo.

Suerte. Carlos