The DISCOVAR assembly was run using a GCloud VM with the configuration: 48 vCPUs, 400G RAM
We started assemblying the LF2 (female) genome by running the following command from the location /home/joao_nunes/lf2-genome-assembly-discovar:
joao_nunes@lf2-genome-assembly-discovar:~$ DiscovarDeNovo READS="raw-data/*fastq.gz" OUT_DIR=/home/joao_nunes/lf2-assembly-discovar/lf2-genome-assembly-discovar PS1: we accidentally created a new folder (lf2-assembly-discovar) to save our output folder (*lf2-genome-assembly-discovar *), while it made more sense to have saved it at the location /home/joao_nunes/lf2-genome-assembly-discovar, from where the command was executed.
PS2: the command started to run at Jan 10th, 11:27 am (even though it was recorded as 13:27 am due to our Linux machine having a different timezone)
Regarding the LF6 genome, we set up the VM machine but could not start it with more processors due to a limit at the us-east1-b zone.
LF2 assembly finished running at 9:30 am, then the process took around 22 hours.
Since the LF2 assembly has finished, we could reduce the number of processors of the VM machine and could start the LF6 machine to run the assembly. The command used to run the assembly with Discovar de novo was (fired at Jan 11th, 10:15 am):
joao_nunes@lf6-genome-assembly-discovar:~$ DiscovarDeNovo READS="raw-data/*fastq.gz" OUT_DIR=/home/joao_nunes/lf6-genome-assembly-discovar/lf2-genome-assembly-discovar 2>&1 | tee DISCOVAR.log; poweroff The differences between this command and the one used to assembly the LF2 genome were:
- it now saves the output generated by Discovar at the terminal in a file called DISCOVAR.log
- once the command is finished (either successfully or failed), it turns down the VM machine
LF6 Assembly started running at Jan 11th, 12:15pm and finish running at Jan 12th, 04:39 am, i.e., total runtime was around 16,4 hours.