Kenneth Durbrow

icon location I've been programming professionally since the 80's. I currently work for National Institutes of Health as team lead for the SRA Toolkit.

Results 8 comments of Kenneth Durbrow

CMake Error: The source directory "/home/shutovo/test/ngs-tools" does not exist.

Thanks. We are forwarding this to the appropriate individual. Hopefully, this will be fixed quickly.

Extreme memory consumption when reading certain SRA records?

The big difference between these two runs is ERR191522 contains alignments and DRR001375 contains only unaligned reads. In the unaligned case, the reads are stored together in one record. The...

Extreme memory consumption when reading certain SRA records?

Ah yes, aligned colorspace! They are broken, and unfortunately they can't (*) be fixed. Is it crucial for you to have these reads? Although I don't have a count, I...

Reduce maximum memory usage while reading SRA data?

Possible? Of course. Feasible? Not so much. Most likely the memory is being used for caching the reference sequences. If you are using an access pattern like `fasterq-dump`, you will...

Reference Workflow for Fastq->SRA File (VDB Conversion)

NCBI has an automated pipeline for SRA submissions. This pipeline is old in software years, it's been in production for over a decade. It's grown over the years, mostly in...

Recognize pre-release tables

The problem with the ones from the SRAO ticket is that KDB does not recognize them as pre-release tables. I thought they'd work for a test case but I was...

configure assumes /usr/bin/make is gmake, and thus make fails on a system where it isn't

> Font packages, png/tiff/etc packages...to download a file? Our code does not introduce any of those dependencies.

configure assumes /usr/bin/make is gmake, and thus make fails on a system where it isn't

> just trying to download a file, not dive down a long list of inter-dependencies Welcome to computers. They've been like this since ... ever. I understand your frustration. It...