Nextflow workflow report

`[naughty_cray]` (resumed run)

Workflow execution completed successfully!

Run times

Wed Feb 14 18:31:58 CET 2018 - Wed Feb 14 18:32:00 CET 2018 (completed 7 years ago, duration: 1.3s)

Nextflow command

/users/rg/epalumbo/bin/nextflow-0.28.0-SNAPSHOT-all run -bg . -with-docker -resume -profile workstation

CPU-Hours: 18.2 (100% cached)
Launch directory: /data/epalumbo/git/sambamba-stats
Work directory: /data/epalumbo/git/sambamba-stats/work
Project directory: /data/epalumbo/git/sambamba-stats
Script name: main.nf
Script ID: 52fa46ca3a7823009485145d6833767e
Workflow profile: workstation
Workflow container
Container engine: docker
Nextflow version: version 0.28.0-SNAPSHOT, build 4757 (14-02-2018 17:29 UTC)
Session ID: c951ebb6-467e-4733-85b7-0c44e47516b5

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU Usage

% Allocated
Raw Usage

Memory Usage

% Allocated
Raw Usage

Job Duration

Disk Read / Write

Number of bytes directly read from disk added to the number of bytes the process originally dirtied in the page-cache for each process.

Tasks

This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.

Show entries

Metrics Metadata All

Search:

task_id	process	tag	status	hash	allocated cpus	%cpu	allocated memory	%mem	vmem	rss	peak_vmem	peak_rss	allocated time	duration	realtime	script	exit	submit	start	complete	rchar	wchar	syscr	syscw	read_bytes	write_bytes	native_id	name	module	container	disk	attempt	scratch	workdir


#!/bin/bash -eu
time sambamba flagstat -t 8 ENCFF044SJL.bam
#!/bin/bash -eu
time samtools flagstat ENCFF044SJL.bam
#!/bin/bash -eu
time sambamba flagstat -t 8 ENCFF044SJL.bam
#!/bin/bash -eu
time samtools flagstat -@8 ENCFF044SJL.bam
#!/bin/bash -eu
time sambamba index -t 8 ENCFF044SJL.bam /dev/null
#!/bin/bash -eu
time sambamba index -t 8 ENCFF044SJL.bam /dev/null
#!/bin/bash -eu
time samtools index ENCFF044SJL.bam /dev/null
#!/bin/bash -eu
time samtools index -@8 ENCFF044SJL.bam /dev/null
#!/bin/bash -eu
time sambamba markdup -t 8 ENCFF044SJL.bam /dev/null
#!/bin/bash -eu
time sambamba markdup -t 8 ENCFF044SJL.bam /dev/null
#!/bin/bash -eu
time samtools rmdup ENCFF044SJL.bam /dev/null
#!/bin/bash -eu
time samtools sort -@{task.cpus} -m 3221225472 -n ENCFF044SJL.bam | samtools fixmate -@{task.cpus} -m - - | samtools sort -@{task.cpus} -m 3221225472 | samtools markdup -@8 - /dev/null
#!/bin/bash -eu
time sambamba sort -t 8 -m 25769803776 -N -o /dev/null ENCFF044SJL.bam
#!/bin/bash -eu
time sambamba sort -t 8 -m 25769803776 -N -o /dev/null ENCFF044SJL.bam
#!/bin/bash -eu
time sambamba view -t 8 -o /dev/null ENCFF044SJL.bam
#!/bin/bash -eu
time samtools sort -@8 -m 3221225472 -n ENCFF044SJL.bam > /dev/null
#!/bin/bash -eu
time samtools sort -@8 -m 3221225472 -n ENCFF044SJL.bam > /dev/null
#!/bin/bash -eu
time sambamba view -t 8 -o /dev/null ENCFF044SJL.bam
#!/bin/bash -eu
time samtools view -@8 ENCFF044SJL.bam > /dev/null
#!/bin/bash -eu
time samtools view -@8 ENCFF044SJL.bam > /dev/null

Showing 1 to 20 of 20 entries