./bsmap -a /Volumes/Bay3/Software/bismark_v0.6.4/filtered_Unlabeled_NoIndex_L003_R1wID_trimmed.fastq -d /Volumes/Bay3\ scratch/tmp/cgigas_alpha_v030.fa -o /Volumes/Bay3\ scratch//tmp/BSMAP_output_trimmed_v0_3_0_A.sam -p 2
BSMAP v2.42
Start at: Mon Mar 12 08:48:02 2012
Load in 272 db seqs, total size 12727468 bp. 1 secs passed
total_kmers: 43046721
Create seed table. 3 secs passed
max mismatches: 2 max multi-hits: 100 max Ns: 5 seed size: 16 index interval: 4
quality cutoff: 0 base quality char: '!'
min fragment size:28 max fragemt size:500
start from read #1 end at read #4294967295
additional alignment: T in reads => C in reference
param.chains:0
mapping strand: ++,-+
Single read alignment(2 threads)
Query: /Volumes/Bay3/Software/bismark_v0.6.4/filtered_Unlabeled_NoIndex_L003_R1wID_trimmed.fastq Reference: /Volumes/Bay3 scratch/tmp/cgigas_alpha_v030.fa Output: /Volumes/Bay3 scratch//tmp/BSMAP_output_trimmed_v0_3_0_A.sam
Total number of aligned reads: 18997752 (14%)
Done.
Finished at Mon Mar 12 09:12:26 2012
Total time consumed: 1464 secs
OUTPUT
methratio
nts - move sam to bsmap folder (next time just write there!)
python methratio.py -d cgigas_alpha_v030.fa -z -o OUTz_methratioBSMAP_v030_A.txt -s /Volumes/Bay3/Software/samtools BSMAP_output_trimmed_v0_3_0_A.sam
OUTPUT
-
python methratio.py -d cgigas_alpha_v030.fa -z -u -o OUTzu_methratioBSMAP_v030_A.txt -s /Volumes/Bay3/Software/samtools BSMAP_output_trimmed_v0_3_0_A.sam
OUTPUT
./bsmap -a /Volumes/Bay3/Software/bismark_v0.6.4/filtered_Unlabeled_NoIndex_L003_R1wID_trimmed.fastq -w 5 -d /Volumes/Bay3\ scratch/tmp/cgigas_alpha_v030.fa -o /Volumes/Bay3\ scratch//tmp/BSMAP_output_trimmed_v0_3_0_B.sam -p 2
Load in 272 db seqs, total size 12727468 bp. 0 secs passed
total_kmers: 43046721
Create seed table. 2 secs passed
max mismatches: 2 max multi-hits: 5 max Ns: 5 seed size: 16 index interval: 4
quality cutoff: 0 base quality char: '!'
min fragment size:28 max fragemt size:500
start from read #1 end at read #4294967295
additional alignment: T in reads => C in reference
param.chains:0
mapping strand: ++,-+
Single read alignment(2 threads)
Query: /Volumes/Bay3/Software/bismark_v0.6.4/filtered_Unlabeled_NoIndex_L003_R1wID_trimmed.fastq Reference: /Volumes/Bay3 scratch/tmp/cgigas_alpha_v030.fa Output: /Volumes/Bay3 scratch//tmp/BSMAP_output_trimmed_v0_3_0_B.sam
Total number of aligned reads: 18997752 (14%)
Done.
Finished at Tue Mar 13 09:38:17 2012
Total time consumed: 1562 secs
OUTPUT
python methratio.py -d cgigas_alpha_v030.fa -z -o OUTzw5_methratioBSMAP_v030_B.txt -s /Volumes/Bay3/Software/samtools BSMAP_output_trimmed_v0_3_0_B.sam
OUTPUT
python methratio.py -d cgigas_alpha_v030.fa -z -u -o OUTzuw5_methratioBSMAP_v030_B.txt -s /Volumes/Bay3/Software/samtools BSMAP_output_trimmed_v0_3_0_B.sam
OUTPUT