BSMAP v2.73
Start at: Wed Feb 12 17:24:10 2014
Input reference file: /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa (format: FASTA)
Load in 7658 db seqs, total size 557717710 bp. 9 secs passed
total_kmers: 43046721
Create seed table. 27 secs passed
max number of mismatches: read_length * 8% max gap size: 0
kmer cut-off ratio:5e-07
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
mapping strand: ++,-+
Single-end alignment(1 threads)
Input read file: /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R1.fastq.gz (format: gzipped FASTQ)
Output file: bsmap_out.sam (format: SAM)
Thread #0: 50000 reads finished. 32 secs passed
Thread #0: 100000 reads finished. 37 secs passed
Thread #0: 150000 reads finished. 42 secs passed
Thread #0: 200000 reads finished. 47 secs passed
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Thread #0: 400000 reads finished. 67 secs passed
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Thread #0: 500000 reads finished. 77 secs passed
Thread #0: 550000 reads finished. 81 secs passed
Thread #0: 600000 reads finished. 86 secs passed
Thread #0: 650000 reads finished. 91 secs passed
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Thread #0: 1000000 reads finished. 126 secs passed
Thread #0: 1050000 reads finished. 131 secs passed
Thread #0: 1100000 reads finished. 136 secs passed
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Thread #0: 1300000 reads finished. 156 secs passed
Thread #0: 1350000 reads finished. 161 secs passed
Thread #0: 1400000 reads finished. 166 secs passed
Thread #0: 1450000 reads finished. 171 secs passed
Thread #0: 1500000 reads finished. 176 secs passed
Thread #0: 1550000 reads finished. 181 secs passed
Thread #0: 1600000 reads finished. 186 secs passed
Thread #0: 1650000 reads finished. 191 secs passed
Thread #0: 1700000 reads finished. 196 secs passed
Thread #0: 1750000 reads finished. 201 secs passed
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Thread #0: 2150000 reads finished. 240 secs passed
Thread #0: 2200000 reads finished. 245 secs passed
Thread #0: 2250000 reads finished. 250 secs passed
Thread #0: 2300000 reads finished. 255 secs passed
Thread #0: 2350000 reads finished. 260 secs passed
Thread #0: 2400000 reads finished. 264 secs passed
Thread #0: 2450000 reads finished. 269 secs passed
Thread #0: 2500000 reads finished. 274 secs passed
Thread #0: 2550000 reads finished. 279 secs passed
Thread #0: 2600000 reads finished. 284 secs passed
Thread #0: 2650000 reads finished. 289 secs passed
Thread #0: 2700000 reads finished. 294 secs passed
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Thread #0: 2800000 reads finished. 304 secs passed
Thread #0: 2850000 reads finished. 309 secs passed
Thread #0: 2900000 reads finished. 314 secs passed
Thread #0: 2950000 reads finished. 319 secs passed
Thread #0: 3000000 reads finished. 324 secs passed
Thread #0: 3050000 reads finished. 329 secs passed
Thread #0: 3100000 reads finished. 334 secs passed
Thread #0: 3150000 reads finished. 339 secs passed
Thread #0: 3200000 reads finished. 344 secs passed
Thread #0: 3250000 reads finished. 348 secs passed
Thread #0: 3300000 reads finished. 353 secs passed
Thread #0: 3350000 reads finished. 358 secs passed
Thread #0: 3400000 reads finished. 363 secs passed
Thread #0: 3450000 reads finished. 369 secs passed
Thread #0: 3500000 reads finished. 374 secs passed
Thread #0: 3550000 reads finished. 378 secs passed
Thread #0: 3600000 reads finished. 383 secs passed
Thread #0: 3617338 reads finished. 385 secs passed
Total number of aligned reads: 2439344 (67%)
Done.
Finished at Wed Feb 12 17:30:35 2014
Total time consumed: 385 secs