Viewing Logs

Nextflow will automatically write a log to .nextflow.log in the directory where you start the pipeline. Each process also produces a log called .command.log, and you can use the nextflow log command to find these:

nextflow log <runId>

The <runId> will be a UUID like “0bf5895b-c504-4d5f-ba06-bf855ea7bd63” or a run name like “admiring_murdock” which is usually printed at the top of your pipeline execution log.

If you are only interested in processes that are part of registration, you can filter like using regular expressions:

nextflow log <runId> -F "process =~ /registration.*/

Or, if you only want the output of “coarse_spots” and “coarse_ransac”:

nextflow log <runId> -F "process =~ /.*coarse.*/"

In addition, if there is an error then the pipeline will typically print the process directory of the process that failed, so you can use that to directly view the complete log of the failed process.

Common Errors

Exit status 130/137

These exit codes indicate that the task ran out of memory. You need to increase the memory setting for the task.

When running with Docker (e.g. on AWS) you will see code 137. On IBM Platform LSF it’s exit code 130.

For example, if a registration:stitch task runs out of memory, you will need to increase the corresponding registration_stitch_memory parameter, e.g. to 30 G.

As a special case, the Janelia LSF Cluster does not respect the memory settings. Instead you need to increase the number of CPUs for the task. CPUs are mapped to slots at Janelia, and each slot gives you an additional 15 GB of memory.

Temporary Files

The pipeline produces various temporary files during processing, and one common problem is running out of space for these files.

Container Builds

The pipeline downloads Docker containers and converts them into Singularity Image Format prior to execution. By default, this uses the /tmp on your system. If the filesystem containing your /tmp directories does not have sufficient space for downloading and extracting the Docker containers, you may see an error like this:

INFO: Converting SIF file to temporary sandbox...
FATAL: while extracting /path/to/.singularity_cache/ 
       root filesystem extraction failed:
       failed to copy content in staging file: 
       write /tmp/rootfs-138799536/archive-375744281: no space left on device

If this happens, you will need to point the SINGULARITY_TMPDIR environment variable to an alternate location, e.g.

export SINGULARITY_TMPDIR=/scratch/tmp

Of course, /scratch/tmp needs to exist on your systems.

If you are using Nextflow Tower you can put the environment variable export in the “Pre-run script” box.

Cached SIF Files

By default, all Singularity images (SIF-format .img files) are cached by the pipeline in ~/.singularity_cache. The main pipeline process will download these files before launching any jobs, so this directory should be accessible from all cluster nodes. You can customize this path by setting the --singularity_cache_dir parameter.

MATLAB cache

The Airfinity spot extraction module must temporarily extract MATLAB code before each job is run. This uses the process directory by default (a unique path inside -workDir) but it can be overriden using --local_scratch_dir.