Questions tagged [aws]
Acronym for Amazon Webservices
8 questions
3 votes
1 answer
152 views
Low Memory Usage with DeepVariant
I am running DeepVariant on a c5.4xlarge instance on AWS EC2 with Ubuntu Server 24.04. I'm using htop to monitor my CPU and memory usage. During make_examples, I noticed that only 8GB of my 32GB of ...
- 33
2 votes
1 answer
66 views
Increasing memory usage in AWS instance
I have 16 CPUs on my AWS EC2 instance and I am trying to use kSNP4 to generate an SNP matrix. I was able to successfully run this with over 150 samples - while it took a while to run it did complete - ...
- 1,063
2 votes
1 answer
147 views
Error Registering Job Definition AWS
I am in the process of creating a bioinformatics pipeline and I am currently trying to setup the AWS infrastructure for which it will run. The script I am running to setup the AWS batch job looks like ...
- 101
0 votes
0 answers
211 views
Why is bcl2fastq2 taking so long to calculate stats?
Our lab has been using bcl2fastq v2.20.0.422 to demultiplex RNA-seq data sequenced on an Illumina Novaseq machine on a beefy EC2 instance and we've run into the strange problem: namely that while ...
- 101
2 votes
1 answer
188 views
How does cromwell and AWS batch decide which compute environment (on-demand or spot) to use?
For processing genomics workflows I make use of widdle and cromwell with an AWS back-end. I have followed all examples on the AWS cromwell tutorial. In my AWS batch console I can see there are 2 job ...
- 21
1 vote
1 answer
124 views
Pointing Cromwell to local EBS mounted storage on AWS Batch
I'm trying to run the WDL tasks from the GTEx RNA-Seq pipeline with Cromwell using AWS Batch as a backend. I store the STAR alignment index on an Elastic Block Store since my Cromwell server instance ...
- 125
3 votes
1 answer
3k views
Downloading SRA Files from AWS
I want to download the original BAM files that the authors had uploaded to SRA. Normally, I would just use sam-dump, but the files are having issues that seem ...
- 651
2 votes
3 answers
705 views
Accessing .bam/.cram files from AWS S3?
What's the best/easiest way for accessing .bam/.cram files from S3? I have .bam/.bai .cram/.crai and .bed + .gff files that I want to make available easily to others so they can browse in IGV and ...
- 2,374