Reports

Execution log

The nextflow log command shows information about executed pipelines in the current folder:

nextflow log <run name> [options]

Note

Both the execution report and the trace file must be specified when the pipeline is first called. By contrast, the log option is useful after a pipeline has already run and is available for every executed pipeline.

By default, log prints the list of executed pipelines:

$ nextflow log
TIMESTAMP            RUN NAME         SESSION ID                            COMMAND
2016-08-01 11:44:51  grave_poincare   18cbe2d3-d1b7-4030-8df4-ae6c42abaa9c  nextflow run hello
2016-08-01 11:44:55  small_goldstine  18cbe2d3-d1b7-4030-8df4-ae6c42abaa9c  nextflow run hello -resume
2016-08-01 11:45:09  goofy_kilby      0a1f1589-bd0e-4cfc-b688-34a03810735e  nextflow run rnatoy -with-docker

Specifying a run name or session id prints tasks executed by that pipeline run:

$ nextflow log goofy_kilby
/Users/../work/0b/be0d1c4b6fd6c778d509caa3565b64
/Users/../work/ec/3100e79e21c28a12ec2204304c1081
/Users/../work/7d/eb4d4471d04cec3c69523aab599fd4
/Users/../work/8f/d5a26b17b40374d37338ccfe967a30
/Users/../work/94/dfdfb63d5816c9c65889ae34511b32

Customizing fields

By default, only the task execution paths are printed. A custom list of fields to print can be provided via the -f (-fields) option. For example:

$ nextflow log goofy_kilby -f hash,name,exit,status
0b/be0d1c  buildIndex (ggal_1_48850000_49020000.Ggal71.500bpflank)  0  COMPLETED
ec/3100e7  mapping (ggal_gut)                                       0  COMPLETED
7d/eb4d44  mapping (ggal_liver)                                     0  COMPLETED
8f/d5a26b  makeTranscript (ggal_liver)                              0  COMPLETED
94/dfdfb6  makeTranscript (ggal_gut)                                0  COMPLETED

The fields accepted by the -f options are the ones in the trace report, as well as: script, stdout, stderr, env. List available fields using the -l (-list-fields) option.

The script field is useful for examining script commands run in each task:

$ nextflow log goofy_kilby -f name,status,script
align_genome      COMPLETED
   bowtie --index /data/genome input.fastq > output
...

Templates

The -t option allows a template (string or file) to be specified. This makes it possible to create complex custom reports in any text-based format. For example, you could save this Markdown snippet to a file:

## $name

script:

    $script

exist status: $exit
task status: $status
task folder: $folder

Then, the following command will output a markdown file containing the script, exit status and folder of all executed tasks:

nextflow log goofy_kilby -t my-template.md > execution-report.md

Filtering

The filter option makes it possible to select which entries to include in the log report. Any valid groovy boolean expression on the log fields can be used to define the filter condition. For example:

nextflow log goofy_kilby -filter 'name =~ /foo.*/ && status == "FAILED"'

Execution report

Nextflow can create an HTML execution report: a single document which includes many useful metrics about a workflow execution. The report is organised in the three main sections: Summary, Resources and Tasks (see below for details).

To enable the creation of this report add the -with-report command line option when launching the pipeline execution. For example:

nextflow run <pipeline> -with-report [file name]

The report file name can be specified as an optional parameter following the report option.

Summary

The Summary section reports the execution status, the launch command, overall execution time and some other workflow metadata. You can see an example below:

Resource Usage

The Resources section plots the distribution of resource usage for each workflow process using the interactive plotly.js plotting library.

Plots are shown for CPU, memory, job duration and disk I/O. They have two (or three) tabs with the raw values and a percentage representation showing what proportion of the requested resources were used. These plots are very helpful to check that task resources are used efficiently.

Learn more about how resource usage is computed in this tutorial.

Tasks

The Tasks section lists all executed tasks, reporting for each of them the status, the actual command script, and many other metrics. You can see an example below:

Note

Nextflow collects these metrics through a background process for each job in the target environment. Make sure the following tools are available in the environment where tasks are executed: awk, date, grep, ps, sed, tail, tee. Moreover, some of these metrics are not reported when running on Mac OS X. See the corresponding note in the trace file section.

Warning

A common problem when using a third party container image is that it does not include one or more of the above utilities, resulting in an empty execution report.

Please read Report scope section to learn more about the execution report configuration details.

Trace file

Nextflow creates an execution tracing file that contains some useful information about each process executed in your pipeline script, including: submission time, start time, completion time, cpu and memory used.

In order to create the execution trace file add the -with-trace command line option when launching the pipeline execution. For example:

nextflow run <pipeline> -with-trace

It will create a file named trace.txt in the current directory. The content looks like the above example:

task_id	hash	native_id	name	status	exit	submit	duration	walltime	%cpu	rss	vmem	rchar	wchar
19	45/ab752a	2032	blast (1)	COMPLETED	0	2014-10-23 16:33:16.288	1m	5s	0.0%	29.8 MB	354 MB	33.3 MB	0
20	72/db873d	2033	blast (2)	COMPLETED	0	2014-10-23 16:34:17.211	30s	10s	35.7%	152.8 MB	428.1 MB	192.7 MB	1 MB
21	53/d13188	2034	blast (3)	COMPLETED	0	2014-10-23 16:34:17.518	29s	20s	4.5%	289.5 MB	381.6 MB	33.3 MB	0
22	26/f65116	2035	blast (4)	COMPLETED	0	2014-10-23 16:34:18.459	30s	9s	6.0%	122.8 MB	353.4 MB	33.3 MB	0
23	88/bc00e4	2036	blast (5)	COMPLETED	0	2014-10-23 16:34:18.507	30s	19s	5.0%	195 MB	395.8 MB	65.3 MB	121 KB
24	74/2556e9	2037	blast (6)	COMPLETED	0	2014-10-23 16:34:18.553	30s	12s	43.6%	140.7 MB	432.2 MB	192.7 MB	182.7 MB
28	b4/0f9613	2041	exonerate (1)	COMPLETED	0	2014-10-23 16:38:19.657	1m 30s	1m 11s	94.3%	611.6 MB	693.8 MB	961.2 GB	6.1 GB
32	af/7f2f57	2044	exonerate (4)	COMPLETED	0	2014-10-23 16:46:50.902	1m 1s	38s	36.6%	115.8 MB	167.8 MB	364 GB	5.1 GB
33	37/ab1fcc	2045	exonerate (5)	COMPLETED	0	2014-10-23 16:47:51.625	30s	12s	59.6%	696 MB	734.6 MB	354.3 GB	420.4 MB
31	d7/eabe51	2042	exonerate (3)	COMPLETED	0	2014-10-23 16:45:50.846	3m 1s	2m 6s	130.1%	703.3 MB	760.9 MB	1.1 TB	28.6 GB
36	c4/d6cc15	2048	exonerate (6)	COMPLETED	0	2014-10-23 16:48:48.718	3m 1s	2m 43s	116.6%	682.1 MB	743.6 MB	868.5 GB	42 GB
30	4f/1ad1f0	2043	exonerate (2)	COMPLETED	0	2014-10-23 16:45:50.961	10m 2s	9m 16s	95.5%	706.2 MB	764 MB	1.6 TB	172.4 GB
52	72/41d0c6	2055	similarity (1)	COMPLETED	0	2014-10-23 17:13:23.543	30s	352ms	0.0%	35.6 MB	58.3 MB	199.3 MB	7.9 MB
57	9b/111b5e	2058	similarity (6)	COMPLETED	0	2014-10-23 17:13:23.655	30s	488ms	0.0%	108.2 MB	158 MB	317.1 MB	9.8 MB
53	3e/bca30f	2061	similarity (2)	COMPLETED	0	2014-10-23 17:13:23.770	30s	238ms	0.0%	6.7 MB	29.6 MB	190 MB	91.2 MB
54	8b/d45b47	2062	similarity (3)	COMPLETED	0	2014-10-23 17:13:23.808	30s	442ms	0.0%	108.1 MB	158 MB	832 MB	565.6 MB
55	51/ac19c6	2064	similarity (4)	COMPLETED	0	2014-10-23 17:13:23.873	30s	6s	0.0%	112.7 MB	162.8 MB	4.9 GB	3.9 GB
56	c3/ec5f4a	2066	similarity (5)	COMPLETED	0	2014-10-23 17:13:23.948	30s	616ms	0.0%	10.4 MB	34.6 MB	238 MB	8.4 MB
98	de/d6c0a6	2099	matrix (1)	COMPLETED	0	2014-10-23 17:14:27.139	30s	1s	0.0%	4.8 MB	42 MB	240.6 MB	79 KB

Trace fields

The following table shows the fields that can be included in the execution report:

task_id

Task ID.

hash

Task hash code.

native_id

Task ID given by the underlying execution system e.g. POSIX process PID when executed locally, job ID when executed by a grid engine, etc.

process

Nextflow process name.

tag

User provided identifier associated this task.

name

Task name.

status

Task status. Possible values are: NEW, SUBMITTED, RUNNING, COMPLETED, FAILED, and ABORTED.

exit

POSIX process exit status.

module

Environment module used to run the task.

container

Docker image name used to execute the task.

cpus

The cpus number request for the task execution.

time

The time request for the task execution

disk

The disk space request for the task execution.

memory

The memory request for the task execution.

attempt

Attempt at which the task completed.

submit

Timestamp when the task has been submitted.

start

Timestamp when the task execution has started.

complete

Timestamp when task execution has completed.

duration

Time elapsed to complete since the submission.

realtime

Task execution time i.e. delta between completion and start timestamp.

queue

The queue that the executor attempted to run the process on.

%cpu

Percentage of CPU used by the process.

%mem

Percentage of memory used by the process.

rss

Real memory (resident set) size of the process. Equivalent to ps -o rss .

vmem

Virtual memory size of the process. Equivalent to ps -o vsize .

peak_rss

Peak of real memory. This data is read from field VmHWM in /proc/$pid/status file.

peak_vmem

Peak of virtual memory. This data is read from field VmPeak in /proc/$pid/status file.

rchar

Number of bytes the process read, using any read-like system call from files, pipes, tty, etc. This data is read from file /proc/$pid/io.

wchar

Number of bytes the process wrote, using any write-like system call. This data is read from file /proc/$pid/io.

syscr

Number of read-like system call invocations that the process performed. This data is read from file /proc/$pid/io.

syscw

Number of write-like system call invocations that the process performed. This data is read from file /proc/$pid/io.

read_bytes

Number of bytes the process directly read from disk. This data is read from file /proc/$pid/io.

write_bytes

Number of bytes the process originally dirtied in the page-cache (assuming they will go to disk later). This data is read from file /proc/$pid/io.

vol_ctxt

Number of voluntary context switches. This data is read from field voluntary_ctxt_switches in /proc/$pid/status file.

inv_ctxt

Number of involuntary context switches. This data is read from field nonvoluntary_ctxt_switches in /proc/$pid/status file.

env

The variables defined in task execution environment.

workdir

The directory path where the task was executed.

script

The task command script.

scratch

The value of the process scratch directive.

error_action

The action applied on errof task failure.

hostname

New in version 22.05.0-edge.

The host on which the task was executed. Supported only for the Kubernetes executor yet. Activate with k8s.fetchNodeName = true in the Nextflow config file.

cpu_model

New in version 22.07.0-edge.

The name of the CPU model used to execute the task. This data is read from file /proc/cpuinfo.

Note

These metrics provide an estimation of the resources used by running tasks. They are not an alternative to low-level performance analysis tools, and they may not be completely accurate, especially for very short-lived tasks (running for less than a few seconds).

Trace report layout and other configuration settings can be specified by using the nextflow.config configuration file.

Please read Trace scope section to learn more about it.

Execution timeline

Nextflow can render an HTML timeline for all processes executed in your pipeline. An example of the execution timeline is shown below:

Each bar represents a process run in the pipeline execution. The bar length represents the task duration time (wall-time). The colored area in each bar represents the real execution time. The grey area to the left of the colored area represents the task scheduling wait time. The grey area to the right of the colored area represents the task termination time (clean-up and file un-staging). The numbers on the x-axis represent the time in absolute units e.g. minutes, hours, etc.

Each bar displays two numbers: the task duration time and the virtual memory size peak.

As each process can spawn many tasks, colors are used to identify those tasks belonging to the same process.

To enable the creation of the execution timeline add the -with-timeline command line option when launching the pipeline execution. For example:

nextflow run <pipeline> -with-timeline [file name]

The report file name can be specified as an optional parameter following the timeline option.

Workflow diagram

A Nextflow pipeline can be represented as a direct acyclic graph (DAG). The vertices in the graph represent the pipeline’s processes and operators, while the edges represent the data dependencies (i.e. channels) between them.

To render the workflow DAG, run your pipeline with the -with-dag option. By default, it creates a file named dag-<timestamp>.html with the workflow DAG rendered as a Mermaid diagram.

The workflow DAG can be rendered in a different format by specifying an output file name with a different extension based on the desired format. For example:

nextflow run <pipeline> -with-dag flowchart.png

New in version 22.06.0-edge: You can use the -preview option with -with-dag to render the workflow DAG without executing any tasks.

Changed in version 23.10.0: The default output format was changed from DOT to HTML.

The following file formats are supported:

dot

Graphviz DOT file

gexf

Graph Exchange XML file (Gephi)

html

HTML file with Mermaid diagram

Changed in version 23.10.0: The HTML format was changed to render a Mermaid diagram instead of a Cytoscape diagram.

mmd

New in version 22.04.0.

Mermaid diagram

pdf

Requires Graphviz to be installed

Graphviz PDF file

png

Requires Graphviz to be installed

Graphviz PNG file

svg

Requires Graphviz to be installed

Graphviz SVG file

Here is the Mermaid diagram produced by Nextflow for the rnaseq-nf pipeline (using the Mermaid Live Editor with the default theme):

nextflow run rnaseq-nf -preview -with-dag

%%{ init: { 'theme': 'base', 'themeVariables': { 'primaryColor': '#B6ECE2', 'primaryTextColor': '#160F26', 'primaryBorderColor': '#065647', 'lineColor': '#545555', 'clusterBkg': '#BABCBD22', 'clusterBorder': '#DDDEDE', 'fontFamily': 'arial' } } }%% flowchart TB subgraph " " v0["Channel.fromFilePairs"] v1["transcriptome"] v7["config"] end subgraph RNASEQ v2([INDEX]) v3([FASTQC]) v4([QUANT]) end v8([MULTIQC]) subgraph " " v9[" "] end v5(( )) v0 --> v3 v0 --> v4 v1 --> v2 v2 --> v4 v3 --> v5 v4 --> v5 v7 --> v8 v5 --> v8 v8 --> v9