I am trying to run a nextflow workflow works great on my EC2 instance, but when I try and run it on AWS batch, I get the error regarding awscli not being able to find the libz library. /usr/local/aws-cli/v2/current/bin/aws: error while loading shared libraries: libz.so.1: cannot open shared object …

Hi @Amit_Indap , sorry we missed your question! Were you able to get this working or do you still need help?

Well, not really because I just removed the tabix from my pipeline because it was blocking me and I couldn’t figure it out. Not sure awscli or something else.

[image] Libz.so missing for AWS CLI in AWS batch tasks Ask for help As a closure for this - we did some analysis by using ldd and it seems the aws v2 CLI does not locate the libz.so.1 that is distributed with its binary. And on a (slim) docker image with no exi…

Awscli can't find libz share object file when running nextflow workflow on AWS Batch

Ask for help

emiller (Edmund Miller) October 13, 2025, 4:10pm 4

This might be the answer!

Topic		Replies	Views
Libz.so missing for AWS CLI in AWS batch tasks Ask for help nextflow , aws	3	176	March 18, 2025
Nf- core/sarek on aws batch error Ask for help nextflow , aws	1	171	April 15, 2025
Aws command not found error Ask for help aws	1	142	October 21, 2024
Nextflow pipeline fails on AWS because it can't find executable in Docker container Ask for help nextflow , aws	8	408	August 30, 2024
How to run nf-core rnaseq pipeline on AWS Ask for help	1	612	June 3, 2024

Awscli can't find libz share object file when running nextflow workflow on AWS Batch

Related topics