Can't download database from zenodo #5789

Dasor · 2025-02-13T17:19:39Z

Dasor
Feb 13, 2025

Bug report

Expected behavior and actual behavior

When running the command:

./nextflow run nf-core/ampliseq -r 2.11.0  \
    -profile docker \
    --input samplesheet.csv \
    --skip_cutadapt \
    --outdir 01_nf-ampliseq_bacterias \
    --illumina_novaseq false \
    --FW_primer CCTACGGGNGGCWGCAG \
    --RV_primer GACTACHVGGGTATCTAATCC \
    --trunclenf 280 --trunclenr 235 \
    --dada_ref_taxonomy "silva=138"

As it tries to download silva138 I get the following error:

 Unable to stage foreign file: https://zenodo.org/record/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz (try 1 of 3) -- Cause: Unable to access path: https://zenodo.org/record/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz

Steps to reproduce the problem

Just run the above code with a valid samplesheet

Program output

The full error is:

WARN: Unable to stage foreign file: https://zenodo.org/record/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz (try 1 of 3) -- Cause: Unable to access path: htt
ps://zenodo.org/record/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz
WARN: Unable to stage foreign file: https://zenodo.org/record/4587955/files/silva_species_assignment_v138.1.fa.gz (try 1 of 3) -- Cause: Unable to access path: https://
zenodo.org/record/4587955/files/silva_species_assignment_v138.1.fa.gz
WARN: Unable to stage foreign file: https://zenodo.org/record/4587955/files/silva_species_assignment_v138.1.fa.gz (try 2 of 3) -- Cause: Unable to access path: https://
zenodo.org/record/4587955/files/silva_species_assignment_v138.1.fa.gz
WARN: Unable to stage foreign file: https://zenodo.org/record/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz (try 2 of 3) -- Cause: Unable to access path: htt
ps://zenodo.org/record/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz
WARN: Unable to stage foreign file: https://zenodo.org/record/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz (try 3 of 3) -- Cause: Unable to access path: htt
ps://zenodo.org/record/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz
WARN: Unable to stage foreign file: https://zenodo.org/record/4587955/files/silva_species_assignment_v138.1.fa.gz (try 3 of 3) -- Cause: Unable to access path: https://
zenodo.org/record/4587955/files/silva_species_assignment_v138.1.fa.gz
ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY'

Caused by:
  Can't stage file https://zenodo.org/record/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz -- reason: Unable to access path: https://zenodo.org/record/458795
5/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz



Container:
  docker.io/biocontainers/biocontainers:v1.2.0_cv1

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details

Environment

Nextflow version: 24.10.4.5934
Java version: 17.0.10
Operating system: Linux
Bash version: GNU bash, version 4.4.19(1)-release (x86_64-redhat-linux-gnu)

Additional context

I believe the error is caused because nextflow tries to access:

https://zenodo.org/record/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz

And this URL redirects to:

https://zenodo.org/records/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz

As it can be seen by running:

$ curl https://zenodo.org/record/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz
<!doctype html>
<html lang=en>
<title>Redirecting...</title>
<h1>Redirecting...</h1>
<p>You should be redirected automatically to the target URL: <a href="/records/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz">/records/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz</a>. If not, click the link.

Is not a network problem for sure since I can download the file with wget. By the way ¿Is there any way I can run the same thing with the files dowloaded locally with wget?

Thanks in advance for the help.

Clockris · 2025-02-25T16:43:44Z

Clockris
Feb 25, 2025

Hi Dasor,

I had the same problem (for the version 2.12.0), and I could not understand why. As a workaround, I just downloaded the

wget https://zenodo.org/records/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz

and I executed the pipeline adding: the following tags:

--dada_ref_tax_custom PATH-TO-JUST-DOWNLOADED-FILE --skip_dada_addspecies

I hope it can help,

best,

Cristiano

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Dasor Feb 13, 2025

Bug report

Expected behavior and actual behavior

Steps to reproduce the problem

Program output

Environment

Additional context

Replies: 1 comment

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Clockris Feb 25, 2025

Dasor
Feb 13, 2025

Clockris
Feb 25, 2025