James Dalgleish

ERROR: Unable to open index file: ucsc.hg19.fa, yet it's in the current directory.

2

bash-4.2$ /data/CCRBioinfo/dalgleishjl/sv_mapping/svaba/bin/svaba run -t PAMHYN_Tumor.realigned.md.bam -n PAMHYN_Normal.realigned.md.bam -a PAMHYN_discovery_chr22 -k chr22 -G ucsc.hg19.fa -p 2 ----------------------------------------------------------- --- Running svaba SV and indel detection on 2 threads ---- --- (inspect *.log...

KeyError(key) in run.neighborhoods.py

4

So, all of the data I'm using is public. I'm trying to create customized ABC regions for lung data. Here is the error I encounter, along with the script I...

HG38 to CHM13v2 VCF liftover using chain

4

I'm having some issues lifting over using the provided chain files. GATK complains that it can't find the reference sequence, yet I'm not precisely sure why. If you know of...

Pre-aligned BAM files, and reversion to single end for HiC-Pro use

26

Hello! I'm having difficulty running the program in a stepwise fashion: After copying two bam files to lscratch, I receive the following error: "Exit: Error: Directory Hierarchy of rawdata '/lscratch/52514766/'...

Tulsa, Alabama

1

There's an error in one of the lines, which will lead to errors in summary stats... there is one homicide listed as Tulsa, AL. Tulsa, Alabama is not the correct...

"Empty output in the score file!!! Program exit"

11

So, the error message is completely accurate. The score files in the "predict_results" folder are all zero bytes, but it doesn't give me an idea why. first 1000 lines of...

INLA: Fail to get good enough initial values using MOcarolinawren_long example data

1

``` library(INLA) library(dplyr) library(tidyr) library(ggplot2) #install_github("andrewzm/STRbook") data("MOcarolinawren_long",package="STRbook") coords

Issue java.lang.ClassNotFoundException: org.apache.commons.cli.ParseException

2

Using the example, I'm getting a bit of an odd java error that popped up just this morning. I previously had used the program successfully. Here's an example using test...

CMAKE_BUILD_TYPE and CUDA_SDK_ROOT_DIR

9

I am attempting to install openmm-tensorflow and am getting a prompt in ccmake about the build type and the CUDA_SDK_ROOT_DIR. ``` Page 1 of 1 **CMAKE_BUILD_TYPE** * CMAKE_INSTALL_PREFIX /usr/local/openmm CUDA_HOST_COMPILER...

What are the typical run times for the pipeline? I have a 40GB fastq and I expect it could be anywhere from 5-15 hours, based on transfer rates.