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Edit and run



In [1]:

    
bsmaploc="/Applications/bioinfo/BSMAP/bsmap-2.74/"



In [2]:

    
cd /Volumes/caviar/wd/2016-10-11









    



/Volumes/caviar/wd/2016-10-11



In [2]:

    
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/1_ATCACG_L001_R1_001.fastq.gz
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/2_CGATGT_L001_R1_001.fastq.gz
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/3_TTAGGC_L001_R1_001.fastq.gz
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/5_ACAGTG_L001_R1_001.fastq.gz
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/6_GCCAAT_L001_R1_001.fastq.gz
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/7_CAGATC_L001_R1_001.fastq.gz
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/8_ACTTGA_L001_R1_001.fastq.gz









    



  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  502M  100  502M    0     0  40.3M      0  0:00:12  0:00:12 --:--:-- 75.3M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  637M  100  637M    0     0  73.3M      0  0:00:08  0:00:08 --:--:-- 73.9M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  633M  100  633M    0     0  41.1M      0  0:00:15  0:00:15 --:--:-- 68.8M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  671M  100  671M    0     0  52.8M      0  0:00:12  0:00:12 --:--:-- 75.2M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  667M  100  667M    0     0  42.3M      0  0:00:15  0:00:15 --:--:-- 70.0M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  548M  100  548M    0     0  68.7M      0  0:00:07  0:00:07 --:--:-- 79.7M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  764M  100  764M    0     0  34.5M      0  0:00:22  0:00:22 --:--:-- 69.6M



In [3]:

    
# Genome



In [3]:

    
cd ../data









    



/Volumes/caviar/wd/data



In [5]:

    
!curl -O http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/Ostrea_lurida.scafSeq









    



  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  761M  100  761M    0     0  49.3M      0  0:00:15  0:00:15 --:--:-- 66.0M



In [6]:

    
!md5 /Volumes/caviar/wd/data/O*









    



MD5 (/Volumes/caviar/wd/data/Ostrea_lurida.scafSeq) = f0a7772d4f1074698b50c913783c6fe2



In [8]:

    
!curl http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/md5.txt | grep scaf









    



  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   913  100   913    0     0   8304      0 --:--:-- --:--:-- --:--:--  8376
f0a7772d4f1074698b50c913783c6fe2  Assembly_Result/Ostrea_lurida.scafSeq



In [4]:

    
ls ../









    



2016-10-11/ 2016-10-18/ data/       misc/



In [5]:

    
cd ../2016-10-11/









    



/Volumes/caviar/wd/2016-10-11



In [7]:

    
ls -lh *.sam









    



-rw-r--r--  1 sr320  staff   208M Oct 15 02:52 bsmap_out_1_ATCACG.sam
-rw-r--r--  1 sr320  staff   254M Oct 16 04:21 bsmap_out_2_CGATGT.sam
-rw-r--r--  1 sr320  staff   253M Oct 17 05:33 bsmap_out_3_TTAGGC.sam
-rw-r--r--  1 sr320  staff   253M Oct 18 08:19 bsmap_out_4_TGACCA.sam
-rw-r--r--  1 sr320  staff    40M Oct 18 10:54 bsmap_out_5_ACAGTG.sam
-rw-r--r--  1 sr320  staff    19M Oct 18 10:55 bsmap_out_6_GCCAAT.sam
-rw-r--r--  1 sr320  staff   215M Oct 19 08:02 bsmap_out_7_CAGATC.sam
-rw-r--r--  1 sr320  staff   1.5G Oct 11 08:06 bsmap_out_M2.sam
-rw-r--r--  1 sr320  staff   1.6G Oct 11 08:10 bsmap_out_M3.sam



In [12]:

    
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/4_TGACCA_L001_R1_001.fastq.gz









    



  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  619M  100  619M    0     0  51.2M      0  0:00:12  0:00:12 --:--:-- 32.3M



In [ ]:

    
for i in ("1_ATCACG","2_CGATGT","3_TTAGGC","4_TGACCA","5_ACAGTG","6_GCCAAT","7_CAGATC","8_ACTTGA"):
    !{bsmaploc}bsmap \
-a {i}_L001_R1_001.fastq.gz \
-d /Volumes/caviar/wd/data/Ostrea_lurida.scafSeq \
-o bsmap_out_{i}.sam \
-p 7









    



BSMAP v2.74
Start at:  Fri Oct 14 06:51:47 2016

Input reference file: /Volumes/caviar/wd/data/Ostrea_lurida.scafSeq 	(format: FASTA)
Load in 765755 db seqs, total size 776306190 bp. 11 secs passed
total_kmers: 43046721



In [8]:

    
for i in ("5_ACAGTG","6_GCCAAT"):
    !{bsmaploc}bsmap \
-a {i}_L001_R1_001.fastq.gz \
-d /Volumes/caviar/wd/data/Ostrea_lurida.scafSeq \
-o bsmap_out_{i}.sam \
-p 4 \
2> bsmap_out_{i}.stderr

^C



In [10]:

    
ls -lh *.sam









    



-rw-r--r--  1 sr320  staff   208M Oct 15 02:52 bsmap_out_1_ATCACG.sam
-rw-r--r--  1 sr320  staff   254M Oct 16 04:21 bsmap_out_2_CGATGT.sam
-rw-r--r--  1 sr320  staff   253M Oct 17 05:33 bsmap_out_3_TTAGGC.sam
-rw-r--r--  1 sr320  staff   253M Oct 18 08:19 bsmap_out_4_TGACCA.sam
-rw-r--r--  1 sr320  staff   264M Oct 20 15:50 bsmap_out_5_ACAGTG.sam
-rw-r--r--  1 sr320  staff   143M Oct 21 04:59 bsmap_out_6_GCCAAT.sam
-rw-r--r--  1 sr320  staff   215M Oct 19 08:02 bsmap_out_7_CAGATC.sam
-rw-r--r--  1 sr320  staff   1.5G Oct 11 08:06 bsmap_out_M2.sam
-rw-r--r--  1 sr320  staff   1.6G Oct 11 08:10 bsmap_out_M3.sam



In [11]:

    
pwd









    Out[11]:





u'/Volumes/caviar/wd/2016-10-11'



In [13]:

    
!tail -4 *.stderr









    



==> bsmap_out_4_TGACCA.stderr <==
Total number of aligned reads: 1259433 (11%)
Done.
Finished at Tue Oct 18 08:19:22 2016
Total time consumed:  88248 secs

==> bsmap_out_5_ACAGTG.stderr <==
Total number of aligned reads: 1319007 (10%)
Done.
Finished at Thu Oct 20 15:50:18 2016
Total time consumed:  93263 secs

==> bsmap_out_6_GCCAAT.stderr <==
Thread #1: 	6150000 reads finished. 46321 secs passed
Thread #3: 	6200000 reads finished. 46733 secs passed
Thread #0: 	6250000 reads finished. 46816 secs passed
Thread #2: 	6300000 reads finished. 47352 secs passed

==> bsmap_out_7_CAGATC.stderr <==
Thread #1: 	9700000 reads finished. 74754 secs passed
Thread #2: 	9750000 reads finished. 75174 secs passed
Thread #3: 	9800000 reads finished. 75483 secs passed
Thread #0: 	9850000 reads finished. 75592 secs passed



In [ ]: