Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.7/samtools' Reference genome folder provided is /Users/sr320/Dropbox/wd/18-03-15/genome/ (absolute path is '/Users/sr320/Dropbox/wd/18-03-15/genome/)' Processing sequences up to read no. 1000 from the input file Input files to be analysed (in current folder '/Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore'): zr2096_10_s1_R1_val_1.fq.gz zr2096_10_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore Now reading in and storing sequence information of the genome specified in: /Users/sr320/Dropbox/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_10_s1_R1_val_1.fq.gz and zr2096_10_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000 from zr2096_10_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_10_s1_R1_val_1.fq.gz to zr2096_10_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_10_s1_R1_val_1.fq.gz to zr2096_10_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_10_s1_R1_val_1.fq.gz (1001 sequences in total) Processing reads up to sequence no. 1000 from zr2096_10_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_10_s1_R2_val_2.fq.gz to zr2096_10_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_10_s1_R2_val_2.fq.gz to zr2096_10_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_10_s1_R2_val_2.fq.gz (1001 sequences in total) Input files are zr2096_10_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_10_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_10_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_10_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Users/sr320/Dropbox/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_10_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_10_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:2:1101:1232:2155_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 ATTGTATTAATTATAAAAAATATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATTTATTATTAAAAATATTAAATA FFFFFFFFFBFFFFFFFFFFFFF#################################<>> Writing bisulfite mapping results to zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_10_s1_R1_val_1.fq.gz and zr2096_10_s1_R2_val_2.fq.gz 1000 reads; of these: 1000 (100.00%) were paired; of these: 903 (90.30%) aligned concordantly 0 times 51 (5.10%) aligned concordantly exactly 1 time 46 (4.60%) aligned concordantly >1 times 9.70% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 907 (90.70%) aligned concordantly 0 times 47 (4.70%) aligned concordantly exactly 1 time 46 (4.60%) aligned concordantly >1 times 9.30% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 900 (90.00%) aligned concordantly 0 times 56 (5.60%) aligned concordantly exactly 1 time 44 (4.40%) aligned concordantly >1 times 10.00% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 902 (90.20%) aligned concordantly 0 times 54 (5.40%) aligned concordantly exactly 1 time 44 (4.40%) aligned concordantly >1 times 9.80% overall alignment rate Processed 1000 sequences in total Successfully deleted the temporary files zr2096_10_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_10_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_10_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_10_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 1000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 5202 Total methylated C's in CpG context: 510 Total methylated C's in CHG context: 16 Total methylated C's in CHH context: 37 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 175 Total unmethylated C's in CHG context: 1138 Total unmethylated C's in CHH context: 3326 Total unmethylated C's in Unknown context: 1 C methylated in CpG context: 74.5% C methylated in CHG context: 1.4% C methylated in CHH context: 1.1% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 24s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.7/samtools' Reference genome folder provided is /Users/sr320/Dropbox/wd/18-03-15/genome/ (absolute path is '/Users/sr320/Dropbox/wd/18-03-15/genome/)' Processing sequences up to read no. 1000 from the input file Input files to be analysed (in current folder '/Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore'): zr2096_1_s1_R1_val_1.fq.gz zr2096_1_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore Now reading in and storing sequence information of the genome specified in: /Users/sr320/Dropbox/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_1_s1_R1_val_1.fq.gz and zr2096_1_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000 from zr2096_1_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_1_s1_R1_val_1.fq.gz to zr2096_1_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_1_s1_R1_val_1.fq.gz to zr2096_1_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_1_s1_R1_val_1.fq.gz (1001 sequences in total) Processing reads up to sequence no. 1000 from zr2096_1_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_1_s1_R2_val_2.fq.gz to zr2096_1_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_1_s1_R2_val_2.fq.gz to zr2096_1_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_1_s1_R2_val_2.fq.gz (1001 sequences in total) Input files are zr2096_1_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_1_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_1_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_1_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Users/sr320/Dropbox/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_1_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_1_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1249:2156_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 GATTATTTGTTGTTTGTTGTTTGTTTGNNNNTNNNTNNGTTTGTTTGTTTGTTTGTTTGTTTGTAAATTTTTTATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFF####<###<##<<>> Writing bisulfite mapping results to zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_1_s1_R1_val_1.fq.gz and zr2096_1_s1_R2_val_2.fq.gz 1000 reads; of these: 1000 (100.00%) were paired; of these: 956 (95.60%) aligned concordantly 0 times 26 (2.60%) aligned concordantly exactly 1 time 18 (1.80%) aligned concordantly >1 times 4.40% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 956 (95.60%) aligned concordantly 0 times 27 (2.70%) aligned concordantly exactly 1 time 17 (1.70%) aligned concordantly >1 times 4.40% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 951 (95.10%) aligned concordantly 0 times 22 (2.20%) aligned concordantly exactly 1 time 27 (2.70%) aligned concordantly >1 times 4.90% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 954 (95.40%) aligned concordantly 0 times 23 (2.30%) aligned concordantly exactly 1 time 23 (2.30%) aligned concordantly >1 times 4.60% overall alignment rate Processed 1000 sequences in total Successfully deleted the temporary files zr2096_1_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_1_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_1_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_1_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 1000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2420 Total methylated C's in CpG context: 221 Total methylated C's in CHG context: 13 Total methylated C's in CHH context: 34 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 71 Total unmethylated C's in CHG context: 515 Total unmethylated C's in CHH context: 1566 Total unmethylated C's in Unknown context: 4 C methylated in CpG context: 75.7% C methylated in CHG context: 2.5% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 33.3% Bismark completed in 0d 0h 0m 18s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.7/samtools' Reference genome folder provided is /Users/sr320/Dropbox/wd/18-03-15/genome/ (absolute path is '/Users/sr320/Dropbox/wd/18-03-15/genome/)' Processing sequences up to read no. 1000 from the input file Input files to be analysed (in current folder '/Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore'): zr2096_2_s1_R1_val_1.fq.gz zr2096_2_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore Now reading in and storing sequence information of the genome specified in: /Users/sr320/Dropbox/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_2_s1_R1_val_1.fq.gz and zr2096_2_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000 from zr2096_2_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_2_s1_R1_val_1.fq.gz to zr2096_2_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_2_s1_R1_val_1.fq.gz to zr2096_2_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_2_s1_R1_val_1.fq.gz (1001 sequences in total) Processing reads up to sequence no. 1000 from zr2096_2_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_2_s1_R2_val_2.fq.gz to zr2096_2_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_2_s1_R2_val_2.fq.gz to zr2096_2_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_2_s1_R2_val_2.fq.gz (1001 sequences in total) Input files are zr2096_2_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_2_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_2_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_2_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Users/sr320/Dropbox/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_2_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_2_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1148:2157_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 AAATTTATTATTTTAAAAATAAAAATTNNNNTNNNTTTTATTATTTTTTTTAATATTTTTTAATATAATTAAATAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFF####<###<<>> Writing bisulfite mapping results to zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_2_s1_R1_val_1.fq.gz and zr2096_2_s1_R2_val_2.fq.gz 1000 reads; of these: 1000 (1000100.00%) were paired; of these: 924 (92.40%) aligned concordantly 0 times 39 (3.90%) aligned concordantly exactly 1 time 37 (3.70%) aligned concordantly >1 times 7.60% overall alignment rate reads; of these: 1000 (100.00%) were paired; of these: 879 (87.90%) aligned concordantly 0 times 67 (6.70%) aligned concordantly exactly 1 time 54 (5.40%) aligned concordantly >1 times 12.10% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 888 (88.80%) aligned concordantly 0 times 54 (5.40%) aligned concordantly exactly 1 time 58 (5.80%) aligned concordantly >1 times 11.20% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 908 (90.80%) aligned concordantly 0 times 61 (6.10%) aligned concordantly exactly 1 time 31 (3.10%) aligned concordantly >1 times 9.20% overall alignment rate Processed 1000 sequences in total Successfully deleted the temporary files zr2096_2_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_2_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_2_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_2_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 1000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 4461 Total methylated C's in CpG context: 524 Total methylated C's in CHG context: 18 Total methylated C's in CHH context: 29 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 121 Total unmethylated C's in CHG context: 1098 Total unmethylated C's in CHH context: 2671 Total unmethylated C's in Unknown context: 5 C methylated in CpG context: 81.2% C methylated in CHG context: 1.6% C methylated in CHH context: 1.1% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 18s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.7/samtools' Reference genome folder provided is /Users/sr320/Dropbox/wd/18-03-15/genome/ (absolute path is '/Users/sr320/Dropbox/wd/18-03-15/genome/)' Processing sequences up to read no. 1000 from the input file Input files to be analysed (in current folder '/Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore'): zr2096_3_s1_R1_val_1.fq.gz zr2096_3_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore Now reading in and storing sequence information of the genome specified in: /Users/sr320/Dropbox/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_3_s1_R1_val_1.fq.gz and zr2096_3_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000 from zr2096_3_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_3_s1_R1_val_1.fq.gz to zr2096_3_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_3_s1_R1_val_1.fq.gz to zr2096_3_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_3_s1_R1_val_1.fq.gz (1001 sequences in total) Processing reads up to sequence no. 1000 from zr2096_3_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_3_s1_R2_val_2.fq.gz to zr2096_3_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_3_s1_R2_val_2.fq.gz to zr2096_3_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_3_s1_R2_val_2.fq.gz (1001 sequences in total) Input files are zr2096_3_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_3_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_3_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_3_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Users/sr320/Dropbox/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_3_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_3_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1059:2153_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 TAATTTAAATAATTTTATATAAATNNNNNNNNNNNNNNNTATTTAAATTAAAAATTTAAATAAATTTTTTTAATTATTTA FFFFFFFFFFFFFFFFFFFFFFFF###############<<>> Writing bisulfite mapping results to zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_3_s1_R1_val_1.fq.gz and zr2096_3_s1_R2_val_2.fq.gz 1000 reads; of these: 1000 (100.00%) were paired; of these: 900 (90.00%) aligned concordantly 0 times 48 (4.80%) aligned concordantly exactly 1 time 52 (5.20%) aligned concordantly >1 times 10.00% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 881 (88.10%) aligned concordantly 0 times 62 (6.20%) aligned concordantly exactly 1 time 57 (5.70%) aligned concordantly >1 times 11.90% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 892 (89.20%) aligned concordantly 0 times 54 (5.40%) aligned concordantly exactly 1 time 54 (5.40%) aligned concordantly >1 times 10.80% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 887 (88.70%) aligned concordantly 0 times 50 (5.00%) aligned concordantly exactly 1 time 63 (6.30%) aligned concordantly >1 times 11.30% overall alignment rate Processed 1000 sequences in total Successfully deleted the temporary files zr2096_3_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_3_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_3_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_3_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 1000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 5367 Total methylated C's in CpG context: 627 Total methylated C's in CHG context: 18 Total methylated C's in CHH context: 40 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 156 Total unmethylated C's in CHG context: 1201 Total unmethylated C's in CHH context: 3325 Total unmethylated C's in Unknown context: 3 C methylated in CpG context: 80.1% C methylated in CHG context: 1.5% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 40.0% Bismark completed in 0d 0h 0m 19s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.7/samtools' Reference genome folder provided is /Users/sr320/Dropbox/wd/18-03-15/genome/ (absolute path is '/Users/sr320/Dropbox/wd/18-03-15/genome/)' Processing sequences up to read no. 1000 from the input file Input files to be analysed (in current folder '/Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore'): zr2096_4_s1_R1_val_1.fq.gz zr2096_4_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore Now reading in and storing sequence information of the genome specified in: /Users/sr320/Dropbox/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_4_s1_R1_val_1.fq.gz and zr2096_4_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000 from zr2096_4_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_4_s1_R1_val_1.fq.gz to zr2096_4_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_4_s1_R1_val_1.fq.gz to zr2096_4_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_4_s1_R1_val_1.fq.gz (1001 sequences in total) Processing reads up to sequence no. 1000 from zr2096_4_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_4_s1_R2_val_2.fq.gz to zr2096_4_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_4_s1_R2_val_2.fq.gz to zr2096_4_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_4_s1_R2_val_2.fq.gz (1001 sequences in total) Input files are zr2096_4_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_4_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_4_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_4_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Users/sr320/Dropbox/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_4_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_4_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1343:2133_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 ATAGTGGTTGTTATGGAAATTAGNNNNNNNNNNNNNNNNNNNNNNNNNTGNANTNTTTTTATTAGAATTGTTAAGGTTT FFFFFFFFFFFFFFFFFFFFFFF#########################<<#<#/#<>> Writing bisulfite mapping results to zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_4_s1_R1_val_1.fq.gz and zr2096_4_s1_R2_val_2.fq.gz 1000 reads; of these: 1000 (100.00%) were paired; of these: 892 (89.20%) aligned concordantly 0 times 60 (6.00%) aligned concordantly exactly 1 time 48 (4.80%) aligned concordantly >1 times 10.80% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 871 (87.10%) aligned concordantly 0 times 66 (6.60%) aligned concordantly exactly 1 time 63 (6.30%) aligned concordantly >1 times 12.90% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 887 (88.70%) aligned concordantly 0 times 61 (6.10%) aligned concordantly exactly 1 time 52 (5.20%) aligned concordantly >1 times 11.30% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 893 (89.30%) aligned concordantly 0 times 59 (5.90%) aligned concordantly exactly 1 time 48 (4.80%) aligned concordantly >1 times 10.70% overall alignment rate Processed 1000 sequences in total Successfully deleted the temporary files zr2096_4_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_4_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_4_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_4_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 1000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 5082 Total methylated C's in CpG context: 512 Total methylated C's in CHG context: 23 Total methylated C's in CHH context: 46 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 174 Total unmethylated C's in CHG context: 1100 Total unmethylated C's in CHH context: 3227 Total unmethylated C's in Unknown context: 2 C methylated in CpG context: 74.6% C methylated in CHG context: 2.0% C methylated in CHH context: 1.4% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 18s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.7/samtools' Reference genome folder provided is /Users/sr320/Dropbox/wd/18-03-15/genome/ (absolute path is '/Users/sr320/Dropbox/wd/18-03-15/genome/)' Processing sequences up to read no. 1000 from the input file Input files to be analysed (in current folder '/Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore'): zr2096_5_s1_R1_val_1.fq.gz zr2096_5_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore Now reading in and storing sequence information of the genome specified in: /Users/sr320/Dropbox/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_5_s1_R1_val_1.fq.gz and zr2096_5_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000 from zr2096_5_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_5_s1_R1_val_1.fq.gz to zr2096_5_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_5_s1_R1_val_1.fq.gz to zr2096_5_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_5_s1_R1_val_1.fq.gz (1001 sequences in total) Processing reads up to sequence no. 1000 from zr2096_5_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_5_s1_R2_val_2.fq.gz to zr2096_5_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_5_s1_R2_val_2.fq.gz to zr2096_5_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_5_s1_R2_val_2.fq.gz (1001 sequences in total) Input files are zr2096_5_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_5_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_5_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_5_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Users/sr320/Dropbox/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_5_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_5_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1218:2142_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TTATTTAAATTTTATTATTTATANNNNNNNNNNNNNNNNNNATTNTTTTTATTATATATATAAAATTATTTTAAAATTAT FFFFFFFFFFFFFFFFFFFFFFF##################<<<#<>> Writing bisulfite mapping results to zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_5_s1_R1_val_1.fq.gz and zr2096_5_s1_R2_val_2.fq.gz 1000 reads; of these: 1000 (100.00%) were paired; of these: 909 (90.90%) aligned concordantly 0 times 47 (4.70%) aligned concordantly exactly 1 time 44 (4.40%) aligned concordantly >1 times 9.10% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 906 (90.60%) aligned concordantly 0 times 55 (5.50%) aligned concordantly exactly 1 time 39 (3.90%) aligned concordantly >1 times 9.40% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 908 (90.80%) aligned concordantly 0 times 56 (5.60%) aligned concordantly exactly 1 time 36 (3.60%) aligned concordantly >1 times 9.20% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 900 (90.00%) aligned concordantly 0 times 56 (5.60%) aligned concordantly exactly 1 time 44 (4.40%) aligned concordantly >1 times 10.00% overall alignment rate Processed 1000 sequences in total Successfully deleted the temporary files zr2096_5_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_5_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_5_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_5_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 1000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 4989 Total methylated C's in CpG context: 525 Total methylated C's in CHG context: 18 Total methylated C's in CHH context: 35 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 126 Total unmethylated C's in CHG context: 1129 Total unmethylated C's in CHH context: 3156 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 80.6% C methylated in CHG context: 1.6% C methylated in CHH context: 1.1% Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 19s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.7/samtools' Reference genome folder provided is /Users/sr320/Dropbox/wd/18-03-15/genome/ (absolute path is '/Users/sr320/Dropbox/wd/18-03-15/genome/)' Processing sequences up to read no. 1000 from the input file Input files to be analysed (in current folder '/Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore'): zr2096_6_s1_R1_val_1.fq.gz zr2096_6_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore Now reading in and storing sequence information of the genome specified in: /Users/sr320/Dropbox/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_6_s1_R1_val_1.fq.gz and zr2096_6_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000 from zr2096_6_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_6_s1_R1_val_1.fq.gz to zr2096_6_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_6_s1_R1_val_1.fq.gz to zr2096_6_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_6_s1_R1_val_1.fq.gz (1001 sequences in total) Processing reads up to sequence no. 1000 from zr2096_6_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_6_s1_R2_val_2.fq.gz to zr2096_6_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_6_s1_R2_val_2.fq.gz to zr2096_6_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_6_s1_R2_val_2.fq.gz (1001 sequences in total) Input files are zr2096_6_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_6_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_6_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_6_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Users/sr320/Dropbox/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_6_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_6_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1093:2134_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 TTAATTTTATTATTAAATAAAAANNNNNNNNNNNNNNNNNNNNNNANNTANANAAATATTAATTAAATATTTTTAAAATA FFFFFFFFFFFFFFFFFFFFFFF######################<##<<#<#<>> Writing bisulfite mapping results to zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_6_s1_R1_val_1.fq.gz and zr2096_6_s1_R2_val_2.fq.gz 1000 reads; of these: 1000 (100.00%) were paired; of these: 880 (88.00%) aligned concordantly 0 times 60 (6.00%) aligned concordantly exactly 1 time 60 (6.00%) aligned concordantly >1 times 12.00% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 887 (88.70%) aligned concordantly 0 times 67 (6.70%) aligned concordantly exactly 1 time 46 (4.60%) aligned concordantly >1 times 11.30% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 870 (87.00%) aligned concordantly 0 times 66 (6.60%) aligned concordantly exactly 1 time 64 (6.40%) aligned concordantly >1 times 13.00% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 907 (90.70%) aligned concordantly 0 times 47 (4.70%) aligned concordantly exactly 1 time 46 (4.60%) aligned concordantly >1 times 9.30% overall alignment rate Processed 1000 sequences in total Successfully deleted the temporary files zr2096_6_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_6_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_6_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_6_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 1000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 5677 Total methylated C's in CpG context: 706 Total methylated C's in CHG context: 8 Total methylated C's in CHH context: 44 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 141 Total unmethylated C's in CHG context: 1315 Total unmethylated C's in CHH context: 3463 Total unmethylated C's in Unknown context: 2 C methylated in CpG context: 83.4% C methylated in CHG context: 0.6% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 19s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.7/samtools' Reference genome folder provided is /Users/sr320/Dropbox/wd/18-03-15/genome/ (absolute path is '/Users/sr320/Dropbox/wd/18-03-15/genome/)' Processing sequences up to read no. 1000 from the input file Input files to be analysed (in current folder '/Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore'): zr2096_7_s1_R1_val_1.fq.gz zr2096_7_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore Now reading in and storing sequence information of the genome specified in: /Users/sr320/Dropbox/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_7_s1_R1_val_1.fq.gz and zr2096_7_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000 from zr2096_7_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_7_s1_R1_val_1.fq.gz to zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_7_s1_R1_val_1.fq.gz to zr2096_7_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_7_s1_R1_val_1.fq.gz (1001 sequences in total) Processing reads up to sequence no. 1000 from zr2096_7_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_7_s1_R2_val_2.fq.gz to zr2096_7_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_7_s1_R2_val_2.fq.gz to zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_7_s1_R2_val_2.fq.gz (1001 sequences in total) Input files are zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_7_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_7_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Users/sr320/Dropbox/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 TTATTATGATGAATTTAAATATTAATAATAAAATTTAAAAAAAATATAAATGTTAAATATTAAATTTTTTAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 141 * 0 0 * * 0 0 TTTTTAAAAAATTTAATATTTAACATTTATATTTTTTTTAAATTTTATTATTAATATTTAAATTCATCATAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFBBFFFFFFBBFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr2096_7_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_7_s1_R2_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 99 NC_035781.1_GA_converted 24539756 32 75M = 24539756 -75 CTACTACAACAAATTCAAATATTAATAACAAAATTTAAAAAAAACATAAACATTAAATATCAAATTCTTCAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:75 YS:i:0 YT:Z:CP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 147 NC_035781.1_GA_converted 24539756 32 75M = 24539756 -75 CTACTACAACAAATTCAAATATTAATAACAAAATTTAAAAAAAACATAAACATTAAATATCAAATTCTTCAAAAA FFFFFFFFFFFFFBBFFFFFFBBFF/FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:75 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr2096_7_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_7_s1_R2_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 83 NC_035780.1_CT_converted 42548691 32 75M = 42548691 -75 TTTTTGAAGAATTTGATATTTAATGTTTATGTTTTTTTTAAATTTTGTTATTAATATTTGAATTTGTTGTAGTAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:75 YS:i:0 YT:Z:CP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 163 NC_035780.1_CT_converted 42548691 32 75M = 42548691 -75 TTTTTGAAGAATTTGATATTTAATGTTTATGTTTTTTTTAAATTTTGTTATTAATATTTGAATTTGTTGTAGTAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFBBFFFFFFBBFFFFFFFFFFFFF AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:75 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 TTATTATGATGAATTTAAATATTAATAATAAAATTTAAAAAAAATATAAATGTTAAATATTAAATTTTTTAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 141 * 0 0 * * 0 0 TTTTTAAAAAATTTAATATTTAACATTTATATTTTTTTTAAATTTTATTATTAATATTTAAATTCATCATAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFBBFFFFFFBBFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_7_s1_R1_val_1.fq.gz and zr2096_7_s1_R2_val_2.fq.gz 1000 reads; of these: 1000 (100.00%) were paired; of these: 906 (90.60%) aligned concordantly 0 times 47 (4.70%) aligned concordantly exactly 1 time 47 (4.70%) aligned concordantly >1 times 9.40% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 882 (88.20%) aligned concordantly 0 times 72 (7.20%) aligned concordantly exactly 1 time 46 (4.60%) aligned concordantly >1 times 11.80% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 912 (91.20%) aligned concordantly 0 times 43 (4.30%) aligned concordantly exactly 1 time 45 (4.50%) aligned concordantly >1 times 8.80% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 886 (88.60%) aligned concordantly 0 times 65 (6.50%) aligned concordantly exactly 1 time 49 (4.90%) aligned concordantly >1 times 11.40% overall alignment rate Processed 1000 sequences in total Successfully deleted the temporary files zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_7_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_7_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 1000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 5558 Total methylated C's in CpG context: 589 Total methylated C's in CHG context: 18 Total methylated C's in CHH context: 62 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 152 Total unmethylated C's in CHG context: 1158 Total unmethylated C's in CHH context: 3579 Total unmethylated C's in Unknown context: 7 C methylated in CpG context: 79.5% C methylated in CHG context: 1.5% C methylated in CHH context: 1.7% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 19s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.7/samtools' Reference genome folder provided is /Users/sr320/Dropbox/wd/18-03-15/genome/ (absolute path is '/Users/sr320/Dropbox/wd/18-03-15/genome/)' Processing sequences up to read no. 1000 from the input file Input files to be analysed (in current folder '/Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore'): zr2096_8_s1_R1_val_1.fq.gz zr2096_8_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore Now reading in and storing sequence information of the genome specified in: /Users/sr320/Dropbox/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_8_s1_R1_val_1.fq.gz and zr2096_8_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000 from zr2096_8_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_8_s1_R1_val_1.fq.gz to zr2096_8_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_8_s1_R1_val_1.fq.gz to zr2096_8_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_8_s1_R1_val_1.fq.gz (1001 sequences in total) Processing reads up to sequence no. 1000 from zr2096_8_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_8_s1_R2_val_2.fq.gz to zr2096_8_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_8_s1_R2_val_2.fq.gz to zr2096_8_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_8_s1_R2_val_2.fq.gz (1001 sequences in total) Input files are zr2096_8_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_8_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_8_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_8_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Users/sr320/Dropbox/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_8_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_8_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1281:2170_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 TTAAAAAATTTATTAAATTTATTATTATTTNTTATTTTTTATAAAAGAAAATAGAGAGAGAGAGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#<>> Writing bisulfite mapping results to zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_8_s1_R1_val_1.fq.gz and zr2096_8_s1_R2_val_2.fq.gz 1000 reads; of these: 1000 (100.00%) were paired; of these: 897 (89.70%) aligned concordantly 0 times 57 (5.70%) aligned concordantly exactly 1 time 46 (4.60%) aligned concordantly >1 times 10.30% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 906 (90.60%) aligned concordantly 0 times 46 (4.60%) aligned concordantly exactly 1 time 48 (4.80%) aligned concordantly >1 times 9.40% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 899 (89.90%) aligned concordantly 0 times 59 (5.90%) aligned concordantly exactly 1 time 42 (4.20%) aligned concordantly >1 times 10.10% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 898 (89.80%) aligned concordantly 0 times 48 (4.80%) aligned concordantly exactly 1 time 54 (5.40%) aligned concordantly >1 times 10.20% overall alignment rate Processed 1000 sequences in total Successfully deleted the temporary files zr2096_8_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_8_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_8_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_8_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 1000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 4674 Total methylated C's in CpG context: 422 Total methylated C's in CHG context: 19 Total methylated C's in CHH context: 58 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 191 Total unmethylated C's in CHG context: 988 Total unmethylated C's in CHH context: 2996 Total unmethylated C's in Unknown context: 5 C methylated in CpG context: 68.8% C methylated in CHG context: 1.9% C methylated in CHH context: 1.9% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 17s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.7/samtools' Reference genome folder provided is /Users/sr320/Dropbox/wd/18-03-15/genome/ (absolute path is '/Users/sr320/Dropbox/wd/18-03-15/genome/)' Processing sequences up to read no. 1000 from the input file Input files to be analysed (in current folder '/Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore'): zr2096_9_s1_R1_val_1.fq.gz zr2096_9_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Users/sr320/Documents/GitHub/project-virginica-oa/data/dignore Now reading in and storing sequence information of the genome specified in: /Users/sr320/Dropbox/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_9_s1_R1_val_1.fq.gz and zr2096_9_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000 from zr2096_9_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_9_s1_R1_val_1.fq.gz to zr2096_9_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_9_s1_R1_val_1.fq.gz to zr2096_9_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_9_s1_R1_val_1.fq.gz (1001 sequences in total) Processing reads up to sequence no. 1000 from zr2096_9_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_9_s1_R2_val_2.fq.gz to zr2096_9_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_9_s1_R2_val_2.fq.gz to zr2096_9_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_9_s1_R2_val_2.fq.gz (1001 sequences in total) Input files are zr2096_9_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_9_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_9_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_9_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Users/sr320/Dropbox/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_9_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_9_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:2:1101:1135:2128_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 AAAATAATAAATAATAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN >> Writing bisulfite mapping results to zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_9_s1_R1_val_1.fq.gz and zr2096_9_s1_R2_val_2.fq.gz 1000 reads; of these: 1000 (100.00%) were paired; of these: 905 (90.50%) aligned concordantly 0 times 56 (5.60%) aligned concordantly exactly 1 time 39 (3.90%) aligned concordantly >1 times 9.50% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 936 (93.60%) aligned concordantly 0 times 36 (3.60%) aligned concordantly exactly 1 time 28 (2.80%) aligned concordantly >1 times 6.40% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 929 (92.90%) aligned concordantly 0 times 39 (3.90%) aligned concordantly exactly 1 time 32 (3.20%) aligned concordantly >1 times 7.10% overall alignment rate 1000 reads; of these: 1000 (100.00%) were paired; of these: 913 (91.30%) aligned concordantly 0 times 53 (5.30%) aligned concordantly exactly 1 time 34 (3.40%) aligned concordantly >1 times 8.70% overall alignment rate Processed 1000 sequences in total Successfully deleted the temporary files zr2096_9_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_9_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_9_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_9_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 1000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 4731 Total methylated C's in CpG context: 578 Total methylated C's in CHG context: 28 Total methylated C's in CHH context: 37 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 82 Total unmethylated C's in CHG context: 1133 Total unmethylated C's in CHH context: 2873 Total unmethylated C's in Unknown context: 1 C methylated in CpG context: 87.6% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 19s ==================== Bismark run complete ====================