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ndaniel / fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data
GNU General Public License v3.0
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failed building database for my organism #176

Closed scseekers closed 3 years ago

scseekers commented 4 years ago

Hi

I am working on the rice genome obtained from the ensemble. I installed fusioncatcher via conda using the commands described in your readme.

I ran the following command to build the database

fusioncatcher-build.py -g oryza_sativa -o /raw/trimmomatic/ensemble_genome/os_db


Downloading the genome of organism 'oryza_sativa' from Ensembl!
230 Login successful.
FTP Error = 550 Failed to change directory.

ERROR: Workflow execution failed at step 4 while executing:
----------------
   get_genome.py \
   --organism oryza_sativa \
   --server ftp.ensembl.org \
   --output /scratch/Asad/E.Coli-Resistant/multiqc_data/tmp/rice_paper_springer/raw/trimmomatic/ensemble_genome/os_db/
----------------

Executing second time the same step/command in order to capture error messages (i.e. STDERR)...

Can't figure out the issue...

ndaniel commented 3 years ago

It looks like here: http://ftp.ensembl.org/pub/current_fasta/ is no organism like Oryza Sativa. This means that it is not supported by FusionCatcher. :-(