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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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No annotation and orthology output #255

Closed Ruiqi-CUB closed 3 years ago

Ruiqi-CUB commented 3 years ago

Hello! I am trying to use eggnog mapper to annotate my transcriptome data but the output annotation and orthology files are empty (only have default output, column names, etc.). I tried the following runs with the same command but just different input fasta file. The results are shown on the table below. It seems that my local eggnog mapper is installed correctly and the genes in the file can be annotated. But for some reason it did not return any results. There are about 0.1M sequences in my transcriptome file.

Run Input Fasta Method Results
1 trinity.fna local eggnog mapper empty outputs without error message
2 trinity.fna online success
3 tests/fixtures/test_queries.fa local eggnog mapper success

The local tggnog mapper was installed from wget, version 2.01b, by 

wget https://github.com/eggnogdb/eggnog-mapper/archive/2.0.1b.tar.gz
tar -xzf 2.0.1b.tar.gz
python2.7 download_eggnog_data.py

Here is the command I run locally:

python2.7 ./eggnog-mapper-2.0.1b/emapper.py -i clean_unique_host_Fscruposum.fna \
--output clean_unique_host_Fscruposum_NOG \
-m diamond

This is the messgae I got above the citation information. From Run 1 image

From Run 3 image

Cantalapiedra commented 3 years ago

Hello @Ruiqi-CUB ,

what kind of data are trinity.fna? Are those transcripts? CDS?

The version of eggnog-mapper you are using accepts as input either CDS or proteins.

Carlos

Ruiqi-CUB commented 3 years ago

They are cds, predicted by Transdecoder. Should I try a different version? They can be anotated online.

On Mon, Dec 7, 2020 at 2:54 AM Carlos P Cantalapiedra < notifications@github.com> wrote:

Hello @Ruiqi-CUB https://github.com/Ruiqi-CUB ,

what kind of data are trinity.fna? Are those transcripts? CDS?

The version of eggnog-mapper you are using accepts as input either CDS or proteins.

Carlos

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/eggnogdb/eggnog-mapper/issues/255#issuecomment-739807259, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALEILITRNIHTP2P44HGOC5LSTSQ5BANCNFSM4UNZ2DMQ .

-- Ruiqi Li PhD Student Dept. of Ecology and Evolutionary Biology University of Colorado Boulder pronouns: he/him/his

Cantalapiedra commented 3 years ago

could you send me a sample of your sequences please?

Ruiqi-CUB commented 3 years ago

Here are 1 thousand sequences from the total 1000 thousand sequences. Please let me know if you want more sequences for testing. Thank you so much

Best Ruiqi

On Mon, Dec 7, 2020 at 4:22 PM Carlos P Cantalapiedra < notifications@github.com> wrote:

could you send me a sample of your sequences please?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/eggnogdb/eggnog-mapper/issues/255#issuecomment-740241448, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALEILIWJ2GEQ2USA23U43M3STVPSRANCNFSM4UNZ2DMQ .

-- Ruiqi Li PhD Student Dept. of Ecology and Evolutionary Biology University of Colorado Boulder pronouns: he/him/his

Cantalapiedra commented 3 years ago

Hi @Ruiqi-CUB ,

where are the sequences?

Ruiqi-CUB commented 3 years ago

I attached it to the email when I replied but it seems that the Github did not show it. I just sent it to your gmail shown on your profile.

On Wed, Dec 9, 2020 at 8:17 AM Carlos P Cantalapiedra < notifications@github.com> wrote:

Hi @Ruiqi-CUB https://github.com/Ruiqi-CUB ,

where are the sequences?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/eggnogdb/eggnog-mapper/issues/255#issuecomment-741838037, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALEILITKQQSRJQWTBT4EA2DST6IJZANCNFSM4UNZ2DMQ .

-- Ruiqi Li PhD Student Dept. of Ecology and Evolutionary Biology University of Colorado Boulder pronouns: he/him/his

Cantalapiedra commented 3 years ago

Hi @Ruiqi-CUB ,

I tested your data with the version under the "refactor" branch, and I got annotations. The command line was:

./emapper.py -m diamond --output_dir ../ruiqi/ --itype CDS -o test --cpu 8 -i ../ruiqi/test_emapper.fna

Next, I will try with the other emapper version. I will report back...

Carlos

Cantalapiedra commented 3 years ago

I am running 2.0.1b and I realized that maybe you were using "diamond blastp", instead of "diamond blastx", and that would be the reason why you don't get any result. You could try adding "--translate" to your command (which is the equivalent to "--itype CDS" in the "refactor" version).

Ruiqi-CUB commented 3 years ago

Thanks! I did not specify --itype CDS in my command. Would that be an issue?

On Thu, Dec 10, 2020 at 1:03 PM Carlos P Cantalapiedra < notifications@github.com> wrote:

Hi @Ruiqi-CUB https://github.com/Ruiqi-CUB ,

I tested your data with the version under the "refactor" branch, and I got annotations. The command line was:

./emapper.py -m diamond --output_dir ../ruiqi/ --itype CDS -o test --cpu 8 -i ../ruiqi/test_emapper.fna

Next, I will try with the other emapper version. I will report back...

Carlos

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/eggnogdb/eggnog-mapper/issues/255#issuecomment-742764056, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALEILIUEZ3RVPYHSTIMBURTSUESPTANCNFSM4UNZ2DMQ .

-- Ruiqi Li PhD Student Dept. of Ecology and Evolutionary Biology University of Colorado Boulder pronouns: he/him/his

Cantalapiedra commented 3 years ago

Hi,

I did test with:

./emapper.py -m diamond --output_dir ../ruiqi/2.0.1b/ --translate -o test --cpu 8 -i ../ruiqi/test_emapper.fna

and I got annotations. So yes, I believe you should specify "--translate" (in version 2.0.1b, or "--itype CDS" in "refactor" version) when annotating CDS (instead of proteins).

Sorry for the delay answering. I hope it is of help!

Best, Carlos

Ruiqi-CUB commented 3 years ago

I really appreciate your help! By the way, is there any difference if I run it locally or online?

On Thu, Dec 10, 2020 at 1:49 PM Carlos P Cantalapiedra < notifications@github.com> wrote:

Hi,

I did test with:

./emapper.py -m diamond --output_dir ../ruiqi/2.0.1b/ --translate -o test --cpu 8 -i ../ruiqi/test_emapper.fna

and I got annotations. So yes, I believe you should specify "--translate" (in version 2.0.1b, or "--itype CDS" in "refactor" version) when annotating CDS (instead of proteins).

Sorry for the delay answering. I hope it is of help!

Best, Carlos

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/eggnogdb/eggnog-mapper/issues/255#issuecomment-742790218, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALEILIQ37JPEATZB7ARBXNTSUEX7BANCNFSM4UNZ2DMQ .

-- Ruiqi Li PhD Student Dept. of Ecology and Evolutionary Biology University of Colorado Boulder pronouns: he/him/his

Cantalapiedra commented 3 years ago

I really appreciate your help!

Glad to be of help.

By the way, is there any difference if I run it locally or online?

There should be no much difference running version 2.0.1b with the online version. However, the "refactor" version is rather different, since the output fields change (some fields removed, some fields added, some fields include more info, specially tax names).

… On Thu, Dec 10, 2020 at 1:49 PM Carlos P Cantalapiedra < @.**> wrote: Hi, I did test with: ./emapper.py -m diamond --output_dir ../ruiqi/2.0.1b/ --translate* -o test --cpu 8 -i ../ruiqi/test_emapper.fna and I got annotations. So yes, I believe you should specify "--translate" (in version 2.0.1b, or "--itype CDS" in "refactor" version) when annotating CDS (instead of proteins). Sorry for the delay answering. I hope it is of help! Best, Carlos — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#255 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALEILIQ37JPEATZB7ARBXNTSUEX7BANCNFSM4UNZ2DMQ . -- Ruiqi Li PhD Student Dept. of Ecology and Evolutionary Biology University of Colorado Boulder pronouns: he/him/his

Cantalapiedra commented 3 years ago

Please, re-open or re-issue if needed.

Best, Carlos