<jupyter_start><jupyter_text><jupyter_code>bsmaploc="/Applications/bioinfo/BSMAP/bsmap-2.74/"

cd /Volumes/caviar/wd/2016-10-11
!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<jupyter_output>% 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   Tim[...]<jupyter_text><jupyter_code># Genome
cd ../data
!curl -O http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/Ostrea_lurida.scafSeq
!md5 /Volumes/caviar/wd/data/O*
!curl http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/md5.txt | grep scaf
ls ../
cd ../2016-10-11/
ls -lh *.sam
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/4_TGACCA_L001_R1_001.fastq.gz
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
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
ls -lh *.sam
pwd
!tail -4 *.stderr<jupyter_output>==> 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
{'fraction_non_alphanumeric': 0.11947533504419731, 'fraction_numerical': 0.11776447105788423, 'mean_word_length': 2.8296943231441047, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 12, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'chain_length': '2', 'dir': 'jupyter-structured-clean-dedup', 'id': '266740', 'license': 'MIT', 'n_tokens_mistral': 1755, 'n_tokens_neox': 1463, 'n_words': 298, 'path': 'jupyter/Olurida/Fidalgo-Siblings-BS.ipynb', 'repo_name': 'sr320/ocattau.github.io', 'size': '3507'}