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Working group bacterial genomics, part 1

  1. transfer the fastq files of the bacteria of your choice to your VM in a dedicated directory
  2. make sure that the directoy contains only the fastq
  3. open a screen session by doing (substitute <screen_name> with your name of choice)
screen -S <screen_name>
  1. then run the follow command (change where needed)
# INNUca basic command

# You should specify where the output goes whenever there is an option to do that
# Whenever possible use the option to specify the number of CPUs/threads to be used

docker run --rm -u $(id -u):$(id -g) -it -v /path/to/data:/data/ ummidock/innuca:3.1 \
       INNUca.py --inputDirectory /data/reads/<your_species_name>/ \
                 --speciesExpected "<your species name with space>" \
                 --genomeSizeExpectedMb <your_species_genome size> \
                 --outdir /data/genomes/<your_species_name>/innuca/ \
                 --threads 8
  1. detach the screen by pressing “Ctrl-A” and “d“. You will not see anything when you press those buttons. The output will be like this:
[detached from 5561.pts-0.193.166.24.142]
cloud-user@193.166.24.142 ~ $
  1. re-attach the screen
screen -r <screen_name>

if you are not sure if you are already in a screen or you do not remember the screen name do as below

screen -ls