Summary of Successful flow in bold-
./bsmap -a /Volumes/betty/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -b /Volumes/betty/filtered_174gm_A_NoIndex_L006_R2.fastq.gz -d /Volumes/betty/oyster_v9.fa -o /Volumes/betty/BiGO_Betty_plain.sam -p 4
582441 read pairs finished. 82016 secs passed
Thread #2: 171500000 read pairs finished. 82026 secs passed
Thread #0: 171550000 read pairs finished. 82032 secs passed
Total number of aligned reads:
pairs: 90102067 (53%)
single a: 17033002 (9.9%)
single b: 15975991 (9.3%)
Done.
Finished at Fri May 17 13:15:23 2013
Total time consumed: 82033 secs
d-128-95-149-219:bsmap-2.74 sr320$ ./bsmap -a /Volumes/betty/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -b /Volumes/betty/filtered_174gm_A_NoIndex_L006_R2.fastq.gz -d /Volumes/betty/oyster_v9.fa -o /Volumes/betty/BiGO_Betty_plain.sam -p 4
python methratio.py -d /Volumes/betty/oyster_v9.fa -u -z -g -o /Volumes/betty/BiGO_betty_plain_methratio_v1.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.73/samtools /Volumes/betty/BiGO_Betty_plain.sam
d-128-95-149-219:bsmap-2.74 sr320$ python methratio.py -d /Volumes/betty/oyster_v9.fa -u -z -g -o /Volumes/betty/BiGO_betty_plain_methratio_v1.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.73/samtools /Volumes/betty/BiGO_Betty_plain.sam
@ Sat May 18 09:16:52 2013: reading reference /Volumes/betty/oyster_v9.fa ...
@ Sat May 18 09:17:20 2013: reading /Volumes/betty/BiGO_Betty_plain.sam ...
[samopen] SAM header is present: 11969 sequences.
@ Sat May 18 09:24:43 2013: read 10000000 lines
@ Sat May 18 09:32:05 2013: read 20000000 lines
@ Sat May 18 09:39:26 2013: read 30000000 lines
@ Sat May 18 09:48:16 2013: read 40000000 lines
@ Sat May 18 09:56:53 2013: read 50000000 lines
@ Sat May 18 10:05:33 2013: read 60000000 lines
@ Sat May 18 10:14:08 2013: read 70000000 lines
@ Sat May 18 10:22:45 2013: read 80000000 lines
@ Sat May 18 11:46:04 2013: read 90000000 lines
@ Sat May 18 11:54:37 2013: read 100000000 lines
@ Sat May 18 12:03:12 2013: read 110000000 lines
@ Sat May 18 12:11:48 2013: read 120000000 lines
@ Sat May 18 12:20:23 2013: read 130000000 lines
@ Sat May 18 12:29:21 2013: read 140000000 lines
@ Sat May 18 12:39:20 2013: read 150000000 lines
@ Sat May 18 12:49:33 2013: read 160000000 lines
@ Sat May 18 13:00:03 2013: read 170000000 lines
@ Sat May 18 13:10:36 2013: read 180000000 lines
@ Sat May 18 13:21:33 2013: read 190000000 lines
@ Sat May 18 13:32:28 2013: read 200000000 lines
@ Sat May 18 13:43:43 2013: read 210000000 lines
@ Sat May 18 13:47:23 2013: combining CpG methylation from both strands ...
@ Sat May 18 13:50:59 2013: writing /Volumes/betty/BiGO_betty_plain_methratio_v1.txt ...
@ Sat May 18 16:54:59 2013: done.
total 167774088 valid mappings, 127192776 covered cytosines, average coverage: 13.23 fold.
d-128-95-149-219:bsmap-2.74 sr320$
./bsmap -a /Volumes/betty/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -b /Volumes/betty/filtered_174gm_A_NoIndex_L006_R2.fastq.gz -d /Volumes/betty/oyster_v9.fa -o /Volumes/betty/BiGO_Betty_plain.bam -p 4
#3: 171350000 read pairs finished. 81910 secs passed
Thread #0: 171400000 read pairs finished. 81925 secs passed
Thread #2: 171450000 read pairs finished. 81942 secs passed
Thread #0: 171582441 read pairs finished. 81977 secs passed
Thread #1: 171500000 read pairs finished. 81981 secs passed
Thread #3: 171550000 read pairs finished. 81983 secs passed
Total number of aligned reads:
pairs: 90102067 (53%)
single a: 17033002 (9.9%)
single b: 15975991 (9.3%)
Done.
Finished at Fri May 17 13:15:22 2013
Total time consumed: 81983 secs
d-128-95-149-219:bsmap-2.74 sr320$ ./bsmap -a /Volumes/betty/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -b /Volumes/betty/filtered_174gm_A_NoIndex_L006_R2.fastq.gz -d /Volumes/betty/oyster_v9.fa -o /Volumes/betty/BiGO_Betty_plain.bam -p 4
./bsmap -a /Volumes/betty/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -b /Volumes/betty/filtered_174gm_A_NoIndex_L006_R2.fastq.gz -d /Volumes/betty/oyster_v9.fa -n 1 -o /Volumes/betty/BiGO_Betty_n1.sam -p 4
finished. 89824 secs passed
Thread #0: 171300000 read pairs finished. 89826 secs passed
Thread #1: 171350000 read pairs finished. 89838 secs passed
Thread #2: 171400000 read pairs finished. 89860 secs passed
Thread #3: 171450000 read pairs finished. 89863 secs passed
Thread #0: 171500000 read pairs finished. 89868 secs passed
Thread #1: 171550000 read pairs finished. 89874 secs passed
Thread #2: 171582441 read pairs finished. 89883 secs passed
Total number of aligned reads:
pairs: 89582942 (52%)
single a: 17594059 (10%)
single b: 16545732 (9.6%)
Done.
Finished at Fri May 17 15:30:28 2013
Total time consumed: 89883 secs
d-128-95-149-219:bsmap-2.74 sr320$ ./bsmap -a /Volumes/betty/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -b /Volumes/betty/filtered_174gm_A_NoIndex_L006_R2.fastq.gz -d /Volumes/betty/oyster_v9.fa -n 1 -o /Volumes/betty/BiGO_Betty_n1.sam -p 4
python methratio.py -d /Volumes/betty/oyster_v9.fa -u -z -g -o /Volumes/betty/BiGO_betty_n1_methratio_v2.txt -s /Users/Shared/Apps/bsmap-2.74/samtools /Volumes/betty/BiGO_Betty_n1.sam
-bash: /Users/Shared/Apps/bsmap-2.74: is a directory
d-128-95-149-219:bsmap-2.74 sr320$ python methratio.py -d /Volumes/betty/oyster_v9.fa -u -z -g -o /Volumes/betty/BiGO_betty_n1_methratio_v2.txt -s /Users/Shared/Apps/bsmap-2.74/samtools /Volumes/betty/BiGO_Betty_n1.sam
@ Sat May 18 09:44:59 2013: reading reference /Volumes/betty/oyster_v9.fa ...
@ Sat May 18 09:45:37 2013: reading /Volumes/betty/BiGO_Betty_n1.sam ...
[samopen] SAM header is present: 11969 sequences.
@ Sat May 18 10:00:06 2013: read 10000000 lines
@ Sat May 18 10:11:27 2013: read 20000000 lines
@ Sat May 18 10:22:48 2013: read 30000000 lines
@ Sat May 18 11:49:29 2013: read 40000000 lines
@ Sat May 18 12:00:43 2013: read 50000000 lines
@ Sat May 18 12:11:48 2013: read 60000000 lines
@ Sat May 18 12:22:48 2013: read 70000000 lines
@ Sat May 18 12:33:14 2013: read 80000000 lines
@ Sat May 18 12:43:15 2013: read 90000000 lines
@ Sat May 18 12:53:02 2013: read 100000000 lines
@ Sat May 18 13:02:52 2013: read 110000000 lines
@ Sat May 18 13:12:28 2013: read 120000000 lines
@ Sat May 18 13:22:02 2013: read 130000000 lines
@ Sat May 18 13:31:27 2013: read 140000000 lines
@ Sat May 18 13:40:57 2013: read 150000000 lines
@ Sat May 18 13:50:33 2013: read 160000000 lines
@ Sat May 18 16:19:32 2013: read 170000000 lines
@ Sat May 18 16:28:59 2013: read 180000000 lines
@ Sat May 18 16:39:03 2013: read 190000000 lines
@ Sat May 18 16:50:11 2013: read 200000000 lines
@ Sat May 18 17:01:05 2013: read 210000000 lines
@ Sat May 18 17:04:39 2013: combining CpG methylation from both strands ...
@ Sat May 18 17:07:33 2013: writing /Volumes/betty/BiGO_betty_n1_methratio_v2.txt ...
@ Sat May 18 17:49:33 2013: done.
total 167885166 valid mappings, 127452697 covered cytosines, average coverage: 13.25 fold.
d-128-95-149-219:bsmap-2.74 sr320$
./bsmap -a /Volumes/betty/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -b /Volumes/betty/filtered_174gm_A_NoIndex_L006_R2.fastq.gz -d /Volumes/betty/oyster_v9.fa -o /Volumes/betty/BiGO_Betty_plain.bsp -p 6