Ryan Golhar
Our users copy/paste to create the samplesheet. They save the samplesheet using Excel. Somewhere along the way a space is added to the end of the index column. When we...
One of our lab operators provided an empty samplesheet intending to fill it out later, but never did. As a result, this run made it into our pipeline where we...
When validating one of my files, I get this error: [ec2-user@master scratch]$ $FASTQVALIDATOR --disableSeqIDCheck --file sample_2.clipped.fastq Finished processing M2GEN-BMS-0715-11192013-LU-FT_L6.D706_2.clipped.fastq with 230767016 lines containing 57691754 sequences. There were a total of...
Would be nice is the quality score encoding scheme is reported, Phred+33, Phred+64, etc.
bcftools should now be used instead of samtools mpileup. Docs need to be updated.
on line 146, source("~/Rscripts/Color.11.R")- this references a file in the user's home directory. I checked to see if the repo has it, and its not here either.
``` sh /opt/amazon-ebs-autoscale/install.sh -d /dev/xvdba -f lvm.ext4 -m /scratch + cat + USAGE=Install Amazon EBS Autoscale /opt/amazon-ebs-autoscale/install.sh [options] [[-m] ] Options -d, --initial-device DEVICE Initial device to use for mountpoint...
When doing so, StarCluster submits the request to AWS, and that part is successful. When StarCluster then queries for the state of the nodes, AWS complains and says "Cannot query...
Sometimes when creating large (200 node) clusters, while waiting for nodes to be in a running state, AWS reports an instance id is not found, probably because it hasn't propogated...
New kernels rename /dev/sd\* to /dev/xda_, however these are used by ephemeral storage drives. So when an instance has ephemeral storage and an assigned EBS volume, there is no way...