assess_specific_genes is taking days

[Malabady]

assess_specific_genes is taking days

[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,

[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

[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]

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