The default build type is Release (optimizations, no assertions). If any crashes are experienced, the first step in addressing them is to redo the run with a Test (optimizations, assertions) or Debug (no optimizations, assertions) build type. This is achieved using, e.g. -DCMAKE_BUILD_TYPE=Test.
Note: The various tools are only built in Test or Debug build types.
FAST5_FILE=$SIMPSONLAB/data/nanopore/ecoli/sqk006/pass/LomanLabz_PC_Ecoli_K12_MG1655_20150924_MAP006_1_5005_1_ch9_file72_strand.fast5
nanocall ${FAST5_FILE} > ${FAST5_FILE}.fa
compute-state-transitions -p .001 -t .1 -k .1 >transitions.tsv
compute-scaled-pore-model -f $FAST5_FILE >model.tsv
get_events $FAST5_FILE | egrep -v '^(#|mean)' | tawk '{print $1,$3,$2,$4}' >events.tsv
run-viterbi -d info -p model.tsv -s transitions.tsv -e events.tsv | { echo ">$(basename $FAST5_FILE)"; cat; } >out.fa
run-viterbi -d debug -p model.tsv -s transitions.tsv -e <(awk 'NR>=100 && NR<200' events.tsv) |& tee log
run-fwbw -d info -p model.tsv -s transitions.tsv -e <(awk 'NR>=100 && NR<200' events.tsv) -o fwbw.tsv