#Setting Variables
#file ID
fid="M1_sept"
#where is bsmap
bsmap="/Users/Shared/Apps/bsmap-2.73/"
#fastq files location R1 location
R1="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/BiGo_Larvae/filtered_BS_CgM1_ACTTGA_L007_R1.fastq.gz"
#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"
#location of sqlshare python client tools
spt="/Users/Mackenzie/sqlshare-pythonclient/tools/"
cd /Volumes/web/Mollusk/bs_larvae_exp/
/Volumes/web/Mollusk/bs_larvae_exp
mkdir {fid}
cd {fid}
/Volumes/web/Mollusk/bs_larvae_exp/M1_sept
!{bsmap}bsmap -a {R1} -d {genome} -o bsmap_out.sam -p 1
BSMAP v2.73 Start at: Wed Feb 12 14:56:40 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. 24 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/BiGo_Larvae/filtered_BS_CgM1_ACTTGA_L007_R1.fastq.gz (format: gzipped FASTQ) Output file: bsmap_out.sam (format: SAM) Thread #0: 50000 reads finished. 29 secs passed Thread #0: 100000 reads finished. 34 secs passed Thread #0: 150000 reads finished. 39 secs passed Thread #0: 200000 reads finished. 43 secs passed Thread #0: 250000 reads finished. 48 secs passed Thread #0: 300000 reads finished. 53 secs passed Thread #0: 350000 reads finished. 58 secs passed Thread #0: 400000 reads finished. 63 secs passed Thread #0: 450000 reads finished. 67 secs passed Thread #0: 500000 reads finished. 72 secs passed Thread #0: 550000 reads finished. 76 secs passed Thread #0: 600000 reads finished. 81 secs passed Thread #0: 650000 reads finished. 86 secs passed Thread #0: 700000 reads finished. 90 secs passed Thread #0: 750000 reads finished. 95 secs passed Thread #0: 800000 reads finished. 100 secs passed Thread #0: 850000 reads finished. 104 secs passed Thread #0: 900000 reads finished. 109 secs passed Thread #0: 950000 reads finished. 114 secs passed Thread #0: 1000000 reads finished. 118 secs passed Thread #0: 1050000 reads finished. 123 secs passed Thread #0: 1100000 reads finished. 128 secs passed Thread #0: 1150000 reads finished. 132 secs passed Thread #0: 1200000 reads finished. 137 secs passed Thread #0: 1250000 reads finished. 141 secs passed Thread #0: 1300000 reads finished. 146 secs passed Thread #0: 1350000 reads finished. 151 secs passed Thread #0: 1400000 reads finished. 155 secs passed Thread #0: 1450000 reads finished. 160 secs passed Thread #0: 1500000 reads finished. 165 secs passed Thread #0: 1550000 reads finished. 169 secs passed Thread #0: 1600000 reads finished. 174 secs passed Thread #0: 1650000 reads finished. 179 secs passed Thread #0: 1700000 reads finished. 183 secs passed Thread #0: 1750000 reads finished. 188 secs passed Thread #0: 1800000 reads finished. 193 secs passed Thread #0: 1850000 reads finished. 198 secs passed Thread #0: 1900000 reads finished. 202 secs passed Thread #0: 1950000 reads finished. 207 secs passed Thread #0: 2000000 reads finished. 212 secs passed Thread #0: 2050000 reads finished. 217 secs passed Thread #0: 2100000 reads finished. 222 secs passed Thread #0: 2150000 reads finished. 227 secs passed Thread #0: 2200000 reads finished. 231 secs passed Thread #0: 2250000 reads finished. 236 secs passed Thread #0: 2300000 reads finished. 241 secs passed Thread #0: 2350000 reads finished. 246 secs passed Thread #0: 2400000 reads finished. 251 secs passed Thread #0: 2450000 reads finished. 264 secs passed Thread #0: 2500000 reads finished. 268 secs passed Thread #0: 2550000 reads finished. 274 secs passed Thread #0: 2600000 reads finished. 279 secs passed Thread #0: 2650000 reads finished. 289 secs passed Thread #0: 2700000 reads finished. 295 secs passed Thread #0: 2750000 reads finished. 299 secs passed 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. 322 secs passed Thread #0: 3000000 reads finished. 333 secs passed Thread #0: 3050000 reads finished. 338 secs passed Thread #0: 3100000 reads finished. 343 secs passed Thread #0: 3150000 reads finished. 351 secs passed Thread #0: 3200000 reads finished. 356 secs passed Thread #0: 3250000 reads finished. 363 secs passed Thread #0: 3300000 reads finished. 368 secs passed Thread #0: 3350000 reads finished. 380 secs passed Thread #0: 3400000 reads finished. 385 secs passed Thread #0: 3450000 reads finished. 390 secs passed Thread #0: 3500000 reads finished. 398 secs passed Thread #0: 3550000 reads finished. 403 secs passed Thread #0: 3600000 reads finished. 408 secs passed Thread #0: 3650000 reads finished. 412 secs passed Thread #0: 3700000 reads finished. 418 secs passed Thread #0: 3750000 reads finished. 424 secs passed Thread #0: 3800000 reads finished. 432 secs passed Thread #0: 3850000 reads finished. 437 secs passed Thread #0: 3900000 reads finished. 443 secs passed Thread #0: 3950000 reads finished. 448 secs passed Thread #0: 4000000 reads finished. 455 secs passed Thread #0: 4050000 reads finished. 462 secs passed Thread #0: 4100000 reads finished. 467 secs passed Thread #0: 4150000 reads finished. 474 secs passed Thread #0: 4200000 reads finished. 479 secs passed Thread #0: 4250000 reads finished. 484 secs passed Thread #0: 4300000 reads finished. 489 secs passed Thread #0: 4350000 reads finished. 494 secs passed Thread #0: 4400000 reads finished. 499 secs passed Thread #0: 4450000 reads finished. 504 secs passed Thread #0: 4500000 reads finished. 509 secs passed Thread #0: 4550000 reads finished. 514 secs passed Thread #0: 4600000 reads finished. 519 secs passed Thread #0: 4650000 reads finished. 524 secs passed Thread #0: 4700000 reads finished. 529 secs passed Thread #0: 4750000 reads finished. 534 secs passed Thread #0: 4800000 reads finished. 539 secs passed Thread #0: 4850000 reads finished. 544 secs passed Thread #0: 4900000 reads finished. 550 secs passed Thread #0: 4950000 reads finished. 555 secs passed Thread #0: 5000000 reads finished. 559 secs passed Thread #0: 5050000 reads finished. 565 secs passed Thread #0: 5100000 reads finished. 570 secs passed Thread #0: 5150000 reads finished. 575 secs passed Thread #0: 5200000 reads finished. 580 secs passed Thread #0: 5250000 reads finished. 585 secs passed Thread #0: 5300000 reads finished. 589 secs passed Thread #0: 5350000 reads finished. 594 secs passed Thread #0: 5400000 reads finished. 600 secs passed Thread #0: 5450000 reads finished. 605 secs passed Thread #0: 5500000 reads finished. 611 secs passed Thread #0: 5543163 reads finished. 616 secs passed Total number of aligned reads: 3687702 (67%) Done. Finished at Wed Feb 12 15:06:57 2014 Total time consumed: 617 secs
!python {bsmap}methratio.py -d {genome} -u -z -g -o methratio_out.txt -s {bsmap}samtools bsmap_out.sam
@ Wed Feb 12 15:06:57 2014: reading reference /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 ... @ Wed Feb 12 15:07:33 2014: reading bsmap_out.sam ... [samopen] SAM header is present: 7658 sequences. @ Wed Feb 12 15:10:09 2014: combining CpG methylation from both strands ... @ Wed Feb 12 15:10:43 2014: writing methratio_out.txt ... @ Wed Feb 12 15:21:48 2014: done. total 2686629 valid mappings, 21854162 covered cytosines, average coverage: 1.35 fold.
!python {spt}singleupload.py -u che625@washington.edu -p 5234162537ce6a35236569c28ab62f65 -d _methratio{fid} methratio_out.txt
Traceback (most recent call last): File "/Users/Mackenzie/sqlshare-pythonclient/tools/singleupload.py", line 42, in <module> main() File "/Users/Mackenzie/sqlshare-pythonclient/tools/singleupload.py", line 39, in main conn.uploadone(args[0], datasetname) File "build/bdist.macosx-10.8-intel/egg/sqlshare/__init__.py", line 166, in uploadone IOError: [Errno 2] No such file or directory: 'methratio_out.txt'