Examining how to best proceed with Larvae Trial samples - which genome etc.
#SR playing around with merge and mapping different genomes
!date
Fri Feb 28 15:25:57 PST 2014
Summary
M1 merge + Esm =
pairs: 3832546 (46%)
single a: 1591687 (19%)
single b: 1349271 (16%)
M1 merge + E =
Total number of aligned reads:
pairs: 2340694 (28%)
single a: 3150081 (38%)
single b: 2811635 (34%)
M1_A8 + Esm =
Total number of aligned reads:
pairs: 2597461 (47%)
single a: 1090241 (20%)
single b: 894626 (16%)
M1_A8 + Erm =
Total number of aligned reads:
pairs: 2174860 (39%)
single a: 1168661 (21%)
single b: 982745 (18%)
M1_A8 + E =
Total number of aligned reads:
pairs: 2597461 (47%)
single a: 1090241 (20%)
single b: 894626 (16%)
filename='BSMAP2view_larvae'
Assumptions- as with most worflows in development - a working directory is used.
!echo 'http://nbviewer.ipython.org/github/sr320/ipython_nb/blob/master/''{filename}''.ipynb'
http://nbviewer.ipython.org/github/sr320/ipython_nb/blob/master/BSMAP2view_larvae.ipynb
#this needs fixing!
!echo 'https://raw.github.com/sr320/ipython_nb/master/''{filename}''.ipynb'
https://raw.github.com/sr320/ipython_nb/master/BSMAP2view_larvae.ipynb
September is known as FCD2CA8: November Core ID FCC39EM
#Will go September then Novemeber
!cat /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R1.fastq \
/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L004_R1.fastq > \
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R1a.fastq \
!cat /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R2.fastq \
/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L004_R2.fastq > \
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R2a.fastq \
R1_A8="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM3/filtered_BS_CgM3_GATCAG_L007_R1.fastq"
R1_EM="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgM3/filtered_BS_CgM3_GATCAG_L004_R1.fastq"
!cat {R1_A8} \
{R1_EM} > \
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_R1a.fastq \
^C
!cat /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R2.fastq \
/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L004_R2.fastq > \
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R2a.fastq \
#file ID
fid="CgM1"
#TIMESTAMP
date=!date +%m%d_%H%M
#working directory (parent)
wd="/Volumes/web/cnidarian/BiGo_larvae_merge/"
#where is bsmap
#bsmap="/Users/Shared/Apps/bsmap-2.73/"
bsmap="/Volumes/Bay3/Software/BSMAP/bsmap-2.74/"
#fastq files location R1 location
R1="/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R1a.fastq"
#fastq files location R2 location
#comment out if SE
R2="/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R2a.fastq"
#genome file
genome="/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"
cd {wd}
/Volumes/web/cnidarian/BiGo_larvae_merge
mkdir {fid}_{date}
cd {fid}_{date}
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0228_0652]
#option - number of processes
!{bsmap}bsmap -a {R1} -b {R2} -d {genome} -o bsmap_out.sam -p 1
BSMAP v2.74 Start at: Fri Feb 28 06:55:11 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. 22 secs passed total_kmers: 43046721 Create seed table. 75 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 (read_1): ++,-+ mapping strand (read_2): +-,-- Pair-end alignment(1 threads) Input read file #1: /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R1a.fastq (format: FASTQ) Input read file #2: /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R2a.fastq (format: FASTQ) Output file: bsmap_out.sam (format: SAM) Thread #0: 50000 read pairs finished. 99 secs passed Thread #0: 100000 read pairs finished. 123 secs passed Thread #0: 150000 read pairs finished. 155 secs passed Thread #0: 200000 read pairs finished. 187 secs passed Thread #0: 250000 read pairs finished. 225 secs passed Thread #0: 300000 read pairs finished. 250 secs passed Thread #0: 350000 read pairs finished. 272 secs passed Thread #0: 400000 read pairs finished. 293 secs passed Thread #0: 450000 read pairs finished. 314 secs passed Thread #0: 500000 read pairs finished. 336 secs passed Thread #0: 550000 read pairs finished. 357 secs passed Thread #0: 600000 read pairs finished. 384 secs passed Thread #0: 650000 read pairs finished. 409 secs passed Thread #0: 700000 read pairs finished. 431 secs passed Thread #0: 750000 read pairs finished. 464 secs passed Thread #0: 800000 read pairs finished. 487 secs passed Thread #0: 850000 read pairs finished. 513 secs passed Thread #0: 900000 read pairs finished. 538 secs passed Thread #0: 950000 read pairs finished. 565 secs passed Thread #0: 1000000 read pairs finished. 614 secs passed Thread #0: 1050000 read pairs finished. 636 secs passed Thread #0: 1100000 read pairs finished. 657 secs passed Thread #0: 1150000 read pairs finished. 677 secs passed Thread #0: 1200000 read pairs finished. 698 secs passed Thread #0: 1250000 read pairs finished. 719 secs passed Thread #0: 1300000 read pairs finished. 743 secs passed Thread #0: 1350000 read pairs finished. 763 secs passed Thread #0: 1400000 read pairs finished. 785 secs passed Thread #0: 1450000 read pairs finished. 806 secs passed Thread #0: 1500000 read pairs finished. 827 secs passed Thread #0: 1550000 read pairs finished. 849 secs passed Thread #0: 1600000 read pairs finished. 870 secs passed Thread #0: 1650000 read pairs finished. 891 secs passed Thread #0: 1700000 read pairs finished. 912 secs passed Thread #0: 1750000 read pairs finished. 932 secs passed Thread #0: 1800000 read pairs finished. 953 secs passed Thread #0: 1850000 read pairs finished. 979 secs passed Thread #0: 1900000 read pairs finished. 1001 secs passed Thread #0: 1950000 read pairs finished. 1021 secs passed Thread #0: 2000000 read pairs finished. 1041 secs passed Thread #0: 2050000 read pairs finished. 1061 secs passed Thread #0: 2100000 read pairs finished. 1081 secs passed Thread #0: 2150000 read pairs finished. 1101 secs passed Thread #0: 2200000 read pairs finished. 1121 secs passed Thread #0: 2250000 read pairs finished. 1141 secs passed Thread #0: 2300000 read pairs finished. 1162 secs passed Thread #0: 2350000 read pairs finished. 1183 secs passed Thread #0: 2400000 read pairs finished. 1204 secs passed Thread #0: 2450000 read pairs finished. 1225 secs passed Thread #0: 2500000 read pairs finished. 1246 secs passed Thread #0: 2550000 read pairs finished. 1266 secs passed Thread #0: 2600000 read pairs finished. 1287 secs passed Thread #0: 2650000 read pairs finished. 1307 secs passed Thread #0: 2700000 read pairs finished. 1329 secs passed Thread #0: 2750000 read pairs finished. 1352 secs passed Thread #0: 2800000 read pairs finished. 1374 secs passed Thread #0: 2850000 read pairs finished. 1395 secs passed Thread #0: 2900000 read pairs finished. 1421 secs passed Thread #0: 2950000 read pairs finished. 1452 secs passed Thread #0: 3000000 read pairs finished. 1476 secs passed Thread #0: 3050000 read pairs finished. 1500 secs passed Thread #0: 3100000 read pairs finished. 1524 secs passed Thread #0: 3150000 read pairs finished. 1546 secs passed Thread #0: 3200000 read pairs finished. 1568 secs passed Thread #0: 3250000 read pairs finished. 1594 secs passed Thread #0: 3300000 read pairs finished. 1618 secs passed Thread #0: 3350000 read pairs finished. 1643 secs passed Thread #0: 3400000 read pairs finished. 1665 secs passed Thread #0: 3450000 read pairs finished. 1689 secs passed Thread #0: 3500000 read pairs finished. 1712 secs passed Thread #0: 3550000 read pairs finished. 1734 secs passed Thread #0: 3600000 read pairs finished. 1764 secs passed Thread #0: 3650000 read pairs finished. 1793 secs passed Thread #0: 3700000 read pairs finished. 1819 secs passed Thread #0: 3750000 read pairs finished. 1850 secs passed Thread #0: 3800000 read pairs finished. 1880 secs passed Thread #0: 3850000 read pairs finished. 1907 secs passed Thread #0: 3900000 read pairs finished. 1940 secs passed Thread #0: 3950000 read pairs finished. 1967 secs passed Thread #0: 4000000 read pairs finished. 1998 secs passed Thread #0: 4050000 read pairs finished. 2021 secs passed Thread #0: 4100000 read pairs finished. 2050 secs passed Thread #0: 4150000 read pairs finished. 2074 secs passed Thread #0: 4200000 read pairs finished. 2104 secs passed Thread #0: 4250000 read pairs finished. 2128 secs passed Thread #0: 4300000 read pairs finished. 2152 secs passed Thread #0: 4350000 read pairs finished. 2175 secs passed Thread #0: 4400000 read pairs finished. 2196 secs passed Thread #0: 4450000 read pairs finished. 2221 secs passed Thread #0: 4500000 read pairs finished. 2250 secs passed Thread #0: 4550000 read pairs finished. 2275 secs passed Thread #0: 4600000 read pairs finished. 2303 secs passed Thread #0: 4650000 read pairs finished. 2331 secs passed Thread #0: 4700000 read pairs finished. 2359 secs passed Thread #0: 4750000 read pairs finished. 2384 secs passed Thread #0: 4800000 read pairs finished. 2405 secs passed Thread #0: 4850000 read pairs finished. 2432 secs passed Thread #0: 4900000 read pairs finished. 2459 secs passed Thread #0: 4950000 read pairs finished. 2480 secs passed Thread #0: 5000000 read pairs finished. 2503 secs passed Thread #0: 5050000 read pairs finished. 2527 secs passed Thread #0: 5100000 read pairs finished. 2548 secs passed Thread #0: 5150000 read pairs finished. 2572 secs passed Thread #0: 5200000 read pairs finished. 2594 secs passed Thread #0: 5250000 read pairs finished. 2621 secs passed Thread #0: 5300000 read pairs finished. 2646 secs passed Thread #0: 5350000 read pairs finished. 2672 secs passed Thread #0: 5400000 read pairs finished. 2695 secs passed Thread #0: 5450000 read pairs finished. 2722 secs passed Thread #0: 5500000 read pairs finished. 2745 secs passed Thread #0: 5550000 read pairs finished. 2769 secs passed Thread #0: 5600000 read pairs finished. 2793 secs passed Thread #0: 5650000 read pairs finished. 2816 secs passed Thread #0: 5700000 read pairs finished. 2840 secs passed Thread #0: 5750000 read pairs finished. 2870 secs passed Thread #0: 5800000 read pairs finished. 2901 secs passed Thread #0: 5850000 read pairs finished. 2928 secs passed Thread #0: 5900000 read pairs finished. 2956 secs passed Thread #0: 5950000 read pairs finished. 2986 secs passed Thread #0: 6000000 read pairs finished. 3016 secs passed Thread #0: 6050000 read pairs finished. 3050 secs passed Thread #0: 6100000 read pairs finished. 3078 secs passed Thread #0: 6150000 read pairs finished. 3107 secs passed Thread #0: 6200000 read pairs finished. 3130 secs passed Thread #0: 6250000 read pairs finished. 3152 secs passed Thread #0: 6300000 read pairs finished. 3174 secs passed Thread #0: 6350000 read pairs finished. 3197 secs passed Thread #0: 6400000 read pairs finished. 3219 secs passed Thread #0: 6450000 read pairs finished. 3244 secs passed Thread #0: 6500000 read pairs finished. 3268 secs passed Thread #0: 6550000 read pairs finished. 3295 secs passed Thread #0: 6600000 read pairs finished. 3321 secs passed Thread #0: 6650000 read pairs finished. 3344 secs passed Thread #0: 6700000 read pairs finished. 3368 secs passed Thread #0: 6750000 read pairs finished. 3393 secs passed Thread #0: 6800000 read pairs finished. 3419 secs passed Thread #0: 6850000 read pairs finished. 3441 secs passed Thread #0: 6900000 read pairs finished. 3468 secs passed Thread #0: 6950000 read pairs finished. 3494 secs passed Thread #0: 7000000 read pairs finished. 3518 secs passed Thread #0: 7050000 read pairs finished. 3543 secs passed Thread #0: 7100000 read pairs finished. 3566 secs passed Thread #0: 7150000 read pairs finished. 3591 secs passed Thread #0: 7200000 read pairs finished. 3615 secs passed Thread #0: 7250000 read pairs finished. 3643 secs passed Thread #0: 7300000 read pairs finished. 3667 secs passed Thread #0: 7350000 read pairs finished. 3691 secs passed Thread #0: 7400000 read pairs finished. 3715 secs passed Thread #0: 7450000 read pairs finished. 3736 secs passed Thread #0: 7500000 read pairs finished. 3760 secs passed Thread #0: 7550000 read pairs finished. 3784 secs passed Thread #0: 7600000 read pairs finished. 3807 secs passed Thread #0: 7650000 read pairs finished. 3831 secs passed Thread #0: 7700000 read pairs finished. 3865 secs passed Thread #0: 7750000 read pairs finished. 3888 secs passed Thread #0: 7800000 read pairs finished. 3931 secs passed Thread #0: 7850000 read pairs finished. 3954 secs passed Thread #0: 7900000 read pairs finished. 3975 secs passed Thread #0: 7950000 read pairs finished. 3999 secs passed Thread #0: 8000000 read pairs finished. 4021 secs passed Thread #0: 8050000 read pairs finished. 4043 secs passed Thread #0: 8100000 read pairs finished. 4066 secs passed Thread #0: 8150000 read pairs finished. 4088 secs passed Thread #0: 8200000 read pairs finished. 4111 secs passed Thread #0: 8250000 read pairs finished. 4137 secs passed Thread #0: 8297202 read pairs finished. 4159 secs passed Total number of aligned reads: pairs: 3832546 (46%) single a: 1591687 (19%) single b: 1349271 (16%) Done. Finished at Fri Feb 28 08:04:30 2014 Total time consumed: 4159 secs
#!python {bsmap}methratio.py -d {genome} -u -z -g -o methratio_out.txt -s {bsmap}samtools bsmap_out.sam
#file ID
fid="CgM1_Enm"
#TIMESTAMP
date=!date +%m%d_%H%M
#working directory (parent)
wd="/Volumes/web/cnidarian/BiGo_larvae_merge/"
#where is bsmap
#bsmap="/Users/Shared/Apps/bsmap-2.73/"
bsmap="/Volumes/Bay3/Software/BSMAP/bsmap-2.74/"
#fastq files location R1 location
R1="/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R1a.fastq"
#fastq files location R2 location
#comment out if SE
R2="/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R2a.fastq"
#genome file
#genome="/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"
genome="/Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna.genome.fa"
cd {wd}
/Volumes/web/cnidarian/BiGo_larvae_merge
mkdir {fid}_{date}
cd {fid}_{date}
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_Enm_[0228_0836]
!{bsmap}bsmap -a {R1} -b {R2} -d {genome} -o bsmap_out.sam -p 2
BSMAP v2.74 Start at: Fri Feb 28 08:37:29 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.genome.fa (format: FASTA) Load in 7658 db seqs, total size 557717710 bp. 22 secs passed total_kmers: 43046721 Create seed table. 72 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 (read_1): ++,-+ mapping strand (read_2): +-,-- Pair-end alignment(2 threads) Input read file #1: /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R1a.fastq (format: FASTQ) Input read file #2: /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R2a.fastq (format: FASTQ) Output file: bsmap_out.sam (format: SAM) Thread #0: 100000 read pairs finished. 105 secs passed Thread #1: 50000 read pairs finished. 105 secs passed Thread #0: 150000 read pairs finished. 136 secs passed Thread #1: 200000 read pairs finished. 136 secs passed Thread #0: 250000 read pairs finished. 163 secs passed Thread #1: 300000 read pairs finished. 164 secs passed Thread #0: 350000 read pairs finished. 188 secs passed Thread #1: 400000 read pairs finished. 190 secs passed Thread #0: 450000 read pairs finished. 227 secs passed Thread #1: 500000 read pairs finished. 229 secs passed Thread #0: 550000 read pairs finished. 258 secs passed Thread #1: 600000 read pairs finished. 261 secs passed Thread #0: 650000 read pairs finished. 285 secs passed Thread #1: 700000 read pairs finished. 287 secs passed Thread #0: 750000 read pairs finished. 311 secs passed Thread #1: 800000 read pairs finished. 313 secs passed Thread #0: 850000 read pairs finished. 336 secs passed Thread #1: 900000 read pairs finished. 340 secs passed Thread #0: 950000 read pairs finished. 376 secs passed Thread #1: 1000000 read pairs finished. 380 secs passed Thread #0: 1050000 read pairs finished. 409 secs passed Thread #1: 1100000 read pairs finished. 411 secs passed Thread #0: 1150000 read pairs finished. 439 secs passed Thread #1: 1200000 read pairs finished. 441 secs passed Thread #0: 1250000 read pairs finished. 464 secs passed Thread #1: 1300000 read pairs finished. 467 secs passed Thread #0: 1350000 read pairs finished. 490 secs passed Thread #1: 1400000 read pairs finished. 492 secs passed Thread #0: 1450000 read pairs finished. 514 secs passed Thread #1: 1500000 read pairs finished. 518 secs passed Thread #0: 1550000 read pairs finished. 544 secs passed Thread #1: 1600000 read pairs finished. 547 secs passed Thread #0: 1650000 read pairs finished. 576 secs passed Thread #1: 1700000 read pairs finished. 580 secs passed Thread #0: 1750000 read pairs finished. 610 secs passed Thread #1: 1800000 read pairs finished. 616 secs passed Thread #0: 1850000 read pairs finished. 644 secs passed Thread #1: 1900000 read pairs finished. 651 secs passed Thread #0: 1950000 read pairs finished. 686 secs passed Thread #1: 2000000 read pairs finished. 693 secs passed Thread #0: 2050000 read pairs finished. 731 secs passed Thread #1: 2100000 read pairs finished. 735 secs passed Thread #0: 2150000 read pairs finished. 772 secs passed Thread #1: 2200000 read pairs finished. 779 secs passed Thread #0: 2250000 read pairs finished. 826 secs passed Thread #1: 2300000 read pairs finished. 832 secs passed Thread #0: 2350000 read pairs finished. 861 secs passed Thread #1: 2400000 read pairs finished. 867 secs passed Thread #0: 2450000 read pairs finished. 901 secs passed Thread #1: 2500000 read pairs finished. 909 secs passed Thread #0: 2550000 read pairs finished. 935 secs passed Thread #1: 2600000 read pairs finished. 942 secs passed Thread #0: 2650000 read pairs finished. 977 secs passed Thread #1: 2700000 read pairs finished. 984 secs passed Thread #0: 2750000 read pairs finished. 1013 secs passed Thread #1: 2800000 read pairs finished. 1018 secs passed Thread #0: 2850000 read pairs finished. 1049 secs passed Thread #1: 2900000 read pairs finished. 1055 secs passed Thread #0: 2950000 read pairs finished. 1084 secs passed Thread #1: 3000000 read pairs finished. 1100 secs passed Thread #0: 3050000 read pairs finished. 1118 secs passed Thread #1: 3100000 read pairs finished. 1141 secs passed Thread #0: 3150000 read pairs finished. 1152 secs passed Thread #1: 3200000 read pairs finished. 1204 secs passed Thread #0: 3250000 read pairs finished. 1212 secs passed Thread #1: 3300000 read pairs finished. 1240 secs passed Thread #0: 3350000 read pairs finished. 1248 secs passed Thread #1: 3400000 read pairs finished. 1276 secs passed Thread #0: 3450000 read pairs finished. 1284 secs passed Thread #1: 3500000 read pairs finished. 1310 secs passed Thread #0: 3550000 read pairs finished. 1319 secs passed Thread #1: 3600000 read pairs finished. 1342 secs passed Thread #0: 3650000 read pairs finished. 1350 secs passed Thread #1: 3700000 read pairs finished. 1389 secs passed Thread #0: 3750000 read pairs finished. 1428 secs passed Thread #1: 3800000 read pairs finished. 1489 secs passed Thread #0: 3850000 read pairs finished. 1516 secs passed Thread #1: 3900000 read pairs finished. 1578 secs passed Thread #0: 3950000 read pairs finished. 1590 secs passed Thread #1: 4000000 read pairs finished. 1633 secs passed Thread #0: 4050000 read pairs finished. 1662 secs passed Thread #1: 4100000 read pairs finished. 1718 secs passed Thread #0: 4150000 read pairs finished. 1813 secs passed Thread #1: 4200000 read pairs finished. 1829 secs passed Thread #0: 4250000 read pairs finished. 1858 secs passed Thread #1: 4300000 read pairs finished. 1866 secs passed Thread #0: 4350000 read pairs finished. 1885 secs passed Thread #1: 4400000 read pairs finished. 1894 secs passed Thread #0: 4450000 read pairs finished. 1914 secs passed Thread #1: 4500000 read pairs finished. 1924 secs passed Thread #0: 4550000 read pairs finished. 1940 secs passed Thread #1: 4600000 read pairs finished. 1954 secs passed Thread #0: 4650000 read pairs finished. 1984 secs passed Thread #1: 4700000 read pairs finished. 1986 secs passed Thread #0: 4750000 read pairs finished. 2012 secs passed Thread #1: 4800000 read pairs finished. 2046 secs passed Thread #0: 4850000 read pairs finished. 2075 secs passed Thread #1: 4900000 read pairs finished. 2080 secs passed Thread #0: 4950000 read pairs finished. 2137 secs passed Thread #1: 5000000 read pairs finished. 2163 secs passed Thread #0: 5050000 read pairs finished. 2172 secs passed Thread #1: 5100000 read pairs finished. 2193 secs passed Thread #0: 5150000 read pairs finished. 2201 secs passed Thread #1: 5200000 read pairs finished. 2251 secs passed Thread #0: 5250000 read pairs finished. 2253 secs passed Thread #1: 5300000 read pairs finished. 2307 secs passed Thread #0: 5350000 read pairs finished. 2309 secs passed Thread #1: 5400000 read pairs finished. 2333 secs passed Thread #0: 5450000 read pairs finished. 2438 secs passed Thread #1: 5500000 read pairs finished. 2439 secs passed Thread #0: 5550000 read pairs finished. 2539 secs passed Thread #1: 5600000 read pairs finished. 2554 secs passed Thread #0: 5650000 read pairs finished. 2567 secs passed Thread #1: 5700000 read pairs finished. 2596 secs passed Thread #0: 5750000 read pairs finished. 2605 secs passed Thread #1: 5800000 read pairs finished. 2662 secs passed Thread #0: 5850000 read pairs finished. 2664 secs passed Thread #1: 5900000 read pairs finished. 2693 secs passed Thread #0: 5950000 read pairs finished. 2723 secs passed Thread #1: 6000000 read pairs finished. 2735 secs passed Thread #0: 6050000 read pairs finished. 2767 secs passed Thread #1: 6100000 read pairs finished. 2769 secs passed Thread #0: 6150000 read pairs finished. 2809 secs passed Thread #1: 6200000 read pairs finished. 2811 secs passed Thread #0: 6250000 read pairs finished. 2871 secs passed Thread #1: 6300000 read pairs finished. 2889 secs passed Thread #0: 6350000 read pairs finished. 2912 secs passed Thread #1: 6400000 read pairs finished. 2934 secs passed Thread #0: 6450000 read pairs finished. 2956 secs passed Thread #1: 6500000 read pairs finished. 2966 secs passed Thread #0: 6550000 read pairs finished. 3008 secs passed Thread #1: 6600000 read pairs finished. 3018 secs passed Thread #0: 6650000 read pairs finished. 3058 secs passed Thread #1: 6700000 read pairs finished. 3100 secs passed Thread #0: 6750000 read pairs finished. 3102 secs passed Thread #1: 6800000 read pairs finished. 3137 secs passed Thread #0: 6850000 read pairs finished. 3139 secs passed Thread #1: 6900000 read pairs finished. 3174 secs passed Thread #0: 6950000 read pairs finished. 3187 secs passed Thread #1: 7000000 read pairs finished. 3211 secs passed Thread #0: 7050000 read pairs finished. 3244 secs passed Thread #1: 7100000 read pairs finished. 3246 secs passed Thread #0: 7150000 read pairs finished. 3284 secs passed Thread #1: 7200000 read pairs finished. 3290 secs passed Thread #0: 7250000 read pairs finished. 3358 secs passed Thread #1: 7300000 read pairs finished. 3361 secs passed Thread #0: 7350000 read pairs finished. 3413 secs passed Thread #1: 7400000 read pairs finished. 3433 secs passed Thread #0: 7450000 read pairs finished. 3456 secs passed Thread #1: 7500000 read pairs finished. 3479 secs passed Thread #0: 7550000 read pairs finished. 3496 secs passed Thread #1: 7600000 read pairs finished. 3512 secs passed Thread #0: 7650000 read pairs finished. 3531 secs passed Thread #1: 7700000 read pairs finished. 3562 secs passed Thread #0: 7750000 read pairs finished. 3571 secs passed Thread #1: 7800000 read pairs finished. 3590 secs passed Thread #0: 7850000 read pairs finished. 3625 secs passed Thread #1: 7900000 read pairs finished. 3629 secs passed Thread #0: 7950000 read pairs finished. 3659 secs passed Thread #1: 8000000 read pairs finished. 3672 secs passed Thread #0: 8050000 read pairs finished. 3702 secs passed Thread #1: 8100000 read pairs finished. 3711 secs passed Thread #0: 8150000 read pairs finished. 3732 secs passed Thread #1: 8200000 read pairs finished. 3791 secs passed Thread #0: 8250000 read pairs finished. 3808 secs passed Total number of aligned reads: pairs: 2340694 (28%) single a: 3150081 (38%) single b: 2811635 (34%) Done. Finished at Fri Feb 28 09:41:09 2014 Total time consumed: 3820 secs
#file ID
fid="CgM1_A8__Esm"
#TIMESTAMP
date=!date +%m%d_%H%M
#working directory (parent)
wd="/Volumes/web/cnidarian/BiGo_larvae_merge/"
#where is bsmap
#bsmap="/Users/Shared/Apps/bsmap-2.73/"
bsmap="/Volumes/Bay3/Software/BSMAP/bsmap-2.74/"
#fastq files location R1 location
#R1="/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R1a.fastq"
R1="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R1.fastq"
#fastq files location R2 location
#comment out if SE
#R2="/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R2a.fastq"
R2="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R2.fastq"
#genome file
genome="/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"
#genome="/Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna.genome.fa"
cd {wd}
/Volumes/web/cnidarian/BiGo_larvae_merge
mkdir {fid}_{date}
cd {fid}_{date}
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_A8__Esm_[0228_0958]
!{bsmap}bsmap -a {R1} -b {R2} -d {genome} -o bsmap_out.sam -p 2
BSMAP v2.74 Start at: Fri Feb 28 09:59:43 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. 629 secs passed total_kmers: 43046721 Create seed table. 683 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 (read_1): ++,-+ mapping strand (read_2): +-,-- Pair-end alignment(2 threads) Input read file #1: /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R1.fastq (format: FASTQ) Input read file #2: /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R2.fastq (format: FASTQ) Output file: bsmap_out.sam (format: SAM) Thread #0: 50000 read pairs finished. 854 secs passed Thread #1: 100000 read pairs finished. 881 secs passed Thread #1: 200000 read pairs finished. 921 secs passed Thread #0: 150000 read pairs finished. 1001 secs passed Thread #1: 250000 read pairs finished. 1040 secs passed Thread #0: 300000 read pairs finished. 1041 secs passed Thread #1: 350000 read pairs finished. 1073 secs passed Thread #0: 400000 read pairs finished. 1074 secs passed Thread #1: 450000 read pairs finished. 1098 secs passed Thread #0: 500000 read pairs finished. 1099 secs passed Thread #1: 550000 read pairs finished. 1129 secs passed Thread #0: 600000 read pairs finished. 1130 secs passed Thread #1: 650000 read pairs finished. 1188 secs passed Thread #0: 700000 read pairs finished. 1192 secs passed Thread #1: 750000 read pairs finished. 1236 secs passed Thread #0: 800000 read pairs finished. 1238 secs passed Thread #1: 850000 read pairs finished. 1273 secs passed Thread #0: 900000 read pairs finished. 1275 secs passed Thread #1: 950000 read pairs finished. 1311 secs passed Thread #0: 1000000 read pairs finished. 1312 secs passed Thread #1: 1050000 read pairs finished. 1345 secs passed Thread #0: 1100000 read pairs finished. 1348 secs passed Thread #1: 1150000 read pairs finished. 1378 secs passed Thread #0: 1200000 read pairs finished. 1382 secs passed Thread #1: 1250000 read pairs finished. 1415 secs passed Thread #0: 1300000 read pairs finished. 1419 secs passed Thread #1: 1350000 read pairs finished. 1451 secs passed Thread #0: 1400000 read pairs finished. 1453 secs passed Thread #1: 1450000 read pairs finished. 1486 secs passed Thread #0: 1500000 read pairs finished. 1490 secs passed Thread #1: 1550000 read pairs finished. 1516 secs passed Thread #0: 1600000 read pairs finished. 1519 secs passed Thread #1: 1650000 read pairs finished. 1548 secs passed Thread #0: 1700000 read pairs finished. 1553 secs passed Thread #1: 1750000 read pairs finished. 1584 secs passed Thread #0: 1800000 read pairs finished. 1588 secs passed Thread #1: 1850000 read pairs finished. 1609 secs passed Thread #0: 1900000 read pairs finished. 1613 secs passed Thread #1: 1950000 read pairs finished. 1637 secs passed Thread #0: 2000000 read pairs finished. 1642 secs passed Thread #1: 2050000 read pairs finished. 1664 secs passed Thread #0: 2100000 read pairs finished. 1667 secs passed Thread #1: 2150000 read pairs finished. 1692 secs passed Thread #0: 2200000 read pairs finished. 1698 secs passed Thread #1: 2250000 read pairs finished. 1722 secs passed Thread #0: 2300000 read pairs finished. 1728 secs passed Thread #1: 2350000 read pairs finished. 1749 secs passed Thread #0: 2400000 read pairs finished. 1756 secs passed Thread #1: 2450000 read pairs finished. 1783 secs passed Thread #0: 2500000 read pairs finished. 1790 secs passed Thread #1: 2550000 read pairs finished. 1810 secs passed Thread #0: 2600000 read pairs finished. 1818 secs passed Thread #1: 2650000 read pairs finished. 1837 secs passed Thread #0: 2700000 read pairs finished. 1843 secs passed Thread #1: 2750000 read pairs finished. 1862 secs passed Thread #0: 2800000 read pairs finished. 1870 secs passed Thread #1: 2850000 read pairs finished. 1891 secs passed Thread #0: 2900000 read pairs finished. 1899 secs passed Thread #1: 2950000 read pairs finished. 1928 secs passed Thread #0: 3000000 read pairs finished. 1939 secs passed Thread #1: 3050000 read pairs finished. 1972 secs passed Thread #0: 3100000 read pairs finished. 1982 secs passed Thread #1: 3150000 read pairs finished. 2002 secs passed Thread #0: 3200000 read pairs finished. 2008 secs passed Thread #1: 3250000 read pairs finished. 2028 secs passed Thread #0: 3300000 read pairs finished. 2036 secs passed Thread #1: 3350000 read pairs finished. 2054 secs passed Thread #0: 3400000 read pairs finished. 2064 secs passed Thread #1: 3450000 read pairs finished. 2084 secs passed Thread #0: 3500000 read pairs finished. 2093 secs passed Thread #1: 3550000 read pairs finished. 2114 secs passed Thread #0: 3600000 read pairs finished. 2122 secs passed Thread #1: 3650000 read pairs finished. 2139 secs passed Thread #0: 3700000 read pairs finished. 2148 secs passed Thread #1: 3750000 read pairs finished. 2169 secs passed Thread #0: 3800000 read pairs finished. 2177 secs passed Thread #1: 3850000 read pairs finished. 2194 secs passed Thread #0: 3900000 read pairs finished. 2203 secs passed Thread #1: 3950000 read pairs finished. 2222 secs passed Thread #0: 4000000 read pairs finished. 2229 secs passed Thread #1: 4050000 read pairs finished. 2246 secs passed Thread #0: 4100000 read pairs finished. 2255 secs passed Thread #1: 4150000 read pairs finished. 2277 secs passed Thread #0: 4200000 read pairs finished. 2287 secs passed Thread #1: 4250000 read pairs finished. 2306 secs passed Thread #0: 4300000 read pairs finished. 2315 secs passed Thread #1: 4350000 read pairs finished. 2332 secs passed Thread #0: 4400000 read pairs finished. 2342 secs passed Thread #1: 4450000 read pairs finished. 2359 secs passed Thread #0: 4500000 read pairs finished. 2368 secs passed Thread #1: 4550000 read pairs finished. 2386 secs passed Thread #0: 4600000 read pairs finished. 2395 secs passed Thread #1: 4650000 read pairs finished. 2415 secs passed Thread #0: 4700000 read pairs finished. 2428 secs passed Thread #1: 4750000 read pairs finished. 2445 secs passed Thread #0: 4800000 read pairs finished. 2456 secs passed Thread #1: 4850000 read pairs finished. 2475 secs passed Thread #0: 4900000 read pairs finished. 2488 secs passed Thread #1: 4950000 read pairs finished. 2504 secs passed Thread #0: 5000000 read pairs finished. 2516 secs passed Thread #1: 5050000 read pairs finished. 2534 secs passed Thread #0: 5100000 read pairs finished. 2545 secs passed Thread #1: 5150000 read pairs finished. 2560 secs passed Thread #0: 5200000 read pairs finished. 2571 secs passed Thread #1: 5250000 read pairs finished. 2587 secs passed Thread #0: 5300000 read pairs finished. 2598 secs passed Thread #1: 5350000 read pairs finished. 2613 secs passed Thread #0: 5400000 read pairs finished. 2625 secs passed Thread #1: 5450000 read pairs finished. 2641 secs passed Thread #0: 5500000 read pairs finished. 2655 secs passed Thread #1: 5543163 read pairs finished. 2664 secs passed Total number of aligned reads: pairs: 2597461 (47%) single a: 1090241 (20%) single b: 894626 (16%) Done. Finished at Fri Feb 28 10:44:07 2014 Total time consumed: 2664 secs
About the same percent map with using unmerged file.
#file ID
fid="CgM1_A8__Erm"
#TIMESTAMP
date=!date +%m%d_%H%M
#working directory (parent)
wd="/Volumes/web/cnidarian/BiGo_larvae_merge/"
#where is bsmap
#bsmap="/Users/Shared/Apps/bsmap-2.73/"
bsmap="/Volumes/Bay3/Software/BSMAP/bsmap-2.74/"
#fastq files location R1 location
#R1="/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R1a.fastq"
R1="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R1.fastq"
#fastq files location R2 location
#comment out if SE
#R2="/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R2a.fastq"
R2="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R2.fastq"
#genome file
genome="/Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_rm.genome.fa"
#genome="/Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna.genome.fa"
cd {wd}
/Volumes/web/cnidarian/BiGo_larvae_merge
mkdir {fid}_{date}
cd {fid}_{date}
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_A8__Erm_[0228_1048]
!{bsmap}bsmap -a {R1} -b {R2} -d {genome} -o bsmap_out.sam -p 2
BSMAP v2.74 Start at: Fri Feb 28 10:49:29 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_rm.genome.fa (format: FASTA) Load in 7658 db seqs, total size 557717710 bp. 87 secs passed total_kmers: 43046721 Create seed table. 134 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 (read_1): ++,-+ mapping strand (read_2): +-,-- Pair-end alignment(2 threads) Input read file #1: /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R1.fastq (format: FASTQ) Input read file #2: /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R2.fastq (format: FASTQ) Output file: bsmap_out.sam (format: SAM) Thread #1: 100000 read pairs finished. 161 secs passed Thread #0: 50000 read pairs finished. 161 secs passed Thread #1: 150000 read pairs finished. 186 secs passed Thread #0: 200000 read pairs finished. 187 secs passed Thread #1: 250000 read pairs finished. 212 secs passed Thread #0: 300000 read pairs finished. 213 secs passed Thread #1: 350000 read pairs finished. 238 secs passed Thread #0: 400000 read pairs finished. 239 secs passed Thread #1: 450000 read pairs finished. 262 secs passed Thread #0: 500000 read pairs finished. 264 secs passed Thread #1: 550000 read pairs finished. 287 secs passed Thread #0: 600000 read pairs finished. 290 secs passed Thread #1: 650000 read pairs finished. 313 secs passed Thread #0: 700000 read pairs finished. 318 secs passed Thread #1: 750000 read pairs finished. 404 secs passed Thread #0: 800000 read pairs finished. 410 secs passed Thread #1: 850000 read pairs finished. 437 secs passed Thread #0: 900000 read pairs finished. 442 secs passed Thread #1: 950000 read pairs finished. 472 secs passed Thread #0: 1000000 read pairs finished. 479 secs passed Thread #1: 1050000 read pairs finished. 517 secs passed Thread #0: 1100000 read pairs finished. 525 secs passed Thread #1: 1150000 read pairs finished. 598 secs passed Thread #0: 1200000 read pairs finished. 605 secs passed Thread #1: 1250000 read pairs finished. 653 secs passed Thread #0: 1300000 read pairs finished. 680 secs passed Thread #1: 1350000 read pairs finished. 777 secs passed Thread #0: 1400000 read pairs finished. 783 secs passed Thread #1: 1450000 read pairs finished. 874 secs passed Thread #0: 1500000 read pairs finished. 892 secs passed Thread #1: 1550000 read pairs finished. 949 secs passed Thread #0: 1600000 read pairs finished. 994 secs passed Thread #1: 1650000 read pairs finished. 1009 secs passed Thread #0: 1700000 read pairs finished. 1056 secs passed Thread #1: 1750000 read pairs finished. 1073 secs passed Thread #0: 1800000 read pairs finished. 1119 secs passed Thread #1: 1850000 read pairs finished. 1131 secs passed Thread #0: 1900000 read pairs finished. 1167 secs passed Thread #1: 1950000 read pairs finished. 1236 secs passed Thread #0: 2000000 read pairs finished. 1281 secs passed Thread #1: 2050000 read pairs finished. 1354 secs passed Thread #0: 2100000 read pairs finished. 1361 secs passed Thread #1: 2150000 read pairs finished. 1417 secs passed Thread #0: 2200000 read pairs finished. 1424 secs passed Thread #1: 2250000 read pairs finished. 1467 secs passed Thread #0: 2300000 read pairs finished. 1470 secs passed Thread #1: 2350000 read pairs finished. 1516 secs passed Thread #0: 2400000 read pairs finished. 1521 secs passed Thread #1: 2450000 read pairs finished. 1568 secs passed Thread #0: 2500000 read pairs finished. 1574 secs passed Thread #1: 2550000 read pairs finished. 1630 secs passed Thread #0: 2600000 read pairs finished. 1668 secs passed Thread #1: 2650000 read pairs finished. 1727 secs passed Thread #0: 2700000 read pairs finished. 1729 secs passed Thread #1: 2750000 read pairs finished. 1774 secs passed Thread #0: 2800000 read pairs finished. 1777 secs passed Thread #1: 2850000 read pairs finished. 1825 secs passed Thread #0: 2900000 read pairs finished. 1827 secs passed Thread #1: 2950000 read pairs finished. 1883 secs passed Thread #0: 3000000 read pairs finished. 1886 secs passed Thread #1: 3050000 read pairs finished. 1938 secs passed Thread #0: 3100000 read pairs finished. 1942 secs passed Thread #1: 3150000 read pairs finished. 1989 secs passed Thread #0: 3200000 read pairs finished. 1994 secs passed Thread #1: 3250000 read pairs finished. 2035 secs passed Thread #0: 3300000 read pairs finished. 2041 secs passed Thread #1: 3350000 read pairs finished. 2080 secs passed Thread #0: 3400000 read pairs finished. 2086 secs passed Thread #1: 3450000 read pairs finished. 2130 secs passed Thread #0: 3500000 read pairs finished. 2136 secs passed Thread #1: 3550000 read pairs finished. 2175 secs passed Thread #0: 3600000 read pairs finished. 2184 secs passed Thread #1: 3650000 read pairs finished. 2238 secs passed Thread #0: 3700000 read pairs finished. 2255 secs passed Thread #1: 3750000 read pairs finished. 2316 secs passed Thread #0: 3800000 read pairs finished. 2328 secs passed Thread #1: 3850000 read pairs finished. 2377 secs passed Thread #0: 3900000 read pairs finished. 2385 secs passed Thread #1: 3950000 read pairs finished. 2426 secs passed Thread #0: 4000000 read pairs finished. 2432 secs passed Thread #1: 4050000 read pairs finished. 2467 secs passed Thread #0: 4100000 read pairs finished. 2476 secs passed Thread #1: 4150000 read pairs finished. 2516 secs passed Thread #0: 4200000 read pairs finished. 2525 secs passed Thread #1: 4250000 read pairs finished. 2573 secs passed Thread #0: 4300000 read pairs finished. 2586 secs passed Thread #1: 4350000 read pairs finished. 2638 secs passed Thread #0: 4400000 read pairs finished. 2650 secs passed Thread #1: 4450000 read pairs finished. 2694 secs passed Thread #0: 4500000 read pairs finished. 2705 secs passed Thread #1: 4550000 read pairs finished. 2740 secs passed Thread #0: 4600000 read pairs finished. 2756 secs passed Thread #1: 4650000 read pairs finished. 2784 secs passed Thread #0: 4700000 read pairs finished. 2795 secs passed Thread #1: 4750000 read pairs finished. 2821 secs passed Thread #0: 4800000 read pairs finished. 2833 secs passed Thread #1: 4850000 read pairs finished. 2857 secs passed Thread #0: 4900000 read pairs finished. 2869 secs passed Thread #1: 4950000 read pairs finished. 2894 secs passed Thread #0: 5000000 read pairs finished. 2907 secs passed Thread #1: 5050000 read pairs finished. 2930 secs passed Thread #0: 5100000 read pairs finished. 2942 secs passed Thread #1: 5150000 read pairs finished. 2965 secs passed Thread #0: 5200000 read pairs finished. 2976 secs passed Thread #1: 5250000 read pairs finished. 2999 secs passed Thread #0: 5300000 read pairs finished. 3012 secs passed Thread #1: 5350000 read pairs finished. 3036 secs passed Thread #0: 5400000 read pairs finished. 3048 secs passed Thread #1: 5450000 read pairs finished. 3070 secs passed Thread #0: 5500000 read pairs finished. 3083 secs passed Thread #1: 5543163 read pairs finished. 3096 secs passed Total number of aligned reads: pairs: 2174860 (39%) single a: 1168661 (21%) single b: 982745 (18%) Done. Finished at Fri Feb 28 11:41:05 2014 Total time consumed: 3096 secs
#file ID
fid="CgM1_A8__E"
#TIMESTAMP
date=!date +%m%d_%H%M
#working directory (parent)
wd="/Volumes/web/cnidarian/BiGo_larvae_merge/"
#where is bsmap
#bsmap="/Users/Shared/Apps/bsmap-2.73/"
bsmap="/Volumes/Bay3/Software/BSMAP/bsmap-2.74/"
#fastq files location R1 location
#R1="/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R1a.fastq"
R1="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R1.fastq"
#fastq files location R2 location
#comment out if SE
#R2="/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R2a.fastq"
R2="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R2.fastq"
#genome file
#genome="/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"
genome="/Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna.genome.fa"
cd {wd}
/Volumes/web/cnidarian/BiGo_larvae_merge
mkdir {fid}_{date}
cd {fid}_{date}
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_A8__E_[0228_1457]
!{bsmap}bsmap -a {R1} -b {R2} -d {genome} -o bsmap_out.sam -p 2
BSMAP v2.74 Start at: Fri Feb 28 14:57:35 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.genome.fa (format: FASTA) Load in 7658 db seqs, total size 557717710 bp. 22 secs passed total_kmers: 43046721 Create seed table. 69 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 (read_1): ++,-+ mapping strand (read_2): +-,-- Pair-end alignment(2 threads) Input read file #1: /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R1.fastq (format: FASTQ) Input read file #2: /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R2.fastq (format: FASTQ) Output file: bsmap_out.sam (format: SAM) Thread #0: 50000 read pairs finished. 98 secs passed Thread #1: 100000 read pairs finished. 99 secs passed Thread #0: 150000 read pairs finished. 126 secs passed Thread #1: 200000 read pairs finished. 126 secs passed Thread #0: 250000 read pairs finished. 152 secs passed Thread #1: 300000 read pairs finished. 153 secs passed Thread #0: 350000 read pairs finished. 187 secs passed Thread #1: 400000 read pairs finished. 189 secs passed Thread #0: 450000 read pairs finished. 225 secs passed Thread #1: 500000 read pairs finished. 228 secs passed Thread #0: 550000 read pairs finished. 268 secs passed Thread #1: 600000 read pairs finished. 270 secs passed Thread #0: 650000 read pairs finished. 299 secs passed Thread #1: 700000 read pairs finished. 302 secs passed Thread #0: 750000 read pairs finished. 334 secs passed Thread #1: 800000 read pairs finished. 337 secs passed Thread #0: 850000 read pairs finished. 368 secs passed Thread #1: 900000 read pairs finished. 371 secs passed Thread #0: 950000 read pairs finished. 402 secs passed Thread #1: 1000000 read pairs finished. 406 secs passed Thread #0: 1050000 read pairs finished. 436 secs passed Thread #1: 1100000 read pairs finished. 440 secs passed Thread #0: 1150000 read pairs finished. 470 secs passed Thread #1: 1200000 read pairs finished. 475 secs passed Thread #0: 1250000 read pairs finished. 499 secs passed Thread #1: 1300000 read pairs finished. 503 secs passed Thread #0: 1350000 read pairs finished. 529 secs passed Thread #1: 1400000 read pairs finished. 533 secs passed Thread #0: 1450000 read pairs finished. 557 secs passed Thread #1: 1500000 read pairs finished. 562 secs passed Thread #0: 1550000 read pairs finished. 586 secs passed Thread #1: 1600000 read pairs finished. 590 secs passed Thread #0: 1650000 read pairs finished. 615 secs passed Thread #1: 1700000 read pairs finished. 621 secs passed Thread #0: 1750000 read pairs finished. 644 secs passed Thread #1: 1800000 read pairs finished. 649 secs passed Thread #0: 1850000 read pairs finished. 672 secs passed Thread #1: 1900000 read pairs finished. 678 secs passed Thread #0: 1950000 read pairs finished. 701 secs passed Thread #1: 2000000 read pairs finished. 706 secs passed Thread #0: 2050000 read pairs finished. 729 secs passed Thread #1: 2100000 read pairs finished. 735 secs passed Thread #0: 2150000 read pairs finished. 757 secs passed Thread #1: 2200000 read pairs finished. 763 secs passed Thread #0: 2250000 read pairs finished. 785 secs passed Thread #1: 2300000 read pairs finished. 792 secs passed Thread #0: 2350000 read pairs finished. 817 secs passed Thread #1: 2400000 read pairs finished. 823 secs passed Thread #0: 2450000 read pairs finished. 845 secs passed Thread #1: 2500000 read pairs finished. 851 secs passed Thread #0: 2550000 read pairs finished. 873 secs passed Thread #1: 2600000 read pairs finished. 879 secs passed Thread #0: 2650000 read pairs finished. 901 secs passed Thread #1: 2700000 read pairs finished. 907 secs passed Thread #0: 2750000 read pairs finished. 930 secs passed Thread #1: 2800000 read pairs finished. 937 secs passed Thread #0: 2850000 read pairs finished. 959 secs passed Thread #1: 2900000 read pairs finished. 965 secs passed Thread #0: 2950000 read pairs finished. 987 secs passed Thread #1: 3000000 read pairs finished. 993 secs passed Thread #0: 3050000 read pairs finished. 1015 secs passed Thread #1: 3100000 read pairs finished. 1021 secs passed Thread #0: 3150000 read pairs finished. 1043 secs passed Thread #1: 3200000 read pairs finished. 1050 secs passed Thread #0: 3250000 read pairs finished. 1070 secs passed Thread #1: 3300000 read pairs finished. 1078 secs passed Thread #0: 3350000 read pairs finished. 1098 secs passed Thread #1: 3400000 read pairs finished. 1106 secs passed Thread #0: 3450000 read pairs finished. 1127 secs passed Thread #1: 3500000 read pairs finished. 1134 secs passed Thread #0: 3550000 read pairs finished. 1154 secs passed Thread #1: 3600000 read pairs finished. 1162 secs passed Thread #0: 3650000 read pairs finished. 1184 secs passed Thread #1: 3700000 read pairs finished. 1192 secs passed Thread #0: 3750000 read pairs finished. 1215 secs passed Thread #1: 3800000 read pairs finished. 1222 secs passed Thread #0: 3850000 read pairs finished. 1241 secs passed Thread #1: 3900000 read pairs finished. 1247 secs passed Thread #0: 3950000 read pairs finished. 1265 secs passed Thread #1: 4000000 read pairs finished. 1271 secs passed Thread #0: 4050000 read pairs finished. 1289 secs passed Thread #1: 4100000 read pairs finished. 1295 secs passed Thread #0: 4150000 read pairs finished. 1315 secs passed Thread #1: 4200000 read pairs finished. 1323 secs passed Thread #0: 4250000 read pairs finished. 1341 secs passed Thread #1: 4300000 read pairs finished. 1348 secs passed Thread #0: 4350000 read pairs finished. 1366 secs passed Thread #1: 4400000 read pairs finished. 1372 secs passed Thread #0: 4450000 read pairs finished. 1394 secs passed Thread #1: 4500000 read pairs finished. 1404 secs passed Thread #0: 4550000 read pairs finished. 1432 secs passed Thread #1: 4600000 read pairs finished. 1443 secs passed Thread #0: 4650000 read pairs finished. 1464 secs passed Thread #1: 4700000 read pairs finished. 1473 secs passed Thread #0: 4750000 read pairs finished. 1494 secs passed Thread #1: 4800000 read pairs finished. 1504 secs passed Thread #0: 4850000 read pairs finished. 1523 secs passed Thread #1: 4900000 read pairs finished. 1531 secs passed Thread #0: 4950000 read pairs finished. 1550 secs passed Thread #1: 5000000 read pairs finished. 1558 secs passed Thread #0: 5050000 read pairs finished. 1577 secs passed Thread #1: 5100000 read pairs finished. 1586 secs passed Thread #0: 5150000 read pairs finished. 1604 secs passed Thread #1: 5200000 read pairs finished. 1613 secs passed Thread #0: 5250000 read pairs finished. 1631 secs passed Thread #1: 5300000 read pairs finished. 1639 secs passed Thread #0: 5350000 read pairs finished. 1657 secs passed Thread #1: 5400000 read pairs finished. 1664 secs passed Thread #0: 5450000 read pairs finished. 1682 secs passed Thread #1: 5500000 read pairs finished. 1689 secs passed Thread #0: 5543163 read pairs finished. 1700 secs passed Total number of aligned reads: pairs: 2597461 (47%) single a: 1090241 (20%) single b: 894626 (16%) Done. Finished at Fri Feb 28 15:25:56 2014 Total time consumed: 1701 secs
!date
Sat Mar 1 06:06:22 PST 2014
First set M1_07 against 3 Ensembl Version
07 is file name differentiator and corresponds to FCD2CA8 / September Run