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Questions tagged [aws]

Acronym for Amazon Webservices

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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 ...
merv's user avatar
  • 651
2 votes
3 answers
559 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 ...
719016's user avatar
  • 2,324
2 votes
1 answer
155 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 ...
user1805473's user avatar
2 votes
1 answer
119 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 ...
Joe_G's user avatar
  • 101
1 vote
1 answer
38 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 - ...
rimo's user avatar
  • 1,003
0 votes
0 answers
146 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 ...
divibisan's user avatar
  • 101
0 votes
1 answer
105 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 ...
Kevin L. Keys's user avatar