# Nf- core/sarek on aws batch error

**URL:** <https://community.seqera.io/t/nf-core-sarek-on-aws-batch-error/2049>\
**Category:** Ask for help\
**Tags:** nextflow, aws\
**Created:** [April 4, 2025, 12:04pm UTC](https://community.seqera.io/t/nf-core-sarek-on-aws-batch-error/2049 "2025-04-04T12:04:40Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![Che\_Martin](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/che_martin/32/1727_2.png) [@Che\_Martin](https://community.seqera.io/u/Che_Martin)\
**Post date:** [April 4, 2025, 12:04pm UTC](https://community.seqera.io/t/nf-core-sarek-on-aws-batch-error/2049/1 "2025-04-04T12:04:40Z")

</div>

Hello all I am a Genomics scientist new to Nextflow. I am trying to run the nf-core/sarek pipeline on an aws batch setup. I run the following command " nextflow run nf-core/sarek -profile awsbatch --awsqueue nf-var-queue --awsregion us-west-1 --input s3://my-bucket/input.csv --outdir s3://my-bucket/output --awscli /usr/bin/aws" and get the error below. I also looked at the AWS logs and the indicated that they could not find aws in a dependent container. See AWS log below also. Any ideas on how to solve?

```auto
[nf-core/sarek] Pipeline completed with errors
ERROR ~ Error executing process > 'NFCORE_SAREK:sarek:FASTP (Tumor1-1)'

Caused by:
  Task failed to start - CannotStartContainerError: Error response from daemon: failed to create task for container: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: error during container init: exec: "/usr/local/env-ex

Command executed:

  [! -f Tumor1-1_1.fastq.gz] && ln -sf ERR3239286_1.fastq.gz Tumor1-1_1.fastq.gz
  [! -f Tumor1-1_2.fastq.gz] && ln -sf ERR3239286_2.fastq.gz Tumor1-1_2.fastq.gz
```

**AWS LOG**

```auto
@entity.Attributes.AWS.ServiceNameSource
ServerIamRole
@entity.Attributes.EC2.InstanceId
i-0d142dc187057eeb8
@entity.Attributes.PlatformType
AWS::EC2
@entity.KeyAttributes.Environment
ec2:default
@entity.KeyAttributes.Name
AWSBatchInstanceRole
@entity.KeyAttributes.Type
Service
@ingestionTime
1743716144388
@log
530856436170:/aws/batch/job
@logStream
nf-quay-io-biocontainers-gawk-5-1-0/default/3c43f62a100f47b4b0e245021c94324d
@message
bash: line 1: /usr/bin/aws: No such file or directory
@timestamp
1743716144275
```

---

<div class="post-metadata">

**Author:** ![maxulysse](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/maxulysse/32/94_2.png) [@maxulysse](https://community.seqera.io/u/maxulysse)\
**Post date:** [April 15, 2025, 6:15am UTC](https://community.seqera.io/t/nf-core-sarek-on-aws-batch-error/2049/2 "2025-04-15T06:15:54Z")

</div>

Using a custom AMI solved the issue.

> **[Amazon Web Services — Nextflow documentation](https://www.nextflow.io/docs/latest/aws.html#custom-ami)**

cf the slack conversation [Slack](https://nfcore.slack.com/archives/CE6SDBX2A/p1743716389264549?thread_ts=1743716389.264549&cid=CE6SDBX2A)

---

<div class="post-metadata">

**Author:** ![system](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/system/32/2402_2.png) [@system](https://community.seqera.io/u/system)\
**Post date:** [April 22, 2025, 6:16am UTC](https://community.seqera.io/t/nf-core-sarek-on-aws-batch-error/2049/3 "2025-04-22T06:16:21Z")

</div>

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.