Wrong configuration file

[mictadlo]

Hi, I ran /mySyntenyPortal/mySyntenyPortal build -p 24 -conf lab.cnf but I got:

Building a website...
##### Read a configuration file #####
 - /QRISdata/Q0231/mysytenyportal/lab.cnf
Wrong configuration file
>LABvsLAB
Done.

Please find below my config file:

# Website name (REQUIRED)
>LABvsLAB
LABvsLABe

# Input Assemblies (REQUIRED)
# FASTA format (https://en.wikipedia.org/wiki/FASTA_format)
>Assemblies
LAB NbV1ChF.fasta

# Divergence times (REQUIRED)
# Example) Human-chimpanzee: near, Human-mouse: medium, Human-chicken: far
>Divtimes
LAB,LAB near

# Resolutions (REQUIRED)
# The minimum size of synteny blocks in base pair
>Resolutions
150000,300000,400000,500000

# Gene annotations of references (OPTIONAL)
# Gene transfer format (GTF) (https://en.wikipedia.org/wiki/Gene_transfer_format)
#>Annotation
#LAB ../data/example_inputs/Homo_sapiens.GRCh38.87.gtf.gz
#Mouse   ../data/example_inputs/Mus_musculus.GRCm38.87.gtf.gz

# Cytogenetic bands (OPTIONAL)
# Column 1: Chromosome
# Column 2: Start position
# Column 3: End position
# Column 4: Name of cytogenetic band
# Column 5: Giemsa stain results
# Refer to the sample files '[mySyntenyPortal_root]/data/example_input/Human.cytoband'
>Cytoband
LAB NbV1ChF.cytoband 

# Pre-built circos plots (OPTIONAL)
# If you want to visualize all chromosomes/scaffolds, you can write 'all' instead of specific chromosomes
>circos1
resolution:150000
LAB:all

# Email address is used to make a contact link in published website. (OPTIONAL)
>Email
Your@e-mail.com

What did I miss?

Thank you in advance

Michal

[jongin333]

Hi, Michal.

I think the '#' in front of the annotation information is wrong. You must remove the '#' like below.

>Annotation

LAB ../data/example_inputs/Homo_sapiens.GRCh38.87.gtf.gz

Mouse ../data/example_inputs/Mus_musculus.GRCm38.87.gtf.gz

==>

Annotation LAB ../data/example_inputs/Homo_sapiens.GRCh38.87.gtf.gz Mouse ../data/example_inputs/Mus_musculus.GRCm38.87.gtf.gz

Thanks, Jongin

[mictadlo]

Hi Jongin, Thank you it works now.

Best wishes,

Michal