I run the nullarbor.pl script but no final report is created.

[jb2cool]

I've finally managed to install Nullarbor on Bio-Linux 8 with the help of Stephen's install script and if I run 'nullarbor.pl --check' then it all looks ok but if I run the makefile against the demo data that Stephen included with his script I don't seem to get any tree generated.

It runs through lots of steps but there is no public_html folder created and no report/index.html that I can find.

I also tried with 'make all -j 4' to try and force it but still no joy

[stephenturner]

Did you happen to run into the issue with prokka and contig IDs being too long? I.e., see the comment at Line 263 and the sed hack.

https://gist.github.com/stephenturner/005d4e4e322b8cf5b991d1d357527859#file-nullarbor-install-ubuntu1404-sh-L263

[jb2cool]

I'm not running this on any of my data yet, just the test/demo data that your script downloads. I'll try and see if your hackjob gets me any further.

Stephen's suggestion did sort me out, thanks

Duplicate of https://github.com/tseemann/nullarbor/issues/81

[jb2cool]

Well I thought it was just the sed hackjob I needed but it's back to doing the same thing on a freshly built machine (Even though it's built with the same script).

I create the samples.tab run the nullarbor.pl to create the makefile 'fix' the makefile with the sed hackjob run the makefile

[kwongj]

Can you post the commands that you used and some of the output that you get?

[jb2cool]

cd genometrackr

nullarbor.pl --name nullarbor --mlst senterica --ref /opt/genomes/senteritidisp125109.fa --input samples.tab --outdir nullarbor --force

sed -i 's/locustag SRR[0-9]*/locustag x/g' nullarbor/Makefile

nice make -j 4 -C /home/jason/genometrackr/nullarbor

Makefile.txt

Once finished in the ~/gemometrackr/nullarbor folder i have folders for the 6 sequences and 4 files; isolates.txt Makefile ref.fa ref.fa.fai

Re-running to capture the output now.

[kwongj]

If you re-run the Makefile again by either running: $ nice make -j 4 -C /home/jason/genometrackr/nullarbor

or entering the nullarbor directory and running the Makefile from there: $ cd /home/jason/genometrackr/nullarbor $ make

Nullarbor should pick up from where it left off.

The 4 files you listed are generated at the start of Nullarbor. Are the folders empty?

[jb2cool]

Folders all have;

abricate.tab contigs.fa denovo.tab kraken.tab megahit.log mlst.tab mlst2.tab prokka directory R1.fq.gz R2.fq.gz SRR1207xxx directory (matches the higher level directory) yield.clean.tab yield.dirty.tab

Two of them (SRR1207483 and SRR1207515) are a bit shorter with only; contigs.fa kraken.tab megahit.log R1.fq.gz R2.fq.gz SRR1207xxx directory (matches the higher level directory) yield.clean.tab yield.dirty.tab

[jb2cool]

here is the output of the job (different name this time) output.txt

I'm not 100% sure that's complete though, i thought there was more to it at the beginning.

[jb2cool]

if i keep re-running the make as you suggest it seems to get a little further every time. I now have denovo.tab, mlst.tab and mlst2.tab in the top level folder as well as a roary directory.

The final error which i can't get past is; "any" is not exported by the List::Util module Can't continue after import errors at /home/jason/.linuxbrew/bin/snippy-core line 5. BEGIN failed--compilation aborted at /home/jason/.linuxbrew/bin/snippy-core line 5. make: *\ [core.aln] Error 255 error.txt

[jb2cool]

List::Util was missing (Even though List::MoreUtils seems to be installed which as i understand it should be sufficient), this seemed to fix it for me; sudo cpan -f -i List::Util

Related issue is in snippy-core https://github.com/tseemann/snippy/issues/51

[kwongj]

Yep - is it working now?

[jb2cool]

Yes, after adding List::Util this seems ok now.

[myebenn]

Hi there, I am experiencing a similar issue with Nullarbor going to completion but failing to generate a final html report (although all individual reports are created within the report folder). The error message I'm getting reads something like this:

[21:42:02] Hello ubuntu [21:42:02] This is nullarbor-report.pl 1.25 [21:42:02] Send complaints to Torsten Seemann torsten.seemann@gmail.com [21:42:02] Folder --outdir /home/ubuntu/efn/seqrun_3_repeat.3/merged.reads18Nov18/nhp.nullarbor.run18Nov18/report already exists. [21:42:02] Identified 72 isolates. [21:42:02] Generating: jobinfo [21:42:02] Generating: seqdata [21:42:02] Generating: identification [21:42:02] Generating: mlst [21:42:02] Generating: serotype [21:42:02] WARNING: no analysis available for serotype [21:42:02] Generating: resistome [21:42:02] Generating: virulome [21:42:03] Generating: assembly [21:42:03] Generating: reference [21:42:03] Generating: core [21:42:03] Generating: snptree [21:42:03] Generating: snpdist [21:42:03] Generating: snpdensity [21:42:03] 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'

Grateful for your kind assistance in resolving this.

Cheers, Ebenn

[sharbie88]

I am getting this error too. What was the solution?

[myebenn]

Hi @sharbie88 The problem didn't go away for me, however, @tseemann suggested that installing the newer version of Nullarbor should solve the issue. I was/am using nullarbor.pl 1.30-dev, whereas the current version is a Nullarbor 2.x. You could try to install the latest version and give it a go.

cheers

[tseemann]

@myebenn nullarbor 1.x uses snippy 3.x which will give you wrong answers. please ugprade if you can!

[myebenn]

👍 👍 I ended up running the individual programmes separately (spades, snippy, prokka, resfinder etc) with up to date versions since then hence did not upgrade, but will do so right away! Thx again @tseemann!

[peflanag]

Hi I am wondering can I reopen this issue? Maybe someone can help? @jb2cool @tseemann

I ran the program on ubuntu in parrelles app on my iMac Pro. It ran first and seemed to work but notiuced there was not a report/index.html file there was only the attached image.

I checked the versions and they all seemed fine and I tried what was mentioned in Snippy-Core Issue #51 running

apt-get install liblist-moreutils-perl

The I ran nullarbor again but it failed with:

[14:57:23] Assigned 2576 locus_tags to CDS and RNA features. [14:57:23] Writing outputs to /tmp/tmp.OFCkn5seeW/ [14:57:24] Generating annotation statistics file [14:57:24] Generating Genbank and Sequin files [14:57:24] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka' -Z \/tmp\/tmp.OFCkn5seeW\/prokka.err -i \/tmp\/tmp.OFCkn5seeW\/prokka.fsa 2> /dev/null [14:57:27] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka' -Z \/tmp\/tmp.OFCkn5seeW\/prokka.err -i \/tmp\/tmp.OFCkn5seeW\/prokka.fsa 2> /dev/null make: *** [Makefile:130: E6206/contigs.gff] Error 2 make: Leaving directory '/media/psf/Home/IMRL_Sequencing/Tanya_MRSA/Nullarbor_Output'

I don't know what to do.