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How do I stop Fasta?

If you start up a Fasta run, and then discover that you're searching the wrong database or have the wrong query sequence, or that the search is simply taking too long, you can stop the program. For Fasta, a 'Ctrl-C' (hold down the Control key, and hit 'c') will stop the search. The program will tell you the best scores it has found so far, and offer to continue with the alignment part of Fasta. Another 'Ctrl-c' at this point will stop Fasta completely, and return you to the helix prompt.

If you just want to 'pause' the program (while you take a look at your query file, for example) use 'Ctrl-z' (hold down the Control key and hit 'z') to suspend the program execution. You will get a helix prompt, and the program will remain in a suspended state until you type 'fg' (for 'foreground') or 'bg' (for 'background'). You can also choose to kill the program after suspending it, by typing 'jobs', and killing the appropriate job. For example, after pausing a Fasta job with 'Ctrl-z': 
helix% jobs
[1]  + Suspended              ( set noglob; $GCGUTILDIR/gcglsf.pl $GCGUTILDIR/fasta )
This tells you that you have one job suspended, and that it is job number 1. 
helix% bg
[1]    ( set noglob; $GCGUTILDIR/gcglsf.pl $GCGUTILDIR/fasta ) &
      1,701 Sequences     675,057 aa searched    SW:AGL1_ARATH
      1,801 Sequences     716,153 aa searched    SW:ALAT_PIG
      1,901 Sequences     754,379 aa searched    SW:ALF_SCHPO
      2,001 Sequences     792,028 aa searched    SW:AMA1_PLAF8
[...etc....]
This puts the job into the background. You have limited control over it now, and will probably not be able to pause, kill or stop it until it is finished. 
helix% fg
( set noglob; $GCGUTILDIR/gcglsf.pl $GCGUTILDIR/fasta x89712.genpept )

      6,001 Sequences   2,332,970 aa searched    SW:CC27_HUMAN
      6,101 Sequences   2,374,535 aa searched    SW:CCKN_MACEU
      6,201 Sequences   2,406,280 aa searched    SW:CD36_HUMAN
      6,301 Sequences   2,437,213 aa searched    SW:CD9_CERAE
      6,401 Sequences   2,479,989 aa searched    SW:CE11_CAEEL
      6,501 Sequences   2,516,827 aa searched    SW:CERB_CERCA
      6,601 Sequences   2,563,151 aa searched    SW:CG2A_DROME
      6,701 Sequences   2,594,679 aa searched    SW:CH10_CAUCR
[...etc...]
This puts the job back into the foreground and it will continue to the end. 
helix% kill %1
[1]    Terminated             ( set noglob; $GCGUTILDIR/gcglsf.pl $GCGUTILDIR/fasta )
This kills the Fasta job.

'fg' and 'bg' should be used with caution, as they interfere with the normal execution of a Fasta job, and in some situations can lead to unexpected results especially if a job is foregrounded or backgrounded more than once. Your job may hang, become unkillable, or leave incomplete files.