running 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_v2.sam -p 14
Total number of aligned reads:
pairs: 90102067 (53%)
single a: 17033002 (9.9%)
single b: 15975991 (9.3%)
CONCERNED about SAM file given error below
-a
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.
Count lines in # 17
7589219 CG
#16
4183705 /Volumes/web/cnidarian/Galaxy16-[combined_CC].tabular
#15
16356996 /Volumes/web/cnidarian/Galaxy15-[combined_CT].tabular
#14
25889528 /Volumes/web/cnidarian/Galaxy14-[combined_CA].tabular
--
Total Cytosines = 82,417,180
Mapping using CLC trimmed data
./bsmap -a /Volumes/web/cnidarian/filtered_174gm_A_NoIndex_L006_R1\ \(paired\)\ trimmed\ \(paired\).fastq -d /Volumes/web/cnidarian/oyster.v9.fa -o /Volumes/web/cnidarian/BiGO_BSMAP_Gonad_CLC_genome_v9_v3.sam -p 4
Total number of aligned reads: 114594586 (34%)
Done.
Finished at Thu Apr 18 19:46:51 2013
Total time consumed: 21376 secs
no
