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Old 04-06-2015, 11:15 AM   #19
lethalfang
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Location: San Francisco, CA

Join Date: Aug 2011
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Quote:
Originally Posted by etal View Post
What files were generated by the second run, if any? Can you show me the status messages or any errors that were printed?

When you run CNVkit with a reference, you don't need the "--targets", "--fasta", "--split" and "--access" arguments as that information has already been captured in the reference file. The default output directory is the current directory ("."). Try this instead:

cnvkit.py batch T1.bam T2.bam T3.bam T4.bam T5.bam T6.bam T7.bam T8.bam T9.bam T10.bam -r N.cnn --scatter --diagram
Thanks. For the second run where I was having question, there is no error message, and a bunch of .targetcoverage.cnn files are generated.

The status messages are:
Code:
Summary: #bins=292, #reads=7633921, mean=26143.5653, min=212.35, max=224646.99
On-target percentage: 37.877 (of 20154547 mapped)
Wrote ./T4.targetcoverage.cnn
Running the CNVkit pipeline on T9.bam ...
Processing reads in T9.bam
Time: 52.775 seconds (154291 reads/sec, 6 bins/sec)
Summary: #bins=292, #reads=8142711, mean=27885.9981, min=268.94, max=279225.27
On-target percentage: 38.472 (of 21165340 mapped)
Wrote ./T3.targetcoverage.cnn
Running the CNVkit pipeline on T10.bam ...
Processing reads in T10.bam
Time: 55.564 seconds (154063 reads/sec, 5 bins/sec)
Summary: #bins=292, #reads=8560291, mean=29316.0670, min=326.38, max=293055.07
On-target percentage: 38.593 (of 22181003 mapped)
Wrote ./T6.targetcoverage.cnn
Time: 57.101 seconds (149544 reads/sec, 5 bins/sec)
Summary: #bins=292, #reads=8539037, mean=29243.2782, min=302.54, max=292123.56
Time: 57.092 seconds (155098 reads/sec, 5 bins/sec)
Summary: #bins=292, #reads=8854878, mean=30324.9281, min=281.23, max=295576.58
Time: 57.155 seconds (147061 reads/sec, 5 bins/sec)
Summary: #bins=292, #reads=8405294, mean=28785.2540, min=254.16, max=285135.1
On-target percentage: 38.485 (of 22188207 mapped)
On-target percentage: 39.087 (of 22654458 mapped)
On-target percentage: 38.633 (of 21757000 mapped)
Wrote ./T2.targetcoverage.cnn
Wrote ./T8.targetcoverage.cnn
Wrote ./T1.targetcoverage.cnn
Time: 58.704 seconds (143289 reads/sec, 5 bins/sec)
Summary: #bins=292, #reads=8411624, mean=28806.9335, min=241.63, max=282191.54
On-target percentage: 38.845 (of 21654563 mapped)
Wrote ./T7.targetcoverage.cnn
Time: 60.050 seconds (150608 reads/sec, 5 bins/sec)
Summary: #bins=292, #reads=9044023, mean=30972.6832, min=298.46, max=306083.6
On-target percentage: 38.815 (of 23300051 mapped)
Wrote ./T5.targetcoverage.cnn
Time: 50.180 seconds (165905 reads/sec, 6 bins/sec)
Summary: #bins=292, #reads=8325083, mean=28510.5614, min=309.7, max=283705.95
On-target percentage: 38.622 (of 21555485 mapped)
Wrote ./T9.targetcoverage.cnn
Time: 51.261 seconds (173281 reads/sec, 6 bins/sec)
Summary: #bins=292, #reads=8882609, mean=30419.8946, min=299.88, max=296973.17
On-target percentage: 38.693 (of 22956916 mapped)
Wrote ./T10.targetcoverage.cnn


I ran again with the command you suggested, and the results are now as expected, i.e., identical to the first run.

Thanks.
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