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From Genome Analysis Wiki
Jump to navigationJump to search→STEP 2 : Run GotCloud Alignment Pipeline
$GCHOME/gotcloud align --conf $GCDATA/[[Alignment Configuration File|GBR60align.conf]] --outdir $GCOUT
$GCHOME/gotcloud align --conf $GCDATA/[[Alignment Configuration File|GBR60align.conf]] --outdir $GCOUT
Upon successful completion of the alignment pipeline, you will see the following message:
Upon successful completion of the alignment pipeline (about 1-2 minutes), you will see the following message:
Commands finished in nn secs with no errors reported
Commands finished in nn secs with no errors reported
