Determining how genome might influence read mapping.

When we did

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



In [11]:

    
ls /Volumes/caviar/wd/2016-10-11/*stderr









    



/Volumes/caviar/wd/2016-10-11/bsmap_out_4_TGACCA.stderr
/Volumes/caviar/wd/2016-10-11/bsmap_out_5_ACAGTG.stderr
/Volumes/caviar/wd/2016-10-11/bsmap_out_6_GCCAAT.stderr
/Volumes/caviar/wd/2016-10-11/bsmap_out_7_CAGATC.stderr
/Volumes/caviar/wd/2016-10-11/bsmap_out_8_ACTTGA.stderr



In [14]:

    
!tail -5 /Volumes/caviar/wd/2016-10-11/*stderr









    



==> /Volumes/caviar/wd/2016-10-11/bsmap_out_4_TGACCA.stderr <==
Thread #3: 	11600000 reads finished. 88248 secs passed
Total number of aligned reads: 1259433 (11%)
Done.
Finished at Tue Oct 18 08:19:22 2016
Total time consumed:  88248 secs

==> /Volumes/caviar/wd/2016-10-11/bsmap_out_5_ACAGTG.stderr <==
Thread #1: 	12550000 reads finished. 93263 secs passed
Total number of aligned reads: 1319007 (10%)
Done.
Finished at Thu Oct 20 15:50:18 2016
Total time consumed:  93263 secs

==> /Volumes/caviar/wd/2016-10-11/bsmap_out_6_GCCAAT.stderr <==
Thread #1: 	12450000 reads finished. 114455 secs passed
Total number of aligned reads: 1312112 (11%)
Done.
Finished at Sat Oct 22 02:37:53 2016
Total time consumed:  114482 secs

==> /Volumes/caviar/wd/2016-10-11/bsmap_out_7_CAGATC.stderr <==
Thread #1: 	10250000 reads finished. 86073 secs passed
Total number of aligned reads: 1105402 (11%)
Done.
Finished at Thu Oct 20 18:49:48 2016
Total time consumed:  86080 secs

==> /Volumes/caviar/wd/2016-10-11/bsmap_out_8_ACTTGA.stderr <==
Thread #7: 	14350000 reads finished. 194158 secs passed
Total number of aligned reads: 1503061 (10%)
Done.
Finished at Wed Oct 19 18:55:06 2016
Total time consumed:  194172 secs

Different Genome



In [17]:

    
!head -1 /Users/sr320/git-repos/student-fish546-2016/data/Ostrea_lurida-Scaff-30k.fa









    



>scaffold114 34.4



In [26]:

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



In [25]:

    
%time









    



CPU times: user 2 µs, sys: 1 µs, total: 3 µs
Wall time: 5.01 µs



In [28]:

    
cd /Volumes/caviar/wd/2016-10-24









    



/Volumes/caviar/wd/2016-10-24



In [30]:

    
%time
for i in ("1_ATCACG","2_CGATGT"):
    !{bsmaploc}bsmap \
-a /Volumes/caviar/wd/2016-10-11/{i}_L001_R1_001.fastq.gz \
-d /Users/sr320/git-repos/student-fish546-2016/data/Ostrea_lurida-Scaff-30k.fa \
-o bsmap_out_{i}.sam \
-p 6 \
2> bsmap_out_{i}.stderr









    



CPU times: user 2 µs, sys: 0 ns, total: 2 µs
Wall time: 5.01 µs



In [31]:

    
!tail -5 *.stderr









    



==> bsmap_out_1_ATCACG.stderr <==
Thread #1: 	9400000 reads finished. 24 secs passed
Total number of aligned reads: 1219262 (13%)
Done.
Finished at Mon Oct 24 15:14:49 2016
Total time consumed:  24 secs

==> bsmap_out_2_CGATGT.stderr <==
Thread #4: 	11950000 reads finished. 29 secs passed
Total number of aligned reads: 1524518 (13%)
Done.
Finished at Mon Oct 24 15:15:18 2016
Total time consumed:  29 secs



In [ ]:

    
/Users/sr320/git-repos/student-fish546-2016/data/Ostrea_lurida-Scaff-10k.fa



In [32]:

    
for i in ("1_ATCACG","2_CGATGT"):
    !{bsmaploc}bsmap \
-a /Volumes/caviar/wd/2016-10-11/{i}_L001_R1_001.fastq.gz \
-d /Users/sr320/git-repos/student-fish546-2016/data/Ostrea_lurida-Scaff-10k.fa \
-o 10k_bsmap_out_{i}.sam \
-p 6 \
2> 10k_bsmap_out_{i}.stderr

!tail -5 *.stderr









    



==> 10k_bsmap_out_1_ATCACG.stderr <==
Thread #3: 	9400000 reads finished. 192 secs passed
Total number of aligned reads: 2189320 (23%)
Done.
Finished at Mon Oct 24 15:28:11 2016
Total time consumed:  192 secs

==> 10k_bsmap_out_2_CGATGT.stderr <==
Thread #2: 	11950000 reads finished. 235 secs passed
Total number of aligned reads: 2732154 (23%)
Done.
Finished at Mon Oct 24 15:32:06 2016
Total time consumed:  235 secs

==> bsmap_out_1_ATCACG.stderr <==
Thread #1: 	9400000 reads finished. 24 secs passed
Total number of aligned reads: 1219262 (13%)
Done.
Finished at Mon Oct 24 15:14:49 2016
Total time consumed:  24 secs

==> bsmap_out_2_CGATGT.stderr <==
Thread #4: 	11950000 reads finished. 29 secs passed
Total number of aligned reads: 1524518 (13%)
Done.
Finished at Mon Oct 24 15:15:18 2016
Total time consumed:  29 secs



In [33]:

    
for i in ("1_ATCACG","2_CGATGT"):
    !{bsmaploc}bsmap \
-a /Volumes/caviar/wd/2016-10-11/{i}_L001_R1_001.fastq.gz \
-d /Users/sr320/git-repos/student-fish546-2016/data/Ostrea_lurida-Scaff-5k.fa \
-o 5k_bsmap_out_{i}.sam \
-p 6 \
2> 5k_bsmap_out_{i}.stderr

!tail -5 *.stderr









    



/bin/sh: line 1: 76994 Abort trap: 6           /Applications/bioinfo/BSMAP/bsmap-2.74/bsmap -a /Volumes/caviar/wd/2016-10-11/2_CGATGT_L001_R1_001.fastq.gz -d /Users/sr320/git-repos/student-fish546-2016/data/Ostrea_lurida-Scaff-5k.fa -o 5k_bsmap_out_2_CGATGT.sam -p 6 2> 5k_bsmap_out_2_CGATGT.stderr
==> 10k_bsmap_out_1_ATCACG.stderr <==
Thread #3: 	9400000 reads finished. 192 secs passed
Total number of aligned reads: 2189320 (23%)
Done.
Finished at Mon Oct 24 15:28:11 2016
Total time consumed:  192 secs

==> 10k_bsmap_out_2_CGATGT.stderr <==
Thread #2: 	11950000 reads finished. 235 secs passed
Total number of aligned reads: 2732154 (23%)
Done.
Finished at Mon Oct 24 15:32:06 2016
Total time consumed:  235 secs

==> 5k_bsmap_out_1_ATCACG.stderr <==
Thread #5: 	9400000 reads finished. 2576 secs passed
Total number of aligned reads: 961476 (10%)
Done.
Finished at Mon Oct 24 16:15:03 2016
Total time consumed:  2577 secs

==> 5k_bsmap_out_2_CGATGT.stderr <==
Thread #2: 	250000 reads finished. 91 secs passed
Thread #0: 	100000 reads finished. 91 secs passed
Thread #4: 	350000 reads finished. 168 secs passed
Thread #1: 	400000 reads finished. 169 secs passed
libc++abi.dylib: terminating with uncaught exception of type std::out_of_range: basic_string::erase

==> bsmap_out_1_ATCACG.stderr <==
Thread #1: 	9400000 reads finished. 24 secs passed
Total number of aligned reads: 1219262 (13%)
Done.
Finished at Mon Oct 24 15:14:49 2016
Total time consumed:  24 secs

==> bsmap_out_2_CGATGT.stderr <==
Thread #4: 	11950000 reads finished. 29 secs passed
Total number of aligned reads: 1524518 (13%)
Done.
Finished at Mon Oct 24 15:15:18 2016
Total time consumed:  29 secs



In [ ]: