Varuni Sarwal

Error in make

1

When I run the command make -f prefix.mak, I get the error fermi.kit/bfc -1s 3g -k 61 -t 16 prefix.ec.fq.gz 2> prefix.flt.fq.gz.log | gzip -1 > prefix.flt.fq.gz /bin/bash: line 1:...

When I try to run the software using: fermi.kit/run-calling -t16 ~/reference.genome/chr19_new.fa prefix.mag.gz | sh, I get the error ERROR: failed to locate the BWA index. Please run 'fermi.kit/bwa index -p...

Alleles not produced in HLAminer output

1

Hi, I am trying to run HLAminer on a set of .fq files. I first index the files using bwa to produce a .sam file. Then, I run HLAminer according...

Empty output file

5

Hi, When I run the tool wham using the command toolPath -e $EXCLUDE -f $reference -t $alignments | perl ${utilsPath}/filtWhamG.pl The tool runs without any error with a non-zero runtime....

Scalability over larger datasets

5

Hi, Is your method scalable over larger datasets? I tried running this method on a dataset of size (10000, 8) and got an estimated run time as below. This should...

Hi! When I try to run PopSV following the instructions given under I don't want to think, how can I run it quickly ? And I run source("automatedPipeline-batchtools.R"), I get...