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3. Exercise 1

Move into the exercise 1 directory and execute the script.

cd /workspace/gitpod/troubleshoot/exercise1
nextflow run

Error message

Nextflow stops the workflow execution and reports the failing task when a process execution exits with a non-zero exit status:

ERROR ~ Error executing process > 'SAMTOOLS_INDEX (2)'

Caused by:
  Process `SAMTOOLS_INDEX (2)` terminated with an error exit status (127)

Command executed:

  samtools index 'reads_father.bam'

Command exit status:

Command output:

Command error: line 2: samtools: command not found

Work dir:

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

-- Check '.nextflow.log' file for details

Caused by: A description of the error cause

Command executed: The command executed

Command exit status: The command exit status

Command output: The command standard output, when available

Command error: The command standard error

Work dir: The command work directory


The command error line 2: samtools: command not found suggests that samtools was not available.

Every process in the pipeline contains a container directive with a relevant container image. However, in this case, docker was not enabled and the samtools tooling was not available locally.

Enabling docker in the nextflow.config file will activate the docker containers for each process and resolve this error.

docker.enabled = true