assess_specific_genes is taking days

[Malabady]

Hello,

I am running the last workflow in the pipeline to assess four specific genes. My analysis included 10 plant species. the problem is that, this step is been running for days and it seems to be stuck at the KAKS analysis, see the following:

``
executor > local (6)
[3d/1f0900] process > DOWNLOAD_GENE_AASEQ [100%] 1 of 1 ✔
[db/177126] process > IDENTIFY_GENES_FROM_ORTHOGROUPS [100%] 1 of 1 ✔
[53/7659f6] process > GENE_EXPANSION_CONTRACTION [100%] 1 of 1 ✔
[ad/25dfde] process > EXTRACT_GENE_CDS [100%] 1 of 1 ✔
[14/f4c9be] process > ALIGN_GENE_CDS [100%] 1 of 1 ✔
[91/6cddca] process > KAKS [ 0%] 0 of 1

``
Is this normal?

[jacquelinemattos]

Hi,
I'm also having some issues in this step. Apparently it's not being able to download the fasta file from NCBI.

@Malabady I see yours passed through this step.
Could you please share how you formatted your "genes.txt" please?

Thanks!

[Malabady]

Hi @jacquelinemattos
Here is my gene.txt file:

GSTU13,Arabidopsis_thaliana,https://www.uniprot.org/uniprotkb/Q9FUS6.fasta
Q3ECW8,Arabidopsis_thaliana,https://www.uniprot.org/uniprotkb/Q3ECW8.fasta
A0A1L7NZV0,Sarracenia_purpurea,https://www.uniprot.org/uniprotkb/A0A1L7NZV0.fasta
A0A1L7NZV4,Sarracenia_purpurea,https://www.uniprot.org/uniprotkb/A0A1L7NZV4.fasta
A0A1L7NZU7,Sarracenia_purpurea,https://www.uniprot.org/uniprotkb/A0A1L7NZU7.fasta

if you are using NCBI links, test the links first with wget.
Good luck.

[jacquelinemattos]

Hi @Malabady

Thanks for the reply and suggestion.
You're right, I tried with wget and the link is not working, for some reason. But when I put it on the web browser it works normally.

This is my genes.txt file:
AGL12,Arabidopsis_thaliana,https://www.ncbi.nlm.nih.gov/nuccore/U20193.1?report=fasta ANR1,Citrus_trifoliata,https://www.ncbi.nlm.nih.gov/nuccore/OP009587.1?report=fasta

Do you have any suggestions?
Thanks!!

[Malabady]

Hi @jacquelinemattos

Your NCBI links are pointing to the HTML report page, not the plain fasta file. so, the workflow is not able to access the sequencing.
I suggest using the uniport database, here is your two genes

https://www.uniprot.org/uniprotkb/Q38841.fasta
https://www.uniprot.org/uniprotkb/Q9SI38.fasta

(please download them with wget to ensure they are the right genes)

Also, I noticed that you're pointing to nucleotide sequences, not protein sequences. I think the tool is expecting protein sequences (please double check).

Cheers,

[Malabady]

sorry, the link to the citrus gene is: https://rest.uniprot.org/uniparc/UPI0003D74F46.fasta

[jacquelinemattos]

Hi @Malabady

Thanks so much for your help. I'm gonna try to use these uniprot links now - they worked using the wget, so let's hope it also works within the pipeline. I'll check if needs to be protein instead of nucleotides.

Thank you very much!
Cheers