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benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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Error "Can't stage file https://files.plutof.ut.ee:" Download of DADA2 ITS fungi-all fail #1987

Open himamura2 opened 3 months ago

himamura2 commented 3 months ago

Hello, I am using NFCORE_AMPLISEQ https://github.com/nf-core/ampliseq/tree/2.10.0, and it uses DADA2. I already posted this issue to https://github.com/nf-core/ampliseq/issues/764 and they metioned that this is the file issue that DADA2 team may be able to resolve.

I am getting this error.

ITS='unite-fungi'
 "  task: name=NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY; work-dir=null
  error [nextflow.exception.ProcessStageException]: Can't stage file 
https://files.plutof.ut.ee/public/orig/1E/25/1E25CA4CC30A31C2E2B8CB2C89824C83D080A7F5A62E6263A0E95B37C6628067.tgz -- reason: Unable to access path: https://files.plutof.ut.ee/public/orig/1E/25/1E25CA4CC30A31C2E2B8CB2C89824C83D080A7F5A62E6263A0E95B37C6628067.tgz
Jul-22 10:29:23.571 [Actor Thread 36] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY'

Caused by:
  Can't stage file https://files.plutof.ut.ee/public/orig/1E/25/1E25CA4CC30A31C2E2B8CB2C89824C83D080A7F5A62E6263A0E95B37C6628067.tgz -- reason: Unable to access path: https://files.plutof.ut.ee/public/orig/1E/25/1E25CA4CC30A31C2E2B8CB2C89824C83D080A7F5A62E6263A0E95B37C6628067.tgz
 "

I contacted "plutof.ut.ee team" about the error and they said:

plutof.ut.ee team wrote I think you have to ask for new URL-s for these files. Last week we closed our legacy file system. I think your files were part of it. In our new file repository solution, you can have more control withe the naming of the files. Sorry for the trouble. All the best, Allan & PlutoF team

So if this is indeed the issue DADA2 team can resolve, could you update the files on plutof.ut.ee?? I attached the log file of ampliseq which uses DADA2. ITS_nextflow.log

best, Hideo

benjjneb commented 3 months ago

The UNITE reference files you are trying to download are managed by UNITE and they (or their partners PlutoF) handle the hosting. We have no influence over that. Given their response, the solution for your issue is to update your download link to their new repository path.

delightsofdecay commented 3 months ago

I'm also having this same issue. Have you found a solution?

JulianaFeliz commented 1 day ago

I managed to solve this problem by setting the link of unite, but it seems like the output its not been generated or recognized by the other programs (as DADA2... etc) . Furthermore, I'm having trouble with the params, and maybe this why the whole process its not working... image

This is how I fix the unite problem ``script: def root_url = "https://s3.hpc.ut.ee/plutof-public/original" if (params.db_release == 'fungi') { url_base = "${root_url}/1E/66" file = "b4d764af-3ec2-46bc-86d3-882df59632b5.gz" """ wget -qO- $url_base/$file | tar xz iconv -f utf-8 -t ascii sh_general_release/.fasta \

unite_fungi.fasta rm -rf sh_general_release* """ } else { url_base = "${root_url}/BF/49" file = "909ba708-b58a-4b81-a17d-7c79f6e4b2a4.gz" """ wget -qO- $url_base/$file \ | gunzip \ | iconv -f utf-8 -t ascii \ unite_all_eukaryotes.fasta rm -f $file """ } } ``

I'm also having this same issue. Have you found a solution?