No nullarbor html report

Ebenn · November 25, 2018, 10:15am

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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: