No nullarbor html report


#1

Please use this template to help us fix your problem quickly! Please don’t include sensitive information (including IP addresses) and fill in sections as appropriate.

CLIMB SERVICE PROBLEMS (Bryn, OpenStack, Launching VMs, Creating and attaching Volumes, etc.)

1. Describe the problem. Are there any error messages you can paste? Can you provide a screenshot of the problem (with sensitive information removed)?
I am running nullarbor2 on a new VM. It goes to completion and generates all the required results in a report directory, except for the report.html. Nullarbor returns the following error message at the end of the whole process:

//For further info see: http://sanger-pathogens.github.io/Roary/

nw_display -S -s -w 1024 -l ‘font-size:12;font-family:sans-serif;’ -i ‘opacity:0’ -b ‘opacity:0’ -v 16 roary/accessory_binary_genes.fa.newick > roary/acc.svg

nullarbor-report.pl --name efn.nhp.18Nov18 --indir . --outdir report

[07:15:32] Hello ubuntu

[07:15:32] This is nullarbor-report.pl 1.25

[07:15:32] Send complaints to Torsten Seemann <torsten.seemann@gmail.com>

[07:15:32] Making folder --outdir /home/ubuntu/efn/seqrun_3_repeat.3/merged.reads18Nov18/nhp.nullarbor.run18Nov18/report

[07:15:32] Identified 96 isolates.

[07:15:32] Generating: jobinfo

[07:15:32] Generating: seqdata

[07:15:34] Generating: identification

[07:15:41] Generating: mlst

[07:15:41] Generating: serotype

[07:15:41] WARNING: no analysis available for serotype

[07:15:41] Generating: resistome

[07:15:45] Generating: virulome

[07:15:54] Generating: assembly

[07:15:54] Generating: reference

[07:15:55] Generating: core

[07:15:55] Generating: snptree

[07:15:55] Generating: snpdist

[07:15:55] Generating: snpdensity

[07:15:55] Can’t open /home/ubuntu/efn/seqrun_3_repeat.3/merged.reads18Nov18/nhp.nullarbor.run18Nov18/core.nway.tab in Nullarbor::Tabular::load

Makefile:48: recipe for target ‘report/index.html’ failed

make: *** [report/index.html] Error 1

make: Leaving directory ‘/home/ubuntu/efn/seqrun_3_repeat.3/merged.reads18Nov18/nhp.nullarbor.run18Nov18’ //

2. What is the name of the VM or volume that the problem is affecting? Ebenn

3. Where is the VM or volume hosted; Birmingham, Cardiff, Swansea or Warwick? Cardiff

4. Is there any other information that you think might be helpful? This is new VM I recently created less than a month ago.

SOFTWARE OR APPLICATION PROBLEMS (Python can’t find the modules I installed, Prokka doesn’t predict any ORFs, etc.)

1. Describe the problem. Include links to any guides that you might be following and a brief history of the commands that you’ve run. Paste any error messages in code-blocks (paste, highlight and press Ctrl+Shift+C).
Below is the error message:

//For further info see: http://sanger-pathogens.github.io/Roary/

nw_display -S -s -w 1024 -l ‘font-size:12;font-family:sans-serif;’ -i ‘opacity:0’ -b ‘opacity:0’ -v 16 roary/accessory_binary_genes.fa.newick > roary/acc.svg

nullarbor-report.pl --name efn.nhp.18Nov18 --indir . --outdir report

[07:15:32] Hello ubuntu

[07:15:32] This is nullarbor-report.pl 1.25

[07:15:32] Send complaints to Torsten Seemann <torsten.seemann@gmail.com>

[07:15:32] Making folder --outdir /home/ubuntu/efn/seqrun_3_repeat.3/merged.reads18Nov18/nhp.nullarbor.run18Nov18/report

[07:15:32] Identified 96 isolates.

[07:15:32] Generating: jobinfo

[07:15:32] Generating: seqdata

[07:15:34] Generating: identification

[07:15:41] Generating: mlst

[07:15:41] Generating: serotype

[07:15:41] WARNING: no analysis available for serotype

[07:15:41] Generating: resistome

[07:15:45] Generating: virulome

[07:15:54] Generating: assembly

[07:15:54] Generating: reference

[07:15:55] Generating: core

[07:15:55] Generating: snptree

[07:15:55] Generating: snpdist

[07:15:55] Generating: snpdensity

[07:15:55] Can’t open /home/ubuntu/efn/seqrun_3_repeat.3/merged.reads18Nov18/nhp.nullarbor.run18Nov18/core.nway.tab in Nullarbor::Tabular::load

Makefile:48: recipe for target ‘report/index.html’ failed

make: *** [report/index.html] Error 1

make: Leaving directory ‘/home/ubuntu/efn/seqrun_3_repeat.3/merged.reads18Nov18/nhp.nullarbor.run18Nov18’ //

2. What operating system are you running; GVL, Ubuntu 16.04, Centos 7, etc.?
Ubuntu

3. Is there any other information that you think might be helpful?

Grateful for your kind assistance!

Cheers,
Ebenn


#2

Hi Ebenn,

I would suggest sending any questions about Nullabor its creator (torsten.seemann@gmail.com) or looking to see if anyone has resolved any similar issues on its github page.

All the best,
Sion


#3

Dear Sion,
Noted. Thx.
Ebenn


#4