examining 

--
python methratio.py -d /Volumes/web/cnidarian/oyster.v9.fa -u -z -g -o  /Volumes/web/cnidarian/BiGO_methratio_v9_A.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.73/samtools /Volumes/web/cnidarian/BiGO_BSMAP_Gonad_genome_v9_v2.sam

g -o  /Volumes/web/cnidarian/BiGO_methratio_v9_A.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.73/samtools /Volumes/web/cnidarian/BiGO_BSMAP_Gonad_genome_v9_v2.sam
@ Fri Apr 19 10:40:45 2013: reading reference /Volumes/web/cnidarian/oyster.v9.fa ...
@ Fri Apr 19 10:41:19 2013: reading /Volumes/web/cnidarian/BiGO_BSMAP_Gonad_genome_v9_v2.sam ...
[samopen] SAM header is present: 11969 sequences.
     @ Fri Apr 19 10:49:03 2013: read 10000000 lines
     @ Fri Apr 19 10:56:48 2013: read 20000000 lines
     @ Fri Apr 19 11:04:31 2013: read 30000000 lines
     @ Fri Apr 19 11:12:12 2013: read 40000000 lines
     @ Fri Apr 19 11:19:54 2013: read 50000000 lines
     @ Fri Apr 19 11:27:37 2013: read 60000000 lines
     @ Fri Apr 19 11:35:17 2013: read 70000000 lines
     @ Fri Apr 19 11:43:12 2013: read 80000000 lines
     @ Fri Apr 19 11:51:19 2013: read 90000000 lines
     @ Fri Apr 19 11:59:06 2013: read 100000000 lines
     @ Fri Apr 19 12:06:52 2013: read 110000000 lines
     @ Fri Apr 19 12:14:40 2013: read 120000000 lines
     @ Fri Apr 19 12:22:26 2013: read 130000000 lines
     @ Fri Apr 19 12:30:10 2013: read 140000000 lines
     @ Fri Apr 19 12:37:55 2013: read 150000000 lines
     @ Fri Apr 19 12:45:40 2013: read 160000000 lines
     @ Fri Apr 19 12:53:21 2013: read 170000000 lines
     @ Fri Apr 19 13:01:04 2013: read 180000000 lines
     @ Fri Apr 19 13:08:48 2013: read 190000000 lines
     @ Fri Apr 19 13:16:32 2013: read 200000000 lines
[sam_read1] reference 'NM:i:0' is recognized as '*'.
Parse error at line 201009682: unmatched CIGAR operation
@ Fri Apr 19 13:17:20 2013: combining CpG methylation from both strands ...
@ Fri Apr 19 13:18:01 2013: writing /Volumes/web/cnidarian/BiGO_methratio_v9_A.txt ...
@ Fri Apr 19 13:54:09 2013: done.
total 158163368 valid mappings, 126786852 covered cytosines, average coverage: 12.52 fold.

--

running 
python methratio.py -d /Volumes/web/cnidarian/oyster.v9.fa -u -z -g -o  /Volumes/web/cnidarian/BiGO_methratio_v9_A2.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.73/samtools /Volumes/web/cnidarian/BiGO_BSMAP_Gonad_genome_v9_v2.sam


same thing


     @ Wed May  1 14:35:48 2013: read 170000000 lines
     @ Wed May  1 14:46:06 2013: read 180000000 lines
     @ Wed May  1 14:55:42 2013: read 190000000 lines
     @ Wed May  1 15:05:38 2013: read 200000000 lines
[sam_read1] reference 'NM:i:0' is recognized as '*'.
Parse error at line 201009682: unmatched CIGAR operation
@ Wed May  1 15:06:42 2013: combining CpG methylation from both strands ...
@ Wed May  1 15:08:28 2013: writing /Volumes/web/cnidarian/BiGO_methratio_v9_A2.txt ...



redo bsmap…..


running in ipython notebook

http://127.0.0.1:8888/c4610fb2-9591-44c8-beaa-f948cdac5793#

Sat still going




http://nbviewer.ipython.org/url/eagle.fish.washington.edu/cnidarian/BiGo%2520-%2520methratio%2520error.ipynb





Running
to bsp on hummingbird

./bsmap -a /Volumes/NGS\ Drive/NGS\ Raw\ Data/Oyster_gonad_Bisulfite/full/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -b  /Volumes/NGS\ Drive/NGS\ Raw\ Data/Oyster_gonad_Bisulfite/full/filtered_174gm_A_NoIndex_L006_R2.fastq.gz -d /Volumes/web/cnidarian/oyster.v9.fa -o /Volumes/web/cnidarian/BiGO_BSMAP_Gonad_genome_v9_v7.bsp -p 10 

finished


Thread #8:      171500000 read pairs finished. 25533 secs passed
Thread #1:      171550000 read pairs finished. 25535 secs passed
Total number of aligned reads:
pairs:       90102067 (53%)
single a:    17033002 (9.9%)
single b:    15975991 (9.3%)
Done.
Finished at Tue May  7 13:40:00 2013
Total time consumed:  25535 secs
d-128-95-149-219:bsmap-2.73 sr320$


methration



python methratio.py -d /Volumes/web/cnidarian/oyster.v9.fa -u -z -g -o  /Volumes/web/cnidarian/BiGO_methratio_v9_A6.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.73/samtools /Volumes/web/cnidarian/BiGO_BSMAP_Gonad_genome_v9_v7.bsp



and 

python methratio.py -d /Volumes/web/cnidarian/oyster.v9.fa -u -z -g -o  /Volumes/web/cnidarian/BiGO_methratio_v9_A7.txt -s /Users/Shared/Apps/bsmap-2.73/samtools /Volumes/web/cnidarian/BiGO_BSMAP_Gonad_genome_v9_v7.bsp



and 

python methratio.py -d /Volumes/web/cnidarian/oyster.v9.fa -u -z -g -o  /Volumes/web/cnidarian/BiGO_methratio_v9_A8.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.74/samtools /Volumes/web/cnidarian/BiGO_BSMAP_Gonad_genome_v9_v7.bsp


all had this error
 Tue May  7 19:20:05 2013: read 200000000 lines
     @ Tue May  7 19:30:24 2013: read 210000000 lines
@ Tue May  7 19:33:43 2013: combining CpG methylation from both strands ...
Traceback (most recent call last):
  File "methratio.py", line 166, in <module>
    methcr[pos] += methcr[pos+1]
OverflowError: unsigned short is greater than maximum
d-128-95-149-219:bsmap-2.73 sr320$


not sure if this is a problem…

try without -g
python methratio.py -d /Volumes/web/cnidarian/oyster.v9.fa -u -z -o  /Volumes/web/cnidarian/BiGO_methratio_v9_A9.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.74/samtools /Volumes/web/cnidarian/BiGO_BSMAP_Gonad_genome_v9_v7.bsp


d-128-95-149-219:bsmap-2.73 sr320$ python methratio.py -d /Volumes/web/cnidarian/oyster.v9.fa -u -z -o  /Volumes/web/cnidarian/BiGO_methratio_v9_A9.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.74/samtools /Volumes/web/cnidarian/BiGO_BSMAP_Gonad_genome_v9_v7.bsp
@ Wed May  8 05:27:35 2013: reading reference /Volumes/web/cnidarian/oyster.v9.fa ...
@ Wed May  8 05:28:09 2013: reading /Volumes/web/cnidarian/BiGO_BSMAP_Gonad_genome_v9_v7.bsp ...
     @ Wed May  8 05:36:54 2013: read 10000000 lines
     @ Wed May  8 05:45:42 2013: read 20000000 lines
     @ Wed May  8 05:54:26 2013: read 30000000 lines
     @ Wed May  8 06:03:11 2013: read 40000000 lines
     @ Wed May  8 06:11:56 2013: read 50000000 lines
     @ Wed May  8 06:20:41 2013: read 60000000 lines
     @ Wed May  8 06:29:24 2013: read 70000000 lines
     @ Wed May  8 06:38:08 2013: read 80000000 lines
     @ Wed May  8 06:46:54 2013: read 90000000 lines
     @ Wed May  8 06:55:39 2013: read 100000000 lines
     @ Wed May  8 07:04:27 2013: read 110000000 lines
     @ Wed May  8 07:13:11 2013: read 120000000 lines
     @ Wed May  8 07:21:57 2013: read 130000000 lines
     @ Wed May  8 07:30:39 2013: read 140000000 lines
     @ Wed May  8 07:39:22 2013: read 150000000 lines
     @ Wed May  8 07:48:04 2013: read 160000000 lines
     @ Wed May  8 07:56:46 2013: read 170000000 lines
     @ Wed May  8 08:05:31 2013: read 180000000 lines
     @ Wed May  8 08:14:16 2013: read 190000000 lines
     @ Wed May  8 08:22:59 2013: read 200000000 lines
     @ Wed May  8 08:31:43 2013: read 210000000 lines
@ Wed May  8 08:34:31 2013: writing /Volumes/web/cnidarian/BiGO_methratio_v9_A9.txt ...
@ Wed May  8 09:13:43 2013: done.
total 167776844 valid mappings, 134938233 covered cytosines, average coverage: 15.01 fold.
d-128-95-149-219:bsmap-2.73 sr320$






^ that worked but want to try a few more things

python methratio.py -d /Volumes/web/cnidarian/oyster.v9.fa -p -z -g -o  /Volumes/web/cnidarian/BiGO_methratio_v9_A11.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.74/samtools /Volumes/web/cnidarian/BiGO_BSMAP_Gonad_genome_v9_v7.bsp


     @ Thu May 16 13:27:50 2013: read 200000000 lines
     @ Thu May 16 13:38:32 2013: read 210000000 lines
@ Thu May 16 13:41:59 2013: combining CpG methylation from both strands ...
Traceback (most recent call last):
  File "methratio.py", line 166, in <module>
    methcr[pos] += methcr[pos+1]
OverflowError: unsigned short is grea





python methratio.py -d /Volumes/web/cnidarian/oyster.v9.fa -z -g -o  /Volumes/web/cnidarian/BiGO_methratio_v9_A12.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.74/samtools /Volumes/web/cnidarian/BiGO_BSMAP_Gonad_genome_v9_v7.bsp



     @ Thu May 16 13:27:50 2013: read 200000000 lines
     @ Thu May 16 13:38:32 2013: read 210000000 lines
@ Thu May 16 13:41:59 2013: combining CpG methylation from both strands ...
Traceback (most recent call last):
  File "methratio.py", line 166, in <module>
    methcr[pos] += methcr[pos+1]
OverflowError: unsigned short is greater than maximum
d-128-95-149-219:bsmap-2.73 sr320$


both running in hummingbird