Running BSMAP

10k cuttoff

Sample	Weight (grams in shell)	Length (mm)	Raw 2bRAD reads
hc1_2B	2.2	17.41	1521
hc1_4B	1.9	20.43	2294290
hc2_15B	2.2	25.33	2498
hc2_17	1.1	19.38	(seq 4x)best = 2964986
hc3_1	2.2	26.79	1863108
hc3_5	1.9	19.5	1915
hc3_7	1.4	18.43	2438612
hc3_10	1.2	19.80	4091281
hc3_11	2.1	20.54	2901608
ss2_9B	1.5	17.2	749
ss2_14B	2.2	21.02	29745
ss2_18B	5.3	35.76	3016
ss3_3B	2.1	22.71	2076769
ss3_14B	2.4	24.71	2661152
ss3_15B	2.6	26.78	2816364
ss3_16B	4.2	39.57	2070520
ss3_20	2.3	26.96	1656456
ss5_18	5.4	27.34	2358172



In [1]:

    
%%bash
date
system_profiler SPSoftwareDataType









    



Wed Nov 23 13:08:33 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: 37 days 1:16



In [2]:

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



In [4]:

    
cd /Volumes/web/halfshell/working-directory/









    



/Volumes/web/halfshell/working-directory



In [5]:

    
!ls -lh









    



total 0
drwxrwxrwx  1 Steven  staff   1.7K Jan 27  2016 16-01-271
drwxrwxrwx  1 Steven  staff   1.7K Jan 27  2016 16-01-27b
drwxrwxrwx  1 Steven  staff   264B Apr  1  2016 16-04-01
drwxrwxrwx  1 Steven  staff   264B Apr  4  2016 16-04-01c
drwxrwxrwx  1 Steven  staff   264B Apr  4  2016 16-04-04
drwxrwxrwx  1 Steven  staff   264B Apr  4  2016 16-04-04b
drwxrwxrwx  1 Steven  staff   1.4K Apr  5  2016 16-04-04c
drwxrwxrwx  1 Steven  staff   264B Apr  4  2016 16-04-04d
drwxrwxrwx  1 Steven  staff   1.1K Apr  5  2016 16-04-05
drwxrwxrwx  1 Steven  staff   3.0K Apr 12  2016 16-04-11
drwxrwxrwx  1 Steven  staff   264B Apr 11  2016 16-04-11-hum-a
drwxrwxrwx  1 Steven  staff   3.0K Apr 13  2016 16-04-12
drwxrwxrwx  1 Steven  staff   2.4K Apr 14  2016 16-04-13
drwxrwxrwx  1 Steven  staff   264B Apr 13  2016 16-04-13b
drwxrwxrwx  1 Steven  staff   6.5K Apr 15  2016 16-04-15
drwxrwxrwx  1 Steven  staff   466B Apr 17  2016 16-04-15b
drwxrwxrwx  1 Steven  staff   264B Apr 15  2016 16-04-15c
drwxrwxrwx  1 Steven  staff   264B Apr 18  2016 16-04-17
drwxrwxrwx  1 Steven  staff   670B May 13  2016 16-05-05
drwxrwxrwx  1 Steven  staff   264B May 12  2016 16-05-12
drwxrwxrwx  1 Steven  staff   432B May 13  2016 16-05-13
drwxrwxrwx  1 Steven  staff   466B May 25  2016 16-05-17
drwxrwxrwx  1 Steven  staff   264B May 17  2016 16-05-17b
drwxrwxrwx  1 Steven  staff   264B May 17  2016 16-05-17c
drwxrwxrwx  1 Steven  staff   432B May 30 14:29 16-05-27
drwxrwxrwx  1 Steven  staff   364B Sep 19 09:53 16-09-19
drwxrwxrwx  1 Steven  staff   602B Oct 29 18:15 16-10-17
drwxrwxrwx  1 Steven  staff   264B Oct 19 07:50 16-10-19
drwxrwxrwx  1 Steven  staff   264B Oct 24 16:05 16-10-24
drwxrwxrwx  1 Steven  staff   772B Oct 25 07:32 16-10-25
drwxrwxrwx  1 Steven  staff   1.1K Oct 29 19:02 16-10-29
drwxrwxrwx  1 Steven  staff   1.8K Jan 27  2016 16-27-01
drwxrwxrwx  1 Steven  staff   264B Jan 27  2016 scripts



In [6]:

    
mkdir 16-11-23



In [7]:

    
cd 16-11-23









    



/Volumes/web/halfshell/working-directory/16-11-23



In [8]:

    
!ls /Volumes/web/nightingales/O_lurida/20160203_mbdseq/*s456.fastq.gz









    



/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_10_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_11_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_12_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_13_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_14_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_15_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_16_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_17_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_18_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_1_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_2_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_3_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_4_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_5_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_6_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_7_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_8_s456.fastq.gz
/Volumes/web/nightingales/O_lurida/20160203_mbdseq/zr1394_9_s456.fastq.gz



In [10]:

    
!cp /Volumes/web/nightingales/O_lurida/20160203_mbdseq/*s456.fastq.gz /Users/Shared/data/Oly_clambay



In [ ]:

    
pwd



In [12]:

    
!cp /Users/Steven/Documents/git-repos/student-fish546-2016/data/Ostrea_lurida-Scaff-10k.fa /Users/Shared/data/Oly_clambay



In [ ]:

    
for i in ("1","2","3", "4", "5", "6", "7", "8","9", "10", "11","12","13", "14", "15", "16", "17", "18"):
    !{bsmaploc}bsmap \
-a /Users/Shared/data/Oly_clambay/zr1394_{i}_s456.fastq.gz \
-d /Users/Shared/data/Oly_clambay/Ostrea_lurida-Scaff-10k.fa \
-o bsmap_out_{i}.sam \
-p 8 \
2> bsmap_out_{i}.stderr



In [28]:

    
!date









    



Sat Oct 29 18:04:27 PDT 2016



In [30]:

    
!tail *err









    



==> bsmap_out_1_ATCACG.stderr <==
Input read file: ../16-10-17/1_ATCACG_L001_R1_001.fastq.gz 	(format: gzipped FASTQ)
Output file: bsmap_out_1_ATCACG.sam	 (format: SAM)
Thread #1: 	171696 reads finished. 11 secs passed
Thread #0: 	50000 reads finished. 13 secs passed
Thread #4: 	100000 reads finished. 13 secs passed
Thread #5: 	150000 reads finished. 13 secs passed
Total number of aligned reads: 41116 (24%)
Done.
Finished at Sat Oct 29 17:16:55 2016
Total time consumed:  14 secs

==> bsmap_out_2_CGATGT.stderr <==
Thread #4: 	11750000 reads finished. 385 secs passed
Thread #7: 	11800000 reads finished. 385 secs passed
Thread #5: 	11850000 reads finished. 385 secs passed
Thread #3: 	11900000 reads finished. 385 secs passed
Thread #6: 	11954873 reads finished. 385 secs passed
Thread #1: 	11950000 reads finished. 389 secs passed
Total number of aligned reads: 2731891 (23%)
Done.
Finished at Sat Oct 29 17:23:25 2016
Total time consumed:  390 secs

==> bsmap_out_3_TTAGGC.stderr <==
Thread #7: 	11600000 reads finished. 372 secs passed
Thread #2: 	11650000 reads finished. 372 secs passed
Thread #1: 	11700000 reads finished. 372 secs passed
Thread #5: 	11817358 reads finished. 373 secs passed
Thread #0: 	11750000 reads finished. 373 secs passed
Thread #3: 	11800000 reads finished. 374 secs passed
Total number of aligned reads: 2681600 (23%)
Done.
Finished at Sat Oct 29 17:29:40 2016
Total time consumed:  375 secs

==> bsmap_out_4_TGACCA.stderr <==
Thread #2: 	11350000 reads finished. 374 secs passed
Thread #5: 	11400000 reads finished. 374 secs passed
Thread #3: 	11450000 reads finished. 375 secs passed
Thread #6: 	11500000 reads finished. 375 secs passed
Thread #4: 	11550000 reads finished. 376 secs passed
Thread #1: 	11600000 reads finished. 377 secs passed
Total number of aligned reads: 2727290 (23%)
Done.
Finished at Sat Oct 29 17:43:23 2016
Total time consumed:  392 secs

==> bsmap_out_5_ACAGTG.stderr <==
Thread #1: 	12350000 reads finished. 418 secs passed
Thread #3: 	12400000 reads finished. 419 secs passed
Thread #0: 	12589609 reads finished. 421 secs passed
Thread #4: 	12450000 reads finished. 424 secs passed
Thread #7: 	12500000 reads finished. 424 secs passed
Thread #6: 	12550000 reads finished. 425 secs passed
Total number of aligned reads: 2817591 (22%)
Done.
Finished at Sat Oct 29 17:36:49 2016
Total time consumed:  427 secs

==> bsmap_out_6_GCCAAT.stderr <==
Thread #7: 	12250000 reads finished. 397 secs passed
Thread #6: 	12300000 reads finished. 397 secs passed
Thread #3: 	12350000 reads finished. 397 secs passed
Thread #5: 	12400000 reads finished. 397 secs passed
Thread #2: 	12450000 reads finished. 398 secs passed
Thread #4: 	12489766 reads finished. 398 secs passed
Total number of aligned reads: 2795408 (22%)
Done.
Finished at Sat Oct 29 17:50:10 2016
Total time consumed:  400 secs

==> bsmap_out_7_CAGATC.stderr <==
Thread #2: 	10050000 reads finished. 351 secs passed
Thread #1: 	10100000 reads finished. 352 secs passed
Thread #0: 	10150000 reads finished. 352 secs passed
Thread #5: 	10295293 reads finished. 362 secs passed
Thread #3: 	10200000 reads finished. 369 secs passed
Thread #4: 	10250000 reads finished. 375 secs passed
Total number of aligned reads: 2394320 (23%)
Done.
Finished at Sat Oct 29 17:56:29 2016
Total time consumed:  377 secs

==> bsmap_out_8_ACTTGA.stderr <==
Thread #0: 	14150000 reads finished. 467 secs passed
Thread #3: 	14200000 reads finished. 467 secs passed
Thread #6: 	14250000 reads finished. 468 secs passed
Thread #2: 	14374642 reads finished. 468 secs passed
Thread #1: 	14300000 reads finished. 470 secs passed
Thread #7: 	14350000 reads finished. 470 secs passed
Total number of aligned reads: 3229689 (22%)
Done.
Finished at Sat Oct 29 18:04:26 2016
Total time consumed:  472 secs



In [35]:

    
for i in ("1_ATCACG","2_CGATGT","3_TTAGGC","5_ACAGTG","4_TGACCA", "6_GCCAAT", "7_CAGATC", "8_ACTTGA"):
    !{bsmaploc}bsmap \
-a ../16-10-17/{i}_L001_R1_001.fastq.gz \
-d Ostrea_lurida-Scaff-10k.fa \
-o bsmap_out_{i}-2.sam \
-p 8 \
2> bsmap_out_{i}-2.stderr



In [38]:

    
ls -lh bsmap*









    



-rw-rw-rw-  1 Steven  staff   411M Oct 29 18:21 bsmap_out_1_ATCACG-2.sam
-rw-rw-rw-  1 Steven  staff    10K Oct 29 18:21 bsmap_out_1_ATCACG-2.stderr
-rw-rw-rw-  1 Steven  staff   8.0M Oct 29 17:16 bsmap_out_1_ATCACG.sam
-rw-rw-rw-  1 Steven  staff   1.0K Oct 29 17:16 bsmap_out_1_ATCACG.stderr
-rw-rw-rw-  1 Steven  staff   513M Oct 29 18:28 bsmap_out_2_CGATGT-2.sam
-rw-rw-rw-  1 Steven  staff    13K Oct 29 18:28 bsmap_out_2_CGATGT-2.stderr
-rw-rw-rw-  1 Steven  staff   513M Oct 29 17:23 bsmap_out_2_CGATGT.sam
-rw-rw-rw-  1 Steven  staff    13K Oct 29 17:23 bsmap_out_2_CGATGT.stderr
-rw-rw-rw-  1 Steven  staff   503M Oct 29 18:36 bsmap_out_3_TTAGGC-2.sam
-rw-rw-rw-  1 Steven  staff    13K Oct 29 18:36 bsmap_out_3_TTAGGC-2.stderr
-rw-rw-rw-  1 Steven  staff   503M Oct 29 17:29 bsmap_out_3_TTAGGC.sam
-rw-rw-rw-  1 Steven  staff    13K Oct 29 17:29 bsmap_out_3_TTAGGC.stderr
-rw-rw-rw-  1 Steven  staff   512M Oct 29 18:49 bsmap_out_4_TGACCA-2.sam
-rw-rw-rw-  1 Steven  staff    13K Oct 29 18:49 bsmap_out_4_TGACCA-2.stderr
-rw-rw-rw-  1 Steven  staff   512M Oct 29 17:43 bsmap_out_4_TGACCA.sam
-rw-rw-rw-  1 Steven  staff    13K Oct 29 17:43 bsmap_out_4_TGACCA.stderr
-rw-rw-rw-  1 Steven  staff   529M Oct 29 18:43 bsmap_out_5_ACAGTG-2.sam
-rw-rw-rw-  1 Steven  staff    14K Oct 29 18:43 bsmap_out_5_ACAGTG-2.stderr
-rw-rw-rw-  1 Steven  staff   529M Oct 29 17:36 bsmap_out_5_ACAGTG.sam
-rw-rw-rw-  1 Steven  staff    14K Oct 29 17:36 bsmap_out_5_ACAGTG.stderr
-rw-rw-rw-  1 Steven  staff   525M Oct 29 18:56 bsmap_out_6_GCCAAT-2.sam
-rw-rw-rw-  1 Steven  staff    14K Oct 29 18:56 bsmap_out_6_GCCAAT-2.stderr
-rw-rw-rw-  1 Steven  staff   525M Oct 29 17:50 bsmap_out_6_GCCAAT.sam
-rw-rw-rw-  1 Steven  staff    14K Oct 29 17:50 bsmap_out_6_GCCAAT.stderr
-rw-rw-rw-  1 Steven  staff   449M Oct 29 19:01 bsmap_out_7_CAGATC-2.sam
-rw-rw-rw-  1 Steven  staff    11K Oct 29 19:01 bsmap_out_7_CAGATC-2.stderr
-rw-rw-rw-  1 Steven  staff   449M Oct 29 17:56 bsmap_out_7_CAGATC.sam
-rw-rw-rw-  1 Steven  staff    11K Oct 29 17:56 bsmap_out_7_CAGATC.stderr
-rw-rw-rw-  1 Steven  staff   606M Oct 29 19:12 bsmap_out_8_ACTTGA-2.sam
-rw-rw-rw-  1 Steven  staff    15K Oct 29 19:12 bsmap_out_8_ACTTGA-2.stderr
-rw-rw-rw-  1 Steven  staff   606M Oct 29 18:04 bsmap_out_8_ACTTGA.sam
-rw-rw-rw-  1 Steven  staff    15K Oct 29 18:04 bsmap_out_8_ACTTGA.stderr



In [ ]: