If you need help connecting to O2, please review the How to login to O2 wiki page.
From Windows, use MobaXterm (preferred) or PuTTY to connect to o2.hms.harvard.edu
and make sure the port is set to the default value of 22.
From a Mac Terminal, use the ssh
command, inserting your HMS ID instead of user123:
ssh user123@o2.hms.harvard.edu |
srun --pty -p interactive -t 0-12:0:0 --mem 2000MB -n 1 /bin/bash mkdir /n/scratch/users/${USER:0:1}/$USER/testSratoolKit cd /n/scratch/users/${USER:0:1}/$USER/testSratoolKit |
# Load sratookit module module load sratoolkit/2.10.7 # Set sratoolkit to use /n/scratch/users/${USER:0:1}/$USER/ncbi as cache space # By default, sratoolkit uses /home/$USER/ncbi as cache. If you download multiple data set, your 100G home space will be filled up quickly. mkdir -p ~/.ncbi # Configure sratoolkit vdb-config --interactive # Directly press x key to quit echo /repository/user/main/public/root = \"/n/scratch/users/${USER:0:1}/$USER/ncbi\" >> ~/.ncbi/user-settings.mkfg |
# Load sratookit module module load sratoolkit/2.10.7 # Use prefetch to download SRA file. prefetch SRR5138775 # Convert SRA file to FASTQ with fastq-dump. fastq-dump --split-files SRR5138775 # Note: The default maximum file size is 20G. When downloading large file more than 20G, it gives error: prefetch SRR7890863 ... 2020-05-27T17:58:24 prefetch.2.9.0 warn: Maximum file size download limit is 20GB 2020-05-27T17:58:24 prefetch.2.9.0: 1) 'SRR7890863' (29GB) is larger than maximum allowed: skipped 2020-05-27T17:58:25 prefetch.2.9.0: 'SRR7890863' has no remote vdbcache ... Download of some files was skipped because they are too large You can change size download limit by setting --min-size and --max-size command line arguments # You can add --max-size 35G: prefetch --max-size 35G SRR7890863 |