Grace’s Notebook: Worked more on R script for adding Qubit data; Started using Mox

Today I worked more on my R script for adding new Qubit files. Everything works great up until the actual joining of files. After joining, there are extra columns that have the extensions “.x” and “.y”… I think it has something to do with the fact that some columns are factors, some are characters, and some are numeric… I also started using Mox today, but am unsure how to upload the .fastq files from the C bairdi transcriptome data. Waiting to hear back on that in a GitHub issue.

R Script

Script here

Issue with the final joining.

Mox

Steven showed me some examples of how to run Trinity on Mox.

 ## Job Name #SBATCH --job-name=trinity ## Allocation Definition #SBATCH --account=srlab #SBATCH --partition=srlab ## Resources ## Nodes (We only get 1, so this is fixed) #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=10-100:00:00 ## Memory per node #SBATCH --mem=100G #SBATCH --mail-type=ALL #SBATCH --mail-user=sr320@uw.edu ## Specify the working directory for this job #SBATCH --workdir=/gscratch/srlab/sr320/analyses/0624b source /gscratch/srlab/programs/scripts/paths.sh /gscratch/srlab/programs/trinity/Trinity \ --seqType fq \ --max_memory 100G \ --left /gscratch/srlab/sr320/data/geoduck-RNA-seq/NR012_S1_L001_R1_001.fastq,\ /gscratch/srlab/sr320/data/geoduck-RNA-seq/NR012_S1_L002_R1_001.fastq \ --right /gscratch/srlab/sr320/data/geoduck-RNA-seq/NR012_S1_L001_R2_001.fastq,\ /gscratch/srlab/sr320/data/geoduck-RNA-seq/NR012_S1_L002_R2_001.fastq \ --trimmomatic \ --CPU 28  

hyak_mox Wiki

To upload files:
File transfers

“`ssh: connect to host 205.175.107.122 port 22: Connection timed out rsync: connection unexpectedly closed (0 bytes received so far) [Receiver] rsync error: unexplained error (code 255) at io.c(605) [Receiver=3.0.9] [graceac9@mox1 ~]$

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