pasted:
python methratio.py -d /Volumes/web/cnidarian/oyster.v9.fa -o /Volumes/web/Mollusk/174gm_analysis/Whole_Genome_Analyses/methratiopython_174gm_v9.txt -s /Users/Shared/Apps/bsmap-2.73/samtools -z -g -u /Volumes/web/Mollusk/174gm_analysis/Whole_Genome_Analyses/BSMAPoutput_174gm_v9.sam
total 24999208 valid mappings, 94087640 covered cytosines, average coverage: 2.67 fold.
-----
will try
python methratio.py -d /Volumes/web/cnidarian/oyster.v9.fa -o /Volumes/web/Mollusk/174gm_analysis/SR_A_Whole_Genome_Analyses/methratiopython_174gm_v9.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.73/samtools -z -g -u /Volumes/web/Mollusk/174gm_analysis/Whole_Genome_Analyses/BSMAPoutput_174gm_v9.sam
[samopen] SAM header is present: 11969 sequences.
@ Wed May 1 10:11:13 2013: read 10000000 lines
@ Wed May 1 10:19:27 2013: read 20000000 lines
@ Wed May 1 10:27:31 2013: read 30000000 lines
[sam_read1] reference 'ZS:Z:+-' is recognized as '*'.
Parse error at line 31774466: invalid CIGAR operation
@ Wed May 1 10:29:00 2013: combining CpG methylation from both strands ...
@ Wed May 1 10:30:04 2013: writing /Volumes/web/Mollusk/174gm_analysis/SR_A_Whole_Genome_Analyses/methratiopython_174gm_v9.txt ...
Traceback (most recent call last):
fout = open(options.outfile, 'w')
IOError: [Errno 2] No such file or directory: '/Volumes/web/Mollusk/174gm_analysis/SR_A_Whole_Genome_Analyses/methratiopython_174gm_v9.txt'
robertsmac:bsmap-2.74 sr320$