Welcome to the Albiorix wiki!

These pages contains information about the Albiorix computer cluster and are intended as a help for users of the system. Want to contribute? Please go ahead and add content.

FAQ

Miscellaneous questions

• How do I contribute to the Albiorix wiki?
• Using SGE to run an analysis on Albiorix
• How do I install additional packaged in BEAST2?

Error messages

Bash

• bash:-qmb8.sh: No such file or directory

git

• Blocked access to SSH keys created by some third-party applications
• fatal: The remote end hung up unexpectedly

mafft

• /usr/local/bin/mafft: line 808: /dev/stderr: Permission denied

Python

• Your Python version is 2.6, but this program requires 2.7

SGE

• Your "qrsh" request could not be scheduled, try again later

• Unable to run job: denied: host "compute-0-2.local is no submit host.

SSH

• ssh: connect to host albiorix.bioenv.gu.se port 22: Connection refused

• ssh_exchange_identification: Connection closed by remote host

• REMOTE HOST IDENTIFICATION HAS CHANGED!

Trinity

• Can't locate COMMON.pm in @INC

Tutorials

SGE

• Launch multiple jobs

Mapping

• Mapping with bowtie2
• Calculate Coverage from BAM file
• Separating mapped and unmapped reads from libraries
• From exonerate to igv: A story about GFF
• Separating mapped and unmapped reads

PacBio SMRT data

• Using PBJelly to gap-close scaffolds
• Using short reads to correct long reads with ECtools
• Using short reads to correct long reads with LSC
• Using short reads to correct long reads with PacBioToCA
• correct uncorrected ECtools reads with LSC

NCBI

• Submitting a genome to NCBI

IGV

• Loading IGV data from Albiorix

Miscellaneous programs

• How to convert your BLAST results into a gff file
• Tobias UCE tutorial
• Using SpeciesGeoCoder
• Creating bacterial phylogenetic trees with PhyloPhlAn
• How to run LogCombiner in Albiorix

Best practices

• Check your downloads with md5sum
• Starting a new bioinformatics project
• Downloading and storing data on Albiorix
• Submitting data to SRA

Transcriptome Quality-Evaluation

• A simple Transrate tutorial

Installed programs

Programs are generally installed in /usr/local/packages. Below are links to information about some of these programs.

Assembly

• CLC-AssemblyCell
• SGA
• Trinity
• Bridger

Phylogeny

• BEAST
• DISSECT
• MrBayes
• PhyloPhlAn

Miscellaneous

• bamtools
• bugreport
• bwa
• CROP
• fastStructure
• LSC
• mafft
• PBJelly
• Prokka
• RADtools
• Structure
• Tassel
• Transrate