I created GVL climb server from the Cardiff cloud system with Nullarbor pipeline already configured, however, When I executed nullarbor pipeline on more than 200 isolates whole genomes fastq files and notice two errors.
First, snippy tool in the pipeline did not detect any SNPs in any of the isolates. I tried using three different reference genomes(FM211187, ATCC_700669, tigre4) but the ouput was the same, no SNP was detected by snippy in the nullarboe pipeline. I upgraded brew and updated all the nullabor tools in the pipeline but could not get any SNPs
Secondly, tbl2san error below is the error Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y āAnnotated using prokka 1.12 from https://github.com/tseemann/prokkaā -Z ERR1065578/prokka/ERR1065578.err -i ERR1065578/prokka/ERR1065578.fsa
I tried the solution suggested in the community issues by still getting the same error
Please any help to will be very much welcome
Please could you paste snps.log from one of the samples to help establish what the problem is?
The tbl2asn problem is an unfortunate mismatch between NCBIās licensing and the way that brew works. I suggest you install your own, system copy of tbl2asn following these steps:
I am having challenges running Nullarbor on my VM which I set up on Cardiff server last week, 14Dec2017. When I type in ānullarbor.pl āhā I get the error message
āread_dir ā/home/linuxbrew/ .linuxbrew/bin/ ā¦/plguinsā ā opendir: No such file or directory at /home/linuxbrew/ .linuxbrew/Cellar/nullarbor/HEAD-1495981/bin/ ā¦/per15/Nullarbor/Plugins.pm line 20ā.
I feel that nullarbor is not properly installed.
I am unsure what Iām doing wrong. Can you please help?
Iām having the same issue, yet, I couldnāt solve it. I unlinked snippy but couldnāt install it again: Here are the last lines I get from:
==> Installing snippy from tseemann/bioinformatics-linux
Error: No available formula with the name "vcflib" (dependency of tseemann/bioinformatics-linux/snippy)
==> Searching for a previously deleted formula (in the last month)...
Warning: homebrew/core is shallow clone. To get complete history run:
git -C "$(brew --repo homebrew/core)" fetch --unshallow
Error: No previously deleted formula found.
==> Searching for similarly named formulae...
==> Searching local taps...
Error: No similarly named formulae found.
==> Searching taps...
==> Searching taps on GitHub...
Error: No formulae found in taps.
This is down to the closing down and subsequent migration of formulae from homebrew/science. You can read about it here.
There will be a transition period where the commonly used homebrew formulae are migrated to homebrew/core and are unavailable.
Fortunately, thanks to the efforts of people like Shaun Jackman and Torsten Seemann, the old repos have been saved from the scrapheap and made available here and here.
You can access these kegs by tapping them:
brew tap brewsci/homebrew-bio brew tap brewsci/homebrew-science
After youāve tapped these kegs, you should be able to
brew install snippy --HEAD
While these repos will provide packages, they do so without any maintenance, except to migrate packages to homebrew/core.