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In [5]:



    


%%bash
date
system_profiler SPSoftwareDataType



    


















    






Fri Nov 25 10:46:53 PST 2016
Software:

    System Software Overview:

      System Version: macOS 10.12 (16A323)
      Kernel Version: Darwin 16.0.0
      Boot Volume: Macintosh HD
      Boot Mode: Normal
      Computer Name: genefish
      User Name: Steven Roberts (Steven)
      Secure Virtual Memory: Enabled
      System Integrity Protection: Enabled
      Time since boot: 38 days 22:54


















In [4]:



    


bsmaploc="/Users/Shared/Apps/bsmap-2.74/"



    











In [7]:



    


mkdir /Volumes/web/halfshell/working-directory/16-11-25



    











In [8]:



    


!{bsmaploc}bsmap \
-a /Users/Shared/data/Oly_clambay/zr1394_1_s456.fastq.gz \
-d /Users/Shared/data/Oly_clambay/Ostrea_lurida-Scaff-10k.fa \
-o /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_Os10k.sam \
-p 8 \
2> /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_Os10k.stderr



    











In [9]:



    


!{bsmaploc}bsmap \
-a /Users/Shared/data/Oly_clambay/zr1394_1_s456.fastq.gz \
-d /Users/Steven/Documents/git-repos/student-fish546-2016/data/Ostrea_lurida-Scaff-30k.fa \
-o /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_O30k.sam \
-p 8 \
2> /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_O30k.stderr



    











In [10]:



    


!{bsmaploc}bsmap \
-a /Users/Shared/data/Oly_clambay/zr1394_1_s456.fastq.gz \
-d /Users/Steven/Documents/git-repos/student-fish546-2016/data/Panopea_generosa-Scaff-70k.fa \
-o /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_P70k.sam \
-p 8 \
2> /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_P70k.stderr



    











In [11]:



    


!{bsmaploc}bsmap \
-a /Users/Shared/data/Oly_clambay/zr1394_1_s456.fastq.gz \
-d /Users/Shared/data/Oly_clambay/Ostrea_lurida-Scaff-10k.fa \
-o /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_Os10k.bsp \
-p 8 \
2> /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_Os10k-bsp.stderr



    











In [12]:



    


!{bsmaploc}bsmap \
-a /Users/Shared/data/Oly_clambay/zr1394_1_s456.fastq.gz \
-d /Users/Steven/Documents/git-repos/student-fish546-2016/data/Ostrea_lurida-Scaff-30k.fa \
-o /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_O30k.bsp \
-p 8 \
2> /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_O30k-bsp.stderr



    











In [13]:



    


!{bsmaploc}bsmap \
-a /Users/Shared/data/Oly_clambay/zr1394_1_s456.fastq.gz \
-d /Users/Steven/Documents/git-repos/student-fish546-2016/data/Panopea_generosa-Scaff-70k.fa \
-o /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_P70k.bsp \
-p 8 \
2> /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_P70k-bsp.stderr



    











In [15]:



    


!tail /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_Os10k-bsp.stderr



    


















    






Thread #2: 	47150000 reads finished. 1429 secs passed
Thread #1: 	47200000 reads finished. 1429 secs passed
Thread #6: 	47250000 reads finished. 1434 secs passed
Thread #3: 	47300000 reads finished. 1434 secs passed
Thread #7: 	47350000 reads finished. 1434 secs passed
Thread #0: 	47399413 reads finished. 1434 secs passed
Total number of aligned reads: 2952762 (6.2%)
Done.
Finished at Fri Nov 25 11:50:10 2016
Total time consumed:  1435 secs

















In [16]:



    


!tail  /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_Os10k.stderr



    


















    






Thread #1: 	47150000 reads finished. 1382 secs passed
Thread #4: 	47200000 reads finished. 1383 secs passed
Thread #0: 	47250000 reads finished. 1386 secs passed
Thread #2: 	47300000 reads finished. 1386 secs passed
Thread #7: 	47350000 reads finished. 1386 secs passed
Thread #6: 	47399413 reads finished. 1386 secs passed
Total number of aligned reads: 2953001 (6.2%)
Done.
Finished at Fri Nov 25 11:22:07 2016
Total time consumed:  1389 secs

















In [17]:



    


!tail /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_O30k.stderr



    


















    






Thread #6: 	47150000 reads finished. 128 secs passed
Thread #7: 	47200000 reads finished. 129 secs passed
Thread #1: 	47250000 reads finished. 129 secs passed
Thread #0: 	47300000 reads finished. 129 secs passed
Thread #3: 	47350000 reads finished. 129 secs passed
Thread #2: 	47399413 reads finished. 129 secs passed
Total number of aligned reads: 1394687 (2.9%)
Done.
Finished at Fri Nov 25 11:24:21 2016
Total time consumed:  133 secs

















In [19]:



    


!tail /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_P70k.stderr



    


















    






Thread #6: 	47150000 reads finished. 105 secs passed
Thread #7: 	47200000 reads finished. 105 secs passed
Thread #0: 	47250000 reads finished. 105 secs passed
Thread #4: 	47300000 reads finished. 106 secs passed
Thread #1: 	47350000 reads finished. 106 secs passed
Thread #3: 	47399413 reads finished. 106 secs passed
Total number of aligned reads: 20423 (0.043%)
Done.
Finished at Fri Nov 25 11:26:08 2016
Total time consumed:  106 secs

















In [20]:



    


!tail /Volumes/web/halfshell/working-directory/16-11-25/bsmap_out_Os10k.sam



    


















    






HWI-C00124:164:C7URDANXX:3:2316:15900:100194	0	s_3622	4089	255	51M	*	0	0	GGGTAAATTTTTTGTTAAGAGTAAATTAGTTAAAATGTTATGGTGTTTATA	B<BBBFFFFFBFFFFFFF//<FFFFBFFFFFFFFFFFBF/F/F<BFBFF/<	NM:i:2	ZS:Z:++
HWI-C00124:164:C7URDANXX:3:2316:15826:100225	256	s_9202	927	255	51M	*	0	0	CTTGGTATTTAATACGGCGGGTGTGATCGGTTAGTAGAGGATGTTTATTTT	BBBBBFF/F<BF/BFF/</BF</</<BB<B/B/<<<BBFF///<FBBFFFF	NM:i:3	ZS:Z:++
HWI-C00124:164:C7URDANXX:3:2316:16427:100059	16	s_3113	1870	255	51M	*	0	0	AAAAAACGAAAATAACGTTTTTCAAAATATAAAATCGAAAAAATCTCGCCT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFF</BBBBB	NM:i:2	ZS:Z:-+
HWI-C00124:164:C7URDANXX:3:2316:16449:100126	0	s_5458	10092	255	51M	*	0	0	TTATTTGTGTTGGGGTGTCGCGAAAAGTAAAATATTAGAGATTATCGCGAC	/<</B/</BFB/BFB</F/F//<BB/<FF/<FF/BFFFF/<<B/<F/F<F7	NM:i:3	ZS:Z:++
HWI-C00124:164:C7URDANXX:3:2316:17137:100074	16	s_2131	4384	255	50M	*	0	0	TAAATATAAAATCTATTATTTAATATCATATTTCAAAAATTACTATTAAG	FFFFF/</FFF<FFF/<FFFFFF<FBFFFFFB/<FFFFFFFFFF<BBBBB	NM:i:3	ZS:Z:-+
HWI-C00124:164:C7URDANXX:3:2316:17605:100102	16	s_335	5506	255	51M	*	0	0	AATATACCGCGATATACCGTAATATTTAAAAAATACCGCGATATATACCAG	FFFF<BF<<F</FFFFFFFFFFFFFFFFFFFFFFFFFFBB/BF/F<BBBBB	NM:i:2	ZS:Z:-+
HWI-C00124:164:C7URDANXX:3:2316:17819:100039	0	s_4157	15400	255	50M	*	0	0	GGCCTTTTAGGATGATAGTATATTATTTGAAGGTGTTCGGAACGATTGTT	BBBBB/FFFF<FBFFFFFFFF<BFFFFFFFFFFFFF<FFF7FBBFFFFFF	NM:i:4	ZS:Z:++
HWI-C00124:164:C7URDANXX:3:2316:2709:100260	256	s_4142	11562	255	47M	*	0	0	ATTATTTTTGTAACGGTTGTATATATTTAATTTAAAATTGTTATATG	/<BBBB/FFFFFFF<<<FF<///<BFFFFFFBBBBF/<<//FFF/B/	NM:i:2	ZS:Z:++
HWI-C00124:164:C7URDANXX:3:2316:4249:100278	272	s_901	13312	255	51M	*	0	0	ATAAAAATACTAAAAAAATAAATAATTAAAACCTCCAAATCAATTCGACAT	BFFBBFFBFFFFFFFFFFF<FFFFFFFFFFBF/FBFFFFFFFFBB/BBBBB	NM:i:0	ZS:Z:-+
HWI-C00124:164:C7URDANXX:3:2316:12989:100298	16	s_6951	9762	255	50M	*	0	0	CTTTCTCGATAAAAACAATCCATATAATCTCTCTCGTAATCATCTCTTAC	FFF/BFFFFFFFFFFFFF<FFFFFFFF<FFB<B<FBFFFBFFFFBBBBBB	NM:i:2	ZS:Z:-+

















In [ ]:

Content source: sr320/sr320.github.io

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