Could not find wireless interface

Using wifite v2 r85.

Scenario. Raspberry pi with 2 wireless cards. wlan0 is set up as a hotspot 
using hosted (hosted creates mon.wlan0 in order to work in AP mode).

wlan1 is an ALFA 036 card and not connected to any interface. I wish to use 
this for wifite.

> wifite -i wlan1 # could not find wireless interface "wlan1"

It then defaults to trying to use mon.wlan0 which causes problems with 
connections to the raspberry pi.

phillips321@raspberrypi ~ $ ifconfig -a
eth0      Link encap:Ethernet  HWaddr b8:27:eb:c8:aa:aa
          UP BROADCAST MULTICAST  MTU:1500  Metric:1
          RX packets:0 errors:0 dropped:0 overruns:0 frame:0
          TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:0 (0.0 B)  TX bytes:0 (0.0 B)

lo        Link encap:Local Loopback
          inet addr:127.0.0.1  Mask:255.0.0.0
          UP LOOPBACK RUNNING  MTU:65536  Metric:1
          RX packets:8 errors:0 dropped:0 overruns:0 frame:0
          TX packets:8 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:0
          RX bytes:1104 (1.0 KiB)  TX bytes:1104 (1.0 KiB)

mon.wlan0 Link encap:UNSPEC  HWaddr 
00-0F-12-89-AA-AA-00-00-00-00-00-00-00-00-00-00
          UP BROADCAST NOTRAILERS RUNNING PROMISC ALLMULTI  MTU:1500  Metric:1
          RX packets:8851 errors:0 dropped:0 overruns:0 frame:0
          TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:1417032 (1.3 MiB)  TX bytes:0 (0.0 B)

wlan0     Link encap:Ethernet  HWaddr 00:0f:12:89:aa:aa
          inet addr:10.0.0.1  Bcast:10.0.0.255  Mask:255.255.255.0
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:8258 errors:0 dropped:140 overruns:0 frame:0
          TX packets:7333 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:653104 (637.7 KiB)  TX bytes:3316054 (3.1 MiB)

wlan1     Link encap:Ethernet  HWaddr 00:c0:ca:38:aa:aa
          UP BROADCAST MULTICAST  MTU:1500  Metric:1
          RX packets:5182 errors:0 dropped:2 overruns:0 frame:0
          TX packets:1686 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:580084 (566.4 KiB)  TX bytes:640297 (625.2 KiB)

phillips321@raspberrypi ~ $ sudo -s
root@raspberrypi:/home/phillips321# ./wifite.py -i wlan1

  .;'                     `;,
 .;'  ,;'             `;,  `;,   WiFite v2 (r85)
.;'  ,;'  ,;'     `;,  `;,  `;,
::   ::   :   ( )   :   ::   ::  automated wireless auditor
':.  ':.  ':. /_\ ,:'  ,:'  ,:'
 ':.  ':.    /___\    ,:'  ,:'   designed for Linux
  ':.       /_____\      ,:'
           /       \

 [+] set interface: wlan1

 [!] the program cowpatty is not required, but is recommended

 [+] scanning for wireless devices...
 [!] could not find wireless interface "wlan1"
 [+] initializing scan (mon.wlan0), updates at 5 sec intervals, CTRL+C when ready.
 [0:00:04] scanning wireless networks. 0 targets and 0 clients found

 [+] scanning (mon.wlan0), updates at 5 sec intervals, CTRL+C when ready.

   NUM ESSID                 CH  ENCR  POWER  WPS?  CLIENT
   --- --------------------  --  ----  -----  ----  ------
    1  TestWiFi               6  WEP   49db    no

 [0:00:05] scanning wireless networks. 1 target and 0 clients found

Any ideas what could be causing this?
Original issue reported on code.google.com by phillips321 on 8 Feb 2014 at 4:10
bloghog2010 / wifite

Could not find wireless interface #135
