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Old 06-06-2014, 02:25 PM   #7
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Location: Vancouver, BC

Join Date: Mar 2010
Posts: 274

Originally Posted by Brian Bushnell View Post


For some reason I can't get COPE to work:

Other programs can see the files fine. I moved them to various places and tried both absolute and relative paths. Any ideas?
Try specifying the files for unconnected pairs. I would try:

./cope -a /dev/shm/sr1.fq -b /dev/shm/sr2.fq -o /dev/shm/cmerged.fq -2 /dev/shm/sr1_unconnected.fq -3 /dev/shm/sr2_unconnected.fq -m 0 -s 33
I know that solution doesn't logicially follow from the error message, but from what I remember, you will get either no messages on failure with this program or nondescript messages. If that doesn't work, I'd check the input again, and then try without the "-s 33" as a last suggestion. It could be the input, but I'm guessing it's just the combination of options, or lack of, that is causing the issue.
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