Going to run our new RRBS Geoduck data through a BSMap analysis run to get some data for next week. This may all be moot, as we’ve not gotten MD5 checksums from Genewiz yet, but I figured I would get started on stuff, on the assumption the data is good.
setwd("~/Documents/Geoduck/")
system("mkdir ~/Documents/Geoduck/untrimmed-Fast-QC")mkdir: cannot create directory ‘/home/sean/Documents/Geoduck/untrimmed-Fast-QC’: File existssystem("fastqc *.gz -o ~/Documents/Geoduck/untrimmed-Fast-QC")Started analysis of EPI-103_S27_L005_R1_001.fastq.gz
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file.names <- list.files(path = ".", pattern = "*.gz")
for(i in 1:(length(file.names) - 1)) {
system(paste("/home/shared/trimgalore/trim_galore --rrbs --paired --fastqc -o ~/Documents/Geoduck/Trimmed-fq", file.names[i], file.names[i + 1], "> trim_galore_output.txt"))
}No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> EPI-103_S27_L005_R1_001.fastq.gz <<)
Found perfect matches for the following adapter sequences:
Adapter type Count Sequence Sequences analysed Percentage
Illumina 150875 AGATCGGAAGAGC 1000000 15.09
smallRNA 2 TGGAATTCTCGG 1000000 0.00
Nextera 0 CTGTCTCTTATA 1000000 0.00
Using Illumina adapter for trimming (count: 150875). Second best hit was smallRNA (count: 2)
gzip: stdout: Broken pipe
Writing report to '/home/sean/Documents/Geoduck/Trimmed-fq/EPI-103_S27_L005_R1_001.fastq.gz_trimming_report.txt'
SUMMARISING RUN PARAMETERS
==========================
Input filename: EPI-103_S27_L005_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.2
Cutadapt version: 1.12
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
File was specified to be an MspI-digested RRBS sample. Sequences with adapter contamination will be trimmed a further 2 bp to remove potential methylation-biased bases from the end-repair reaction
Running FastQC on the data once trimming has completed
Output file(s) will be GZIP compressed
>>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<<
This is cutadapt 1.12 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -a X EPI-103_S27_L005_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
10000000 sequences processed
20000000 sequences processed
Finished in 339.56 s (17 us/read; 3.61 M reads/minute).
=== Summary ===
Total reads processed: 20,420,261
Reads with adapters: 0 (0.0%)
Reads written (passing filters): 20,420,261 (100.0%)
Total basepairs processed: 2,062,446,361 bp
Quality-trimmed: 8,319,695 bp (0.4%)
Total written (filtered): 2,054,126,666 bp (99.6%)
=== Adapter 1 ===
Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times.
>>> Quality trimming completed <<<
20420261 sequences processed in total
Writing final adapter and quality trimmed output to EPI-103_S27_L005_R1_001_trimmed.fq.gz
>>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file EPI-103_S27_L005_R1_001.fastq.gz_qual_trimmed.fastq <<<
10000000 sequences processed
20000000 sequences processed
This is cutadapt 1.12 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /home/sean/Documents/Geoduck/Trimmed-fq/EPI-103_S27_L005_R1_001.fastq.gz_qual_trimmed.fastq
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 414.36 s (20 us/read; 2.96 M reads/minute).
=== Summary ===
Total reads processed: 20,420,261
Reads with adapters: 10,283,712 (50.4%)
Reads written (passing filters): 20,420,261 (100.0%)
Total basepairs processed: 2,054,126,666 bp
Total written (filtered): 1,925,748,290 bp (93.8%)
=== Adapter 1 ===
Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10283712 times.
No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1
Bases preceding removed adapters:
A: 26.7%
C: 5.9%
G: 24.5%
T: 42.9%
none/other: 0.0%
Overview of removed sequences
length count expect max.err error counts
1 4475714 5105065.2 0 4475714
2 1023849 1276266.3 0 1023849
3 388885 319066.6 0 388885
4 258450 79766.6 0 258450
5 111458 19941.7 0 111458
6 115643 4985.4 0 115643
7 106247 1246.4 0 106247
8 141870 311.6 0 141870
9 107898 77.9 0 106798 1100
10 98957 19.5 1 93927 5030
11 102966 4.9 1 96927 6039
12 95747 1.2 1 90547 5200
13 87695 0.3 1 82877 4818
14 101667 0.3 1 94968 6699
15 93139 0.3 1 87800 5339
16 103499 0.3 1 96374 7125
17 95053 0.3 1 89414 5639
18 87319 0.3 1 82373 4946
19 93614 0.3 1 87354 6260
20 83374 0.3 1 78697 4677
21 94369 0.3 1 88145 6224
22 87215 0.3 1 82399 4816
23 81878 0.3 1 76955 4923
24 84292 0.3 1 78848 5444
25 75958 0.3 1 71702 4256
26 85493 0.3 1 79989 5504
27 75013 0.3 1 70780 4233
28 69434 0.3 1 65743 3691
29 76872 0.3 1 72314 4558
30 70549 0.3 1 66780 3769
31 76672 0.3 1 72027 4645
32 65989 0.3 1 62622 3367
33 77921 0.3 1 73000 4921
34 64015 0.3 1 60557 3458
35 65390 0.3 1 61390 4000
36 69532 0.3 1 65320 4212
37 62340 0.3 1 58957 3383
38 61893 0.3 1 58232 3661
39 59034 0.3 1 55683 3351
40 60466 0.3 1 56940 3526
41 85039 0.3 1 81239 3800
42 48849 0.3 1 46798 2051
43 21450 0.3 1 19928 1522
44 48314 0.3 1 45718 2596
45 45581 0.3 1 43091 2490
46 43704 0.3 1 41474 2230
47 46686 0.3 1 44129 2557
48 44652 0.3 1 42070 2582
49 44260 0.3 1 41731 2529
50 38780 0.3 1 36820 1960
51 36753 0.3 1 34893 1860
52 34328 0.3 1 32602 1726
53 32419 0.3 1 30876 1543
54 32948 0.3 1 31303 1645
55 32703 0.3 1 31200 1503
56 31231 0.3 1 29705 1526
57 30278 0.3 1 28832 1446
58 27855 0.3 1 26666 1189
59 27604 0.3 1 26347 1257
60 24122 0.3 1 23057 1065
61 23675 0.3 1 22682 993
62 24513 0.3 1 23477 1036
63 23046 0.3 1 22005 1041
64 22440 0.3 1 21524 916
65 20291 0.3 1 19482 809
66 18819 0.3 1 18005 814
67 17210 0.3 1 16470 740
68 14805 0.3 1 14163 642
69 14715 0.3 1 14065 650
70 13133 0.3 1 12521 612
71 12548 0.3 1 12020 528
72 11994 0.3 1 11476 518
73 11872 0.3 1 11190 682
74 18800 0.3 1 18184 616
75 7934 0.3 1 7639 295
76 3757 0.3 1 3618 139
77 2203 0.3 1 2106 97
78 1531 0.3 1 1470 61
79 1078 0.3 1 1043 35
80 755 0.3 1 716 39
81 508 0.3 1 483 25
82 324 0.3 1 311 13
83 230 0.3 1 220 10
84 142 0.3 1 132 10
85 110 0.3 1 103 7
86 59 0.3 1 50 9
87 46 0.3 1 39 7
88 61 0.3 1 52 9
89 53 0.3 1 48 5
90 66 0.3 1 55 11
91 82 0.3 1 73 9
92 124 0.3 1 107 17
93 190 0.3 1 169 21
94 305 0.3 1 277 28
95 464 0.3 1 429 35
96 389 0.3 1 358 31
97 180 0.3 1 159 21
98 73 0.3 1 58 15
99 41 0.3 1 36 5
100 58 0.3 1 42 16
101 163 0.3 1 99 64
Successfully deleted temporary file EPI-103_S27_L005_R1_001.fastq.gz_qual_trimmed.fastq
RUN STATISTICS FOR INPUT FILE: EPI-103_S27_L005_R1_001.fastq.gz
=============================================
20420261 sequences processed in total
Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2158450 (10.6%)
The length threshold of paired-end sequences gets evaluated later on (in the validation step)
RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 10282845 (50.4%)
Writing report to '/home/sean/Documents/Geoduck/Trimmed-fq/EPI-103_S27_L005_R1_001.fastq.gz_qual_trimmed.fastq_trimming_report.txt'
SUMMARISING RUN PARAMETERS
==========================
Input filename: EPI-103_S27_L005_R1_001.fastq.gz_qual_trimmed.fastq
Trimming mode: paired-end
Trim Galore version: 0.4.2
Cutadapt version: 1.12
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
File was specified to be an MspI-digested RRBS sample. Sequences with adapter contamination will be trimmed a further 2 bp to remove potential methylation-biased bases from the end-repair reaction
Running FastQC on the data once trimming has completed
Output file(s) will be GZIP compressed
>>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<<
This is cutadapt 1.12 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -a X EPI-103_S27_L005_R1_001.fastq.gz_qual_trimmed.fastq
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
cutadapt: error: FASTQ file ended prematurely
>>> Quality trimming completed <<<
148470 sequences processed in total
Unable to close QUAL filehandle:
gzip: stdout: Broken pipe
No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> EPI-103_S27_L005_R1_001.fastq.gz_qual_trimmed.fastq <<)
Found perfect matches for the following adapter sequences:
Adapter type Count Sequence Sequences analysed Percentage
Illumina 22628 AGATCGGAAGAGC 148470 15.24
smallRNA 1 TGGAATTCTCGG 148470 0.00
Nextera 0 CTGTCTCTTATA 148470 0.00
Using Illumina adapter for trimming (count: 22628). Second best hit was smallRNA (count: 1)
Writing report to '/home/sean/Documents/Geoduck/Trimmed-fq/EPI-103_S27_L005_R1_001.fastq.gz_qual_trimmed.fastq_trimming_report.txt'
SUMMARISING RUN PARAMETERS
==========================
Input filename: EPI-103_S27_L005_R1_001.fastq.gz_qual_trimmed.fastq
Trimming mode: paired-end
Trim Galore version: 0.4.2
Cutadapt version: 1.12
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
File was specified to be an MspI-digested RRBS sample. Sequences with adapter contamination will be trimmed a further 2 bp to remove potential methylation-biased bases from the end-repair reaction
Running FastQC on the data once trimming has completed
>>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<<
This is cutadapt 1.12 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -a X EPI-103_S27_L005_R1_001.fastq.gz_qual_trimmed.fastq
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
cutadapt: error: FASTQ file ended prematurely
>>> Quality trimming completed <<<
148470 sequences processed in total
Unable to close QUAL filehandle:
No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> EPI-103_S27_L005_R1_001.fastq.gz_trimming_report.txt <<)
Found perfect matches for the following adapter sequences:
Adapter type Count Sequence Sequences analysed Percentage
Illumina 1 AGATCGGAAGAGC 4 25.00
Nextera 0 CTGTCTCTTATA 4 0.00
smallRNA 0 TGGAATTCTCGG 4 0.00
Using Illumina adapter for trimming (count: 1). Second best hit was Nextera (count: 0)
Writing report to '/home/sean/Documents/Geoduck/Trimmed-fq/EPI-103_S27_L005_R1_001.fastq.gz_trimming_report.txt_trimming_report.txt'
SUMMARISING RUN PARAMETERS
==========================
Input filename: EPI-103_S27_L005_R1_001.fastq.gz_trimming_report.txt
Trimming mode: paired-end
Trim Galore version: 0.4.2
Cutadapt version: 1.12
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
File was specified to be an MspI-digested RRBS sample. Sequences with adapter contamination will be trimmed a further 2 bp to remove potential methylation-biased bases from the end-repair reaction
Running FastQC on the data once trimming has completed
>>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<<
This is cutadapt 1.12 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -a X EPI-103_S27_L005_R1_001.fastq.gz_trimming_report.txt
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
cutadapt: error: Line 1 in FASTQ file is expected to start with '@', but found '\n'
>>> Quality trimming completed <<<
0 sequences processed in total
Unable to close QUAL filehandle:
No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> EPI-103_S27_L005_R2_001.fastq.gz <<)
Found perfect matches for the following adapter sequences:
Adapter type Count Sequence Sequences analysed Percentage
Illumina 150921 AGATCGGAAGAGC 1000000 15.09
Nextera 3 CTGTCTCTTATA 1000000 0.00
smallRNA 0 TGGAATTCTCGG 1000000 0.00
Using Illumina adapter for trimming (count: 150921). Second best hit was Nextera (count: 3)
gzip: stdout: Broken pipe
Writing report to '/home/sean/Documents/Geoduck/Trimmed-fq/EPI-103_S27_L005_R2_001.fastq.gz_trimming_report.txt'
SUMMARISING RUN PARAMETERS
==========================
Input filename: EPI-103_S27_L005_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.2
Cutadapt version: 1.12
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
File was specified to be an MspI-digested RRBS sample. Sequences with adapter contamination will be trimmed a further 2 bp to remove potential methylation-biased bases from the end-repair reaction
Running FastQC on the data once trimming has completed
Output file(s) will be GZIP compressed
>>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<<
This is cutadapt 1.12 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -a X EPI-103_S27_L005_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
10000000 sequences processed
20000000 sequences processed
Finished in 327.83 s (16 us/read; 3.74 M reads/minute).
=== Summary ===
Total reads processed: 20,420,261
Reads with adapters: 0 (0.0%)
Reads written (passing filters): 20,420,261 (100.0%)
Total basepairs processed: 2,062,446,361 bp
Quality-trimmed: 15,714,712 bp (0.8%)
Total written (filtered): 2,046,731,649 bp (99.2%)
=== Adapter 1 ===
Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times.
>>> Quality trimming completed <<<
20420261 sequences processed in total
Writing final adapter and quality trimmed output to EPI-103_S27_L005_R2_001_trimmed.fq.gz
>>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file EPI-103_S27_L005_R2_001.fastq.gz_qual_trimmed.fastq <<< Cancelled the trimming to get just raw data processed quickly.
for(i in seq(from = 1, to = (length(file.names) - 1), by = 2)) {
system(paste0("bsmap -p 16 -d ~/Documents/Geoduck/Panopea_generosa-Scaff-10k.fa -a ", file.names[i], " -b ", file.names[i + 1], " -o ~/Documents/Geoduck/bsmap-output/", substr(file.names[i], 1, 16), ".sam > bsmap_output_", substr(file.names[i], 1, 16), ".txt"))
}
[bsmap] @Fri Dec 30 12:07:01 2016 loading reference file: /home/sean/Documents/Geoduck/Panopea_generosa-Scaff-10k.fa (format: FASTA)
[bsmap] @Fri Dec 30 12:07:04 2016 19539 reference seqs loaded, total size 314618376 bp. 3 secs passed
[bsmap] @Fri Dec 30 12:07:14 2016 create seed table. 13 secs passed
[bsmap] @Fri Dec 30 12:07:14 2016 Pair-end alignment(16 threads),
Input read file #1: EPI-103_S27_L005_R1_001.fastq.gz (format: gzipped FASTQ)
Input read file #2: EPI-103_S27_L005_R2_001.fastq.gz (format: gzipped FASTQ)
Output file: /home/sean/Documents/Geoduck/bsmap-output/EPI-103_S27_L005.sam (format: SAM)
[bsmap] @Fri Dec 30 13:32:35 2016 total read pairs: 20420261 total time consumed: 5134 secs
aligned pairs: 2517366 (12.3%), unique pairs: 2336090 (11.4%), non-unique pairs: 181276 (0.9%)
unpaired read #1: 1172671 (5.7%), unique reads: 915318 (4.5%), non-unique reads: 257353 (1.3%)
unpaired read #2: 1098935 (5.4%), unique reads: 854437 (4.2%), non-unique reads: 244498 (1.2%)
[bsmap] @Fri Dec 30 13:32:35 2016 loading reference file: /home/sean/Documents/Geoduck/Panopea_generosa-Scaff-10k.fa (format: FASTA)
[bsmap] @Fri Dec 30 13:32:38 2016 19539 reference seqs loaded, total size 314618376 bp. 3 secs passed
[bsmap] @Fri Dec 30 13:32:48 2016 create seed table. 13 secs passed
[bsmap] @Fri Dec 30 13:32:48 2016 Pair-end alignment(16 threads),
Input read file #1: EPI-104_S28_L005_R1_001.fastq.gz (format: gzipped FASTQ)
Input read file #2: EPI-104_S28_L005_R2_001.fastq.gz (format: gzipped FASTQ)
Output file: /home/sean/Documents/Geoduck/bsmap-output/EPI-104_S28_L005.sam (format: SAM)
[bsmap] @Fri Dec 30 15:39:01 2016 total read pairs: 30166064 total time consumed: 7586 secs
aligned pairs: 3697105 (12.3%), unique pairs: 3420145 (11.3%), non-unique pairs: 276960 (0.9%)
unpaired read #1: 1621376 (5.4%), unique reads: 1264027 (4.2%), non-unique reads: 357349 (1.2%)
unpaired read #2: 1538258 (5.1%), unique reads: 1198037 (4.0%), non-unique reads: 340221 (1.1%)
[bsmap] @Fri Dec 30 15:39:01 2016 loading reference file: /home/sean/Documents/Geoduck/Panopea_generosa-Scaff-10k.fa (format: FASTA)
[bsmap] @Fri Dec 30 15:39:04 2016 19539 reference seqs loaded, total size 314618376 bp. 3 secs passed
[bsmap] @Fri Dec 30 15:39:14 2016 create seed table. 13 secs passed
[bsmap] @Fri Dec 30 15:39:14 2016 Pair-end alignment(16 threads),
Input read file #1: EPI-111_S29_L005_R1_001.fastq.gz (format: gzipped FASTQ)
Input read file #2: EPI-111_S29_L005_R2_001.fastq.gz (format: gzipped FASTQ)
Output file: /home/sean/Documents/Geoduck/bsmap-output/EPI-111_S29_L005.sam (format: SAM)
[bsmap] @Fri Dec 30 17:32:32 2016 total read pairs: 27105772 total time consumed: 6811 secs
aligned pairs: 3282200 (12.1%), unique pairs: 3041425 (11.2%), non-unique pairs: 240775 (0.9%)
unpaired read #1: 1415839 (5.2%), unique reads: 1110086 (4.1%), non-unique reads: 305753 (1.1%)
unpaired read #2: 1339689 (4.9%), unique reads: 1042560 (3.8%), non-unique reads: 297129 (1.1%)
[bsmap] @Fri Dec 30 17:32:32 2016 loading reference file: /home/sean/Documents/Geoduck/Panopea_generosa-Scaff-10k.fa (format: FASTA)
[bsmap] @Fri Dec 30 17:32:35 2016 19539 reference seqs loaded, total size 314618376 bp. 3 secs passed
[bsmap] @Fri Dec 30 17:32:45 2016 create seed table. 13 secs passed
[bsmap] @Fri Dec 30 17:32:45 2016 Pair-end alignment(16 threads),
Input read file #1: EPI-113_S30_L005_R1_001.fastq.gz (format: gzipped FASTQ)
Input read file #2: EPI-113_S30_L005_R2_001.fastq.gz (format: gzipped FASTQ)
Output file: /home/sean/Documents/Geoduck/bsmap-output/EPI-113_S30_L005.sam (format: SAM)
[bsmap] @Fri Dec 30 19:23:19 2016 total read pairs: 26402719 total time consumed: 6647 secs
aligned pairs: 3154150 (11.9%), unique pairs: 2926861 (11.1%), non-unique pairs: 227289 (0.9%)
unpaired read #1: 1424412 (5.4%), unique reads: 1114346 (4.2%), non-unique reads: 310066 (1.2%)
unpaired read #2: 1362250 (5.2%), unique reads: 1061756 (4.0%), non-unique reads: 300494 (1.1%)
[bsmap] @Fri Dec 30 19:23:19 2016 loading reference file: /home/sean/Documents/Geoduck/Panopea_generosa-Scaff-10k.fa (format: FASTA)
[bsmap] @Fri Dec 30 19:23:22 2016 19539 reference seqs loaded, total size 314618376 bp. 3 secs passed
[bsmap] @Fri Dec 30 19:23:32 2016 create seed table. 13 secs passed
[bsmap] @Fri Dec 30 19:23:32 2016 Pair-end alignment(16 threads),
Input read file #1: EPI-119_S31_L005_R1_001.fastq.gz (format: gzipped FASTQ)
Input read file #2: EPI-119_S31_L005_R2_001.fastq.gz (format: gzipped FASTQ)
Output file: /home/sean/Documents/Geoduck/bsmap-output/EPI-119_S31_L005.sam (format: SAM)
[bsmap] @Fri Dec 30 21:24:39 2016 total read pairs: 29018872 total time consumed: 7280 secs
aligned pairs: 3373571 (11.6%), unique pairs: 3141307 (10.8%), non-unique pairs: 232264 (0.8%)
unpaired read #1: 1615333 (5.6%), unique reads: 1264246 (4.4%), non-unique reads: 351087 (1.2%)
unpaired read #2: 1533635 (5.3%), unique reads: 1190562 (4.1%), non-unique reads: 343073 (1.2%)
[bsmap] @Fri Dec 30 21:24:39 2016 loading reference file: /home/sean/Documents/Geoduck/Panopea_generosa-Scaff-10k.fa (format: FASTA)
[bsmap] @Fri Dec 30 21:24:41 2016 19539 reference seqs loaded, total size 314618376 bp. 2 secs passed
[bsmap] @Fri Dec 30 21:24:52 2016 create seed table. 13 secs passed
[bsmap] @Fri Dec 30 21:24:52 2016 Pair-end alignment(16 threads),
Input read file #1: EPI-120_S32_L005_R1_001.fastq.gz (format: gzipped FASTQ)
Input read file #2: EPI-120_S32_L005_R2_001.fastq.gz (format: gzipped FASTQ)
Output file: /home/sean/Documents/Geoduck/bsmap-output/EPI-120_S32_L005.sam (format: SAM)
[bsmap] @Fri Dec 30 23:06:34 2016 total read pairs: 24230515 total time consumed: 6115 secs
aligned pairs: 3049585 (12.6%), unique pairs: 2833486 (11.7%), non-unique pairs: 216099 (0.9%)
unpaired read #1: 1396478 (5.8%), unique reads: 1094292 (4.5%), non-unique reads: 302186 (1.2%)
unpaired read #2: 1329580 (5.5%), unique reads: 1034666 (4.3%), non-unique reads: 294914 (1.2%)
[bsmap] @Fri Dec 30 23:06:34 2016 loading reference file: /home/sean/Documents/Geoduck/Panopea_generosa-Scaff-10k.fa (format: FASTA)
[bsmap] @Fri Dec 30 23:06:37 2016 19539 reference seqs loaded, total size 314618376 bp. 3 secs passed
[bsmap] @Fri Dec 30 23:06:47 2016 create seed table. 13 secs passed
[bsmap] @Fri Dec 30 23:06:47 2016 Pair-end alignment(16 threads),
Input read file #1: EPI-127_S33_L005_R1_001.fastq.gz (format: gzipped FASTQ)
Input read file #2: EPI-127_S33_L005_R2_001.fastq.gz (format: gzipped FASTQ)
Output file: /home/sean/Documents/Geoduck/bsmap-output/EPI-127_S33_L005.sam (format: SAM)
[bsmap] @Sat Dec 31 00:40:16 2016 total read pairs: 22355686 total time consumed: 5622 secs
aligned pairs: 2804076 (12.5%), unique pairs: 2604191 (11.6%), non-unique pairs: 199885 (0.9%)
unpaired read #1: 1291005 (5.8%), unique reads: 1008876 (4.5%), non-unique reads: 282129 (1.3%)
unpaired read #2: 1228688 (5.5%), unique reads: 953980 (4.3%), non-unique reads: 274708 (1.2%)
[bsmap] @Sat Dec 31 00:40:16 2016 loading reference file: /home/sean/Documents/Geoduck/Panopea_generosa-Scaff-10k.fa (format: FASTA)
[bsmap] @Sat Dec 31 00:40:19 2016 19539 reference seqs loaded, total size 314618376 bp. 3 secs passed
[bsmap] @Sat Dec 31 00:40:29 2016 create seed table. 13 secs passed
[bsmap] @Sat Dec 31 00:40:29 2016 Pair-end alignment(16 threads),
Input read file #1: EPI-128_S34_L005_R1_001.fastq.gz (format: gzipped FASTQ)
Input read file #2: EPI-128_S34_L005_R2_001.fastq.gz (format: gzipped FASTQ)
Output file: /home/sean/Documents/Geoduck/bsmap-output/EPI-128_S34_L005.sam (format: SAM)
[bsmap] @Sat Dec 31 02:23:58 2016 total read pairs: 24692504 total time consumed: 6222 secs
aligned pairs: 3045683 (12.3%), unique pairs: 2828479 (11.5%), non-unique pairs: 217204 (0.9%)
unpaired read #1: 1433756 (5.8%), unique reads: 1123524 (4.6%), non-unique reads: 310232 (1.3%)
unpaired read #2: 1340187 (5.4%), unique reads: 1039299 (4.2%), non-unique reads: 300888 (1.2%)
[bsmap] @Sat Dec 31 02:23:58 2016 loading reference file: /home/sean/Documents/Geoduck/Panopea_generosa-Scaff-10k.fa (format: FASTA)
[bsmap] @Sat Dec 31 02:24:01 2016 19539 reference seqs loaded, total size 314618376 bp. 3 secs passed
[bsmap] @Sat Dec 31 02:24:11 2016 create seed table. 13 secs passed
[bsmap] @Sat Dec 31 02:24:11 2016 Pair-end alignment(16 threads),
Input read file #1: EPI-135_S35_L005_R1_001.fastq.gz (format: gzipped FASTQ)
Input read file #2: EPI-135_S35_L005_R2_001.fastq.gz (format: gzipped FASTQ)
Output file: /home/sean/Documents/Geoduck/bsmap-output/EPI-135_S35_L005.sam (format: SAM)
[bsmap] @Sat Dec 31 04:25:17 2016 total read pairs: 28955967 total time consumed: 7279 secs
aligned pairs: 3188523 (11.0%), unique pairs: 2949004 (10.2%), non-unique pairs: 239519 (0.8%)
unpaired read #1: 1404490 (4.9%), unique reads: 1101052 (3.8%), non-unique reads: 303438 (1.0%)
unpaired read #2: 1312702 (4.5%), unique reads: 1019696 (3.5%), non-unique reads: 293006 (1.0%)
[bsmap] @Sat Dec 31 04:25:17 2016 loading reference file: /home/sean/Documents/Geoduck/Panopea_generosa-Scaff-10k.fa (format: FASTA)
[bsmap] @Sat Dec 31 04:25:20 2016 19539 reference seqs loaded, total size 314618376 bp. 3 secs passed
[bsmap] @Sat Dec 31 04:25:30 2016 create seed table. 13 secs passed
[bsmap] @Sat Dec 31 04:25:30 2016 Pair-end alignment(16 threads),
Input read file #1: EPI-136_S36_L005_R1_001.fastq.gz (format: gzipped FASTQ)
Input read file #2: EPI-136_S36_L005_R2_001.fastq.gz (format: gzipped FASTQ)
Output file: /home/sean/Documents/Geoduck/bsmap-output/EPI-136_S36_L005.sam (format: SAM)
[bsmap] @Sat Dec 31 06:22:08 2016 total read pairs: 27877100 total time consumed: 7011 secs
aligned pairs: 3061099 (11.0%), unique pairs: 2828993 (10.1%), non-unique pairs: 232106 (0.8%)
unpaired read #1: 1339415 (4.8%), unique reads: 1050035 (3.8%), non-unique reads: 289380 (1.0%)
unpaired read #2: 1276208 (4.6%), unique reads: 994615 (3.6%), non-unique reads: 281593 (1.0%)
[bsmap] @Sat Dec 31 06:22:08 2016 loading reference file: /home/sean/Documents/Geoduck/Panopea_generosa-Scaff-10k.fa (format: FASTA)
[bsmap] @Sat Dec 31 06:22:10 2016 19539 reference seqs loaded, total size 314618376 bp. 2 secs passed
[bsmap] @Sat Dec 31 06:22:20 2016 create seed table. 12 secs passed
[bsmap] @Sat Dec 31 06:22:20 2016 Pair-end alignment(16 threads),
Input read file #1: EPI-143_S37_L005_R1_001.fastq.gz (format: gzipped FASTQ)
Input read file #2: EPI-143_S37_L005_R2_001.fastq.gz (format: gzipped FASTQ)
Output file: /home/sean/Documents/Geoduck/bsmap-output/EPI-143_S37_L005.sam (format: SAM)
[bsmap] @Sat Dec 31 07:51:22 2016 total read pairs: 21282370 total time consumed: 5354 secs
aligned pairs: 2538558 (11.9%), unique pairs: 2356364 (11.1%), non-unique pairs: 182194 (0.9%)
unpaired read #1: 1219939 (5.7%), unique reads: 954258 (4.5%), non-unique reads: 265681 (1.2%)
unpaired read #2: 1114102 (5.2%), unique reads: 863281 (4.1%), non-unique reads: 250821 (1.2%)
[bsmap] @Sat Dec 31 07:51:22 2016 loading reference file: /home/sean/Documents/Geoduck/Panopea_generosa-Scaff-10k.fa (format: FASTA)
[bsmap] @Sat Dec 31 07:51:25 2016 19539 reference seqs loaded, total size 314618376 bp. 3 secs passed
[bsmap] @Sat Dec 31 07:51:35 2016 create seed table. 13 secs passed
[bsmap] @Sat Dec 31 07:51:35 2016 Pair-end alignment(16 threads),
Input read file #1: EPI-145_S38_L005_R1_001.fastq.gz (format: gzipped FASTQ)
Input read file #2: EPI-145_S38_L005_R2_001.fastq.gz (format: gzipped FASTQ)
Output file: /home/sean/Documents/Geoduck/bsmap-output/EPI-145_S38_L005.sam (format: SAM)
[bsmap] @Sat Dec 31 09:38:26 2016 total read pairs: 25512585 total time consumed: 6424 secs
aligned pairs: 3095359 (12.1%), unique pairs: 2872361 (11.3%), non-unique pairs: 222998 (0.9%)
unpaired read #1: 1432883 (5.6%), unique reads: 1118827 (4.4%), non-unique reads: 314056 (1.2%)
unpaired read #2: 1360450 (5.3%), unique reads: 1056084 (4.1%), non-unique reads: 304366 (1.2%)Add a new chunk by clicking the Insert Chunk button on the toolbar or by pressing Ctrl+Alt+I.
When you save the notebook, an HTML file containing the code and output will be saved alongside it (click the Preview button or press Ctrl+Shift+K to preview the HTML file).