diff --git a/tasks/task_consensus_call.wdl b/tasks/task_consensus_call.wdl index b7cff278..ed8daebc 100644 --- a/tasks/task_consensus_call.wdl +++ b/tasks/task_consensus_call.wdl @@ -160,7 +160,7 @@ task consensus { echo $num_ACTG | tee NUM_ACTG # calculate percent coverage (Wu Han-1 genome length: 29903bp) - python -c "print ( round( ($num_ACTG / 29903 ) * 100, 2 ) )" | tee PERCENT_REF_COVERAGE + python3 -c "print ( round( ($num_ACTG / 29903 ) * 100, 2 ) )" | tee PERCENT_REF_COVERAGE num_degenerate=$( grep -v ">" ${samplename}.consensus.fa | grep -o -E "B|D|E|F|H|I|J|K|L|M|O|P|Q|R|S|U|V|W|X|Y|Z" | wc -l ) if [ -z "$num_degenerate" ] ; then num_degenerate="0" ; fi