Error executing process > bowtie indices... mirBase issue?

[nf-core]

Error executing process > bowtie indices... mirBase issue?

[Shellfishgene]

Changing the download links in the smrnaseq nextflow.config from the ftp version to

mature = "https://mirbase.org/ftp/CURRENT/mature.fa.gz"
hairpin = "https://mirbase.org/ftp/CURRENT/hairpin.fa.gz"

works also.

[evchambers]

Hi @hesham123457887, I am also experiencing this issue. Seems to be a problem connecting to mirbase.

[DoctorBioinformatics]

Hi @hesham123457887, I am also experiencing this issue. Seems to be a problem connecting to mirbase.

Yah.. couldn't really find a workaround. Did you mange to fix it?

[lpantano]

through the web page this is working, worst case they change the url and we need to update. you could pass the parameters pointing to the right file if this is the issue. i can check back tomorrow.

[DoctorBioinformatics]

you could pass the parameters pointing to the right file if this is the issue.

Sure, which parameters then? Is it the --fasta one or something else should be joined in the command? thx!

[Shellfishgene]

I also noticed this, from Linux I get connection refused (with wget, curl and via smrnaseq), and Firefox downloads a 0 byte file with the ftp links. The download links on the website are https, not ftp as the pipeline tries, maybe this was changed recently.
The options for pointing to the already downloaded files are --mature and --hairpin.

[DoctorBioinformatics]

The options for pointing to the already downloaded files are --mature and --hairpin.

Perfect... It runs now without the error.. Will see till the end thx!

P.S: For the mature and hairpin fa files, are those mouse, human, or a combined fasta file?
I Couldn't find this info online.. thx

[evchambers]

@Shellfishgene thank you so much for this. Manually downloading the files and passing --hairpin and --mature has bypassed the problem.

@hesham123457887 I believe they are combined fasta files.

[apeltzer]

This should be addressed in the current dev branch now - so you may just run that version for now -r dev to get around the issue 👍🏻

Release coming soon ™️ I suppose, but when looking at the current dev branch it looks like things should work for you when directly using the dev branch.

Please re-open if this is not the case and/or open a new issue then 👍🏻