run Roary

export PERL5LIB=$CONDA_PREFIX/lib/perl5/site_perl/5.22.0/ roary -p 4 -f ./roary -i 95 -cd 99 -s -e -n -v prokka/BK036327/BK036327.gff prokka/SX003539/SX003539.gff prokka/SX010463/SX010463.gff prokka/SX11227/SX11227.gff prokka/SX21888/SX21888.gff prokka/SX3282/SX3282.gff prokka/SX6010/SX6010.gff prokka/UR033452/UR033452.gff prokka/VA005892/VA005892.gff prokka/VA10744/VA10744.gff prokka/VA11956/VA11956.gff prokka/VA22627/VA22627.gff prokka/VA42437/VA42437.gff prokka/VA9181/VA9181.gff prokka/BK230/BK230.gff prokka/SX008197/SX008197.gff prokka/SX011228/SX011228.gff prokka/SX11809/SX11809.gff prokka/SX22080/SX22080.gff prokka/SX4175/SX4175.gff prokka/SX7227/SX7227.gff prokka/UR033513/UR033513.gff prokka/VA006555/VA006555.gff prokka/VA11214/VA11214.gff prokka/VA15614/VA15614.gff prokka/VA22707/VA22707.gff prokka/VA44411/VA44411.gff prokka/BK6793/BK6793.gff prokka/SX008376/SX008376.gff prokka/SX013593/SX013593.gff prokka/SX13129/SX13129.gff prokka/SX2890/SX2890.gff prokka/SX47920/SX47920.gff prokka/UR004699/UR004699.gff prokka/UR033547/UR033547.gff prokka/VA021269/VA021269.gff prokka/VA11590/VA11590.gff prokka/VA18232/VA18232.gff prokka/VA33823/VA33823.gff prokka/VA47956/VA47956.gff prokka/SX000196/SX000196.gff prokka/SX008379/SX008379.gff prokka/SX048572/SX048572.gff prokka/SX13636/SX13636.gff prokka/SX29836/SX29836.gff prokka/SX488/SX488.gff prokka/UR029020/UR029020.gff prokka/UR36289/UR36289.gff prokka/VA041877/VA041877.gff prokka/VA11620/VA11620.gff prokka/VA21241/VA21241.gff prokka/VA34370/VA34370.gff prokka/VA47966/VA47966.gff prokka/SX003010/SX003010.gff prokka/SX009323/SX009323.gff prokka/SX048970/SX048970.gff prokka/SX16398/SX16398.gff prokka/SX31281/SX31281.gff prokka/SX50013/SX50013.gff prokka/UR030652/UR030652.gff prokka/UR3900/UR3900.gff prokka/VA073169/VA073169.gff prokka/VA11749/VA11749.gff prokka/VA22326/VA22326.gff prokka/VA35455/VA35455.gff prokka/VA7035/VA7035.gff

roary -p 3 -f ./roary -i 95 -cd 99 -s -e -n -v prokka/BK036327/BK036327.gff prokka/BK230/BK230.gff prokka/BK6793/BK6793.gff prokka/SX013593/SX013593.gff prokka/SX2890/SX2890.gff prokka/SX3282/SX3282.gff prokka/SX4175/SX4175.gff prokka/SX488/SX488.gff prokka/SX6010/SX6010.gff prokka/SX7227/SX7227.gff prokka/UR030652/UR030652.gff prokka/UR3900/UR3900.gff prokka/VA005892/VA005892.gff prokka/VA006555/VA006555.gff prokka/VA041877/VA041877.gff prokka/VA073169/VA073169.gff prokka/VA10744/VA10744.gff prokka/VA11214/VA11214.gff prokka/VA11590/VA11590.gff prokka/VA11620/VA11620.gff prokka/VA11749/VA11749.gff prokka/VA11956/VA11956.gff prokka/VA15614/VA15614.gff prokka/VA18232/VA18232.gff prokka/VA21241/VA21241.gff prokka/VA22326/VA22326.gff prokka/VA22627/VA22627.gff prokka/VA22707/VA22707.gff prokka/VA33823/VA33823.gff prokka/VA34370/VA34370.gff prokka/VA35455/VA35455.gff prokka/VA42437/VA42437.gff prokka/VA44411/VA44411.gff prokka/VA47956/VA47956.gff prokka/VA47966/VA47966.gff prokka/VA7035/VA7035.gff

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