Unable to Fetch Some Archives

[Samiah-Kanwar]

Hi @mlin yesterday I cloned updated idseq-workflows but got an error while running the following command: docker build -t idseq-consensus-genome idseq-workflows/consensus-genome

The error is at 12/17 step:

RUN apt-get install -y python3-cffi python3-h5py python3-intervaltree python3-edlib muscle git
 ---> Running in 819cc4b4d14a

Get:41 http://us-west-2.ec2.archive.ubuntu.com/ubuntu focal/universe amd64 python3-h5py amd64 2.10.0-2build2 [873 kB]
Get:42 http://us-west-2.ec2.archive.ubuntu.com/ubuntu focal/main amd64 python3-sortedcontainers all 2.1.0-2 [27.3 kB]
Get:43 http://us-west-2.ec2.archive.ubuntu.com/ubuntu focal/universe amd64 python3-intervaltree all 3.0.2-1.1 [22.4 kB]
Fetched 17.3 MB in 46s (377 kB/s)
E: Failed to fetch http://security.ubuntu.com/ubuntu/pool/main/g/git/git-man_2.25.1-1ubuntu3.1_all.deb  404  Not Found [IP: 34.210.25.51 80]
E: Failed to fetch http://security.ubuntu.com/ubuntu/pool/main/g/git/git_2.25.1-1ubuntu3.1_amd64.deb  404  Not Found [IP: 34.210.25.51 80]
E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?
The command '/bin/sh -c apt-get install -y python3-cffi python3-h5py python3-intervaltree python3-edlib muscle git' returned a non-zero code: 100

My workstation is fully updated and upgraded, I retried after installing the packages manually but still got the same error. I have attached the detailed error file.

My Workstation's Specs are:

OS Name: Ubuntu 21.04
OS Type: 64-bit

Thank you in Advance.

Ideseq_error_Samiah.txt

[rzlim08]

Hi @Samiah-Kanwar, could you try running with

docker build --no-cache -t idseq-consensus-genome idseq-workflows/consensus-genome. This will rebuild the image from scratch.

I think sometimes docker's caching system can cause discrepancies in apt.

Thanks, Ryan

[Samiah-Kanwar]

Thank you very much @rzlim08 it worked.