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usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
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Download reads from NCBI SRA fails #90

Closed kjetilkl closed 1 year ago

kjetilkl commented 1 year ago

The tool "Faster Download and Extract Reads in FASTQ format from NCBI SRA" (and possibly the two other tools in the SRA Tools suite also) fails with the error:

ls: *.fastq: No such file or directory

Output to STDOUT includes the following

Failed to call external services.
Prefetch attempt 1 of 3 exited with code 1
Failed to call external services.
Prefetch attempt 2 of 3 exited with code 1
Failed to call external services.
Prefetch attempt 3 of 3 exited with code 1

There are some notes in the accompanying README.rst file for this tool repository,

kjetilkl commented 1 year ago

The tool has been run 85 times since 2020 (in six different versions) and has never worked.

The cause of the problem was that Singularity was not able to mount the /etc/resolv.conf file from the host inside the container. This file defines how the system uses DNS to resolve host names and IP addresses. Since it was missing, the tool was not able to connect to the NCBI server.

I suspect that the containers - which were automatically built on our system from Conda packages - were missing a required bind point for this configuration file (ref). The problem was fixed by replacing the existing container image with a functional image downloaded from http://datacache.galaxyproject.org/singularity/m/u/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a%3A5ba01bc7e5b4a6b4b710393faa4156d843145afb-0.