3. Exercise 1¶
Move into the exercise 1 directory and execute the hello-gatk.nf script.
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:
127
Command output:
(empty)
Command error:
.command.sh: line 2: samtools: command not found
Work dir:
/workspace/gitpod/troubleshoot/exercise1/work/46/e01f274e2ef1735164061d62c51169
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
Solution
The command error .command.sh: line 2: samtools: command not found suggests that samtools was not available.
Every process in the hello-gatk.nf 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.
| nextflow.config | |
|---|---|