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
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 ~]$