./bsmap -a //Volumes/NGS\ Drive/NGS\ Raw\ Data/Oyster_BSseq/filtered_Unlabeled_NoIndex_L003_R1.fastq.gz -d /Volumes/web/cnidarian/oyster.v9.fa -o /Volumes/web/cnidarian/BiGill_BSMAP_GillMBD_genome_v9_v1.sam -p 16

Total number of aligned reads: 120734940 (86%)
Done.
Finished at Wed Apr 17 09:09:59 2013
Total time consumed:  8235 secs



http://eagle.fish.washington.edu/cnidarian/BiGill_BSMAP_GiIlMBD_genome_v9_v1.sam



python methratio.py -d /Volumes/web/cnidarian/oyster.v9.fa -u -z -g -o  /Volumes/web/cnidarian/BiGill_methratio_v9_A.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.73/samtools /Volumes/web/cnidarian/BiGill_BSMAP_GiIlMBD_genome_v9_v1.sam


@ Wed Apr 17 09:34:51 2013: reading reference /Volumes/web/cnidarian/oyster.v9.fa ...
@ Wed Apr 17 09:35:36 2013: reading /Volumes/web/cnidarian/BiGill_BSMAP_GiIlMBD_genome_v9_v1.sam ...
[samopen] SAM header is present: 11969 sequences.
     @ Wed Apr 17 09:41:11 2013: read 10000000 lines
     @ Wed Apr 17 09:46:34 2013: read 20000000 lines
     @ Wed Apr 17 09:51:39 2013: read 30000000 lines
     @ Wed Apr 17 09:56:50 2013: read 40000000 lines
     @ Wed Apr 17 10:01:59 2013: read 50000000 lines
     @ Wed Apr 17 10:07:03 2013: read 60000000 lines
     @ Wed Apr 17 10:11:56 2013: read 70000000 lines
     @ Wed Apr 17 10:16:55 2013: read 80000000 lines
     @ Wed Apr 17 10:22:21 2013: read 90000000 lines
     @ Wed Apr 17 10:27:34 2013: read 100000000 lines
     @ Wed Apr 17 10:32:44 2013: read 110000000 lines
     @ Wed Apr 17 10:37:36 2013: read 120000000 lines
@ Wed Apr 17 10:37:57 2013: combining CpG methylation from both strands ...
@ Wed Apr 17 10:38:38 2013: writing /Volumes/web/cnidarian/BiGill_methratio_v9_A.txt ...
@ Wed Apr 17 11:11:30 2013: done.
total 76206216 valid mappings, 91981690 covered cytosines, average coverage: 4.83 fold.


http://eagle.fish.washington.edu/cnidarian/BiGill_methratio_v9_A.txt


python singleupload.py sr320@washington.edu c8c52036bdecbbc798d3248bcc15c15c /Volumes/web/cnidarian/BiGill_methratio_v9_A.txt
/Volumes/web/cnidarian/BiGill_methratio_v9_A.txt




python methratio.py -d /Volumes/web/cnidarian/oyster.v9.fa -u -g -o  /Volumes/web/cnidarian/BiGill_methratio_v9_B.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.73/samtools /Volumes/web/cnidarian/BiGill_BSMAP_GiIlMBD_genome_v9_v1.sam



@ Wed Apr 17 09:57:07 2013: reading reference /Volumes/web/cnidarian/oyster.v9.fa ...
@ Wed Apr 17 09:57:35 2013: reading /Volumes/web/cnidarian/BiGill_BSMAP_GiIlMBD_genome_v9_v1.sam ...
[samopen] SAM header is present: 11969 sequences.
     @ Wed Apr 17 10:02:12 2013: read 10000000 lines
     @ Wed Apr 17 10:06:49 2013: read 20000000 lines
     @ Wed Apr 17 10:11:28 2013: read 30000000 lines
     @ Wed Apr 17 12:41:31 2013: read 40000000 lines
     @ Wed Apr 17 13:30:11 2013: read 50000000 lines
     @ Wed Apr 17 13:34:53 2013: read 60000000 lines
     @ Wed Apr 17 13:39:33 2013: read 70000000 lines
     @ Wed Apr 17 13:44:10 2013: read 80000000 lines
     @ Wed Apr 17 13:48:49 2013: read 90000000 lines
     @ Wed Apr 17 13:53:35 2013: read 100000000 lines
     @ Wed Apr 17 13:58:13 2013: read 110000000 lines
     @ Wed Apr 17 14:02:52 2013: read 120000000 lines
@ Wed Apr 17 14:03:12 2013: combining CpG methylation from both strands ...
@ Wed Apr 17 14:03:55 2013: writing /Volumes/web/cnidarian/BiGill_methratio_v9_B.txt ...
@ Wed Apr 17 14:12:44 2013: done.
total 76206216 valid mappings, 91981690 covered cytosines, average coverage: 4.83 fold.


http://eagle.fish.washington.edu/cnidarian/BiGill_methratio_v9_B.txt