Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/local/bin/samtools' Reference genome folder provided is /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ (absolute path is '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/)' Processing sequences up to read no. 10000 from the input file Input files to be analysed (in current folder '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing'): /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_10_s1_R1_val_1.fq.gz /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing Now reading in and storing sequence information of the genome specified in: /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_10_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_10_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 sequences in total) Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 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/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ with the specified options: -q --score-min L,0,-0.9 -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,-0.9 -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 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_10_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_10_s1_R2_val_2.fq.gz 1000010000 reads; of these:10000 reads; of these: reads; of these:10000 reads; of these: 10000 ( 1000010000 ( 100.00 100.00% () were paired; of these:% ) were paired; of these:10000 ( 100.00%) were paired; of these:100.007523 % ( 75.23) were paired; of these: 7441% ) aligned concordantly 0 times7444 (104174.41% ( () aligned concordantly 0 times7417 ( 74.17108510.41 (%74.4410.85%) aligned concordantly 0 times) aligned concordantly exactly 1 time %% ) aligned concordantly 0 times) aligned concordantly exactly 1 time 1436 1120 (147411.20 ( (14.36 14.74%1046%) aligned concordantly >1 times) aligned concordantly >1 times (%10.46%) aligned concordantly exactly 1 time 24.771463%25.59 (%14.63%) aligned concordantly exactly 1 time overall alignment rate overall alignment rate ) aligned concordantly >1 times1510 ( 15.1025.83% overall alignment rate %) aligned concordantly >1 times 25.56% overall alignment rate Processed 10000 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: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 124884 Total methylated C's in CpG context: 12539 Total methylated C's in CHG context: 631 Total methylated C's in CHH context: 2516 Total methylated C's in Unknown context: 148 Total unmethylated C's in CpG context: 4967 Total unmethylated C's in CHG context: 27708 Total unmethylated C's in CHH context: 76523 Total unmethylated C's in Unknown context: 825 C methylated in CpG context: 71.6% C methylated in CHG context: 2.2% C methylated in CHH context: 3.2% C methylated in unknown context (CN or CHN): 15.2% Bismark completed in 0d 0h 0m 26s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/local/bin/samtools' Reference genome folder provided is /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ (absolute path is '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/)' Processing sequences up to read no. 10000 from the input file Input files to be analysed (in current folder '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing'): /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_1_s1_R1_val_1.fq.gz /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing Now reading in and storing sequence information of the genome specified in: /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_1_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_1_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 sequences in total) Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 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/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ with the specified options: -q --score-min L,0,-0.9 -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,-0.9 -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 99 NC_035780.1_CT_converted 54035224 6 27M4I48M = 54035615 471 GATTATTTGTTGTTTGTTGTTTGTTTGNNNNTNNNTNNGTTTGTTTGTTTGTTTGTTTGTTTGTAAATTTTTTATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFF####<###<##<<>> Writing bisulfite mapping results to zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_1_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_1_s1_R2_val_2.fq.gz 10000 reads; of these: 10000 (100.00%) were paired; of these: 8826 (88.26%) aligned concordantly 0 times 495 (4.95%) aligned concordantly exactly 1 time 679 (6.79%) aligned concordantly >1 times 11.74% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8836 (88.36%) aligned concordantly 0 times 465 (4.65%) aligned concordantly exactly 1 time 699 (6.99%) aligned concordantly >1 times 11.64% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8812 (88.12%) aligned concordantly 0 times 485 (4.85%) aligned concordantly exactly 1 time 703 (7.03%) aligned concordantly >1 times 11.88% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8841 (88.41%) aligned concordantly 0 times 470 (4.70%) aligned concordantly exactly 1 time 689 (6.89%) aligned concordantly >1 times 11.59% overall alignment rate Processed 10000 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: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 52326 Total methylated C's in CpG context: 5052 Total methylated C's in CHG context: 266 Total methylated C's in CHH context: 1864 Total methylated C's in Unknown context: 120 Total unmethylated C's in CpG context: 1821 Total unmethylated C's in CHG context: 10917 Total unmethylated C's in CHH context: 32406 Total unmethylated C's in Unknown context: 445 C methylated in CpG context: 73.5% C methylated in CHG context: 2.4% C methylated in CHH context: 5.4% C methylated in unknown context (CN or CHN): 21.2% Bismark completed in 0d 0h 0m 22s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/local/bin/samtools' Reference genome folder provided is /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ (absolute path is '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/)' Processing sequences up to read no. 10000 from the input file Input files to be analysed (in current folder '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing'): /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_2_s1_R1_val_1.fq.gz /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing Now reading in and storing sequence information of the genome specified in: /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_2_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_2_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 sequences in total) Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 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/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ with the specified options: -q --score-min L,0,-0.9 -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,-0.9 -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 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_2_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_2_s1_R2_val_2.fq.gz 10000 reads; of these:10000 reads; of these: 10000 (100.00%) were paired; of these: 7488 ( 10000 (100.00%) were paired; of these: 7413 (74.13%) aligned concordantly 0 times 1014 (10.14%) aligned concordantly exactly 1 time 1573 (15.73%) aligned concordantly >1 times 25.87% overall alignment rate 74.88%) aligned concordantly 0 times 958 (9.58%) aligned concordantly exactly 1 time 1554 (15.54%) aligned concordantly >1 times 25.12% overall alignment rate 10000 reads; of these: 10000 (100.0010000 reads; of these:% ) were paired; of these: 7435 ( 10000 (74.35%100.00) aligned concordantly 0 times %) were paired; of these:1020 ( 10.20%) aligned concordantly exactly 1 time 15457415 ( (15.4574.15%%) aligned concordantly >1 times ) aligned concordantly 0 times 1006 (25.6510.06%% overall alignment rate) aligned concordantly exactly 1 time 1579 (15.79%) aligned concordantly >1 times 25.85% overall alignment rate Processed 10000 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: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 102111 Total methylated C's in CpG context: 10038 Total methylated C's in CHG context: 566 Total methylated C's in CHH context: 3104 Total methylated C's in Unknown context: 202 Total unmethylated C's in CpG context: 3813 Total unmethylated C's in CHG context: 22530 Total unmethylated C's in CHH context: 62060 Total unmethylated C's in Unknown context: 786 C methylated in CpG context: 72.5% C methylated in CHG context: 2.5% C methylated in CHH context: 4.8% C methylated in unknown context (CN or CHN): 20.4% Bismark completed in 0d 0h 0m 25s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/local/bin/samtools' Reference genome folder provided is /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ (absolute path is '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/)' Processing sequences up to read no. 10000 from the input file Input files to be analysed (in current folder '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing'): /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_3_s1_R1_val_1.fq.gz /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing Now reading in and storing sequence information of the genome specified in: /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_3_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_3_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 sequences in total) Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 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/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ with the specified options: -q --score-min L,0,-0.9 -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,-0.9 -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 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_3_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_3_s1_R2_val_2.fq.gz 1000010000 reads; of these: reads; of these: 10000 reads; of these: 10000 10000 10000 ( ( (100.00%) were paired; of these:100.00 7275%100.00%) were paired; of these: ) were paired; of these:7329 ( 73.29 ( 72.75%7309) aligned concordantly 0 times10000 ( %73.09 reads; of these:) aligned concordantly 0 times% ) aligned concordantly 0 times 1089 1126 (1000010.891135 (% ( (11.35%100.00) aligned concordantly exactly 1 time) aligned concordantly exactly 1 time 11.26 %1582) were paired; of these:% () aligned concordantly exactly 1 time15.82 1565 ( %) aligned concordantly >1 times7329159015.65 (%73.29 () aligned concordantly >1 times15.90 % ) aligned concordantly 0 times26.71 %% overall alignment rate110026.91 () aligned concordantly >1 times 11.0027.25%% overall alignment rate % overall alignment rate ) aligned concordantly exactly 1 time 1571 (15.71%) aligned concordantly >1 times 26.71% overall alignment rate Processed 10000 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: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 126332 Total methylated C's in CpG context: 14736 Total methylated C's in CHG context: 617 Total methylated C's in CHH context: 2228 Total methylated C's in Unknown context: 184 Total unmethylated C's in CpG context: 3805 Total unmethylated C's in CHG context: 27577 Total unmethylated C's in CHH context: 77369 Total unmethylated C's in Unknown context: 981 C methylated in CpG context: 79.5% C methylated in CHG context: 2.2% C methylated in CHH context: 2.8% C methylated in unknown context (CN or CHN): 15.8% Bismark completed in 0d 0h 0m 26s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/local/bin/samtools' Reference genome folder provided is /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ (absolute path is '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/)' Processing sequences up to read no. 10000 from the input file Input files to be analysed (in current folder '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing'): /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_4_s1_R1_val_1.fq.gz /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing Now reading in and storing sequence information of the genome specified in: /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_4_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_4_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 sequences in total) Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 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/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ with the specified options: -q --score-min L,0,-0.9 -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,-0.9 -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 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_4_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_4_s1_R2_val_2.fq.gz 10000 reads; of these: 10000 (100.00%) were paired; of these: 7134 (71.34%) aligned concordantly 0 times 1132 (11.32%) aligned concordantly exactly 1 time 1734 (17.34%) aligned concordantly >1 times 28.66% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7321 (10000 reads; of these:73.21 %) aligned concordantly 0 times 1117 (11.17 %) aligned concordantly exactly 1 time 1562 (1000010000 (15.62%) aligned concordantly >1 times100.00% 26.79 reads; of these:% overall alignment rate 10000 (100.00%) were paired; of these: ) were paired; of these: 7125 ( 7363 (73.63%71.25) aligned concordantly 0 times % ) aligned concordantly 0 times 1073 (1131 (11.3110.73%%) aligned concordantly exactly 1 time 1744 (17.44%) aligned concordantly >1 times ) aligned concordantly exactly 1 time 1564 (15.64%) aligned concordantly >1 times 28.7526.37% overall alignment rate% overall alignment rate Processed 10000 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: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 114960 Total methylated C's in CpG context: 10494 Total methylated C's in CHG context: 540 Total methylated C's in CHH context: 2602 Total methylated C's in Unknown context: 188 Total unmethylated C's in CpG context: 4594 Total unmethylated C's in CHG context: 24865 Total unmethylated C's in CHH context: 71865 Total unmethylated C's in Unknown context: 922 C methylated in CpG context: 69.6% C methylated in CHG context: 2.1% C methylated in CHH context: 3.5% C methylated in unknown context (CN or CHN): 16.9% Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/local/bin/samtools' Reference genome folder provided is /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ (absolute path is '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/)' Processing sequences up to read no. 10000 from the input file Input files to be analysed (in current folder '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing'): /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_5_s1_R1_val_1.fq.gz /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing Now reading in and storing sequence information of the genome specified in: /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_5_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_5_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 sequences in total) Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 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/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ with the specified options: -q --score-min L,0,-0.9 -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,-0.9 -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 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_5_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_5_s1_R2_val_2.fq.gz 10000 reads; of these: 10000 (100.00%) were paired; of these: 7494 (74.94%) aligned concordantly 0 times 1049 (10.49%) aligned concordantly exactly 1 time 1457 (14.57%) aligned concordantly >1 times 25.06% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7526 (75.26%) aligned concordantly 0 times 1062 (10.62%) aligned concordantly exactly 1 time 1412 (14.12%) aligned concordantly >1 times 24.74% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7554 (75.54%) aligned concordantly 0 times 1035 (10.35%) aligned concordantly exactly 1 time 1411 (14.11%) aligned concordantly >1 times 24.46% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7521 (75.21%) aligned concordantly 0 times 1004 (10.04%) aligned concordantly exactly 1 time 1475 (14.75%) aligned concordantly >1 times 24.79% overall alignment rate Processed 10000 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: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 114130 Total methylated C's in CpG context: 10183 Total methylated C's in CHG context: 586 Total methylated C's in CHH context: 2285 Total methylated C's in Unknown context: 158 Total unmethylated C's in CpG context: 4347 Total unmethylated C's in CHG context: 23923 Total unmethylated C's in CHH context: 72806 Total unmethylated C's in Unknown context: 832 C methylated in CpG context: 70.1% C methylated in CHG context: 2.4% C methylated in CHH context: 3.0% C methylated in unknown context (CN or CHN): 16.0% 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' [2.3.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/local/bin/samtools' Reference genome folder provided is /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ (absolute path is '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/)' Processing sequences up to read no. 10000 from the input file Input files to be analysed (in current folder '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing'): /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_6_s1_R1_val_1.fq.gz /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing Now reading in and storing sequence information of the genome specified in: /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_6_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_6_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 sequences in total) Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 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/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ with the specified options: -q --score-min L,0,-0.9 -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,-0.9 -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 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_6_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_6_s1_R2_val_2.fq.gz 10000 reads; of these: 10000 (100.00%) were paired; of these: 7066 (70.66%) aligned concordantly 0 times 1204 (12.04%) aligned concordantly exactly 1 time 1730 (17.30%) aligned concordantly >1 times 29.34% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7357 (73.57%) aligned concordantly 0 times 1061 (10.61%) aligned concordantly exactly 1 time 1582 (15.82%) aligned concordantly >1 times 26.43% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7079 (70.79%) aligned concordantly 0 times 1209 (12.09%) aligned concordantly exactly 1 time 1712 (17.12%) aligned concordantly >1 times 29.21% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7371 (73.71%) aligned concordantly 0 times 1083 (10.83%) aligned concordantly exactly 1 time 1546 (15.46%) aligned concordantly >1 times 26.29% overall alignment rate Processed 10000 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: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 116472 Total methylated C's in CpG context: 11898 Total methylated C's in CHG context: 465 Total methylated C's in CHH context: 2420 Total methylated C's in Unknown context: 146 Total unmethylated C's in CpG context: 3804 Total unmethylated C's in CHG context: 25393 Total unmethylated C's in CHH context: 72492 Total unmethylated C's in Unknown context: 812 C methylated in CpG context: 75.8% C methylated in CHG context: 1.8% C methylated in CHH context: 3.2% C methylated in unknown context (CN or CHN): 15.2% Bismark completed in 0d 0h 0m 25s ==================== Bismark run complete ==================== Path to Bowtie 2 specified as: bowtie2 Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/local/bin/samtools' Reference genome folder provided is /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ (absolute path is '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/)' Processing sequences up to read no. 10000 from the input file Input files to be analysed (in current folder '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing'): /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_7_s1_R1_val_1.fq.gz /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing Now reading in and storing sequence information of the genome specified in: /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_7_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_7_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 sequences in total) Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 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/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ with the specified options: -q --score-min L,0,-0.9 -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,-0.9 -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,-0.9 -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 6 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 6 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,-0.9 -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 6 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 6 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,-0.9 -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 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_7_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_7_s1_R2_val_2.fq.gz 10000 reads; of these: 10000 (100.00%) were paired; of these: 7535 (75.35%) aligned concordantly 0 times 1065 (10.65%) aligned concordantly exactly 1 time 1400 (14.00%) aligned concordantly >1 times 24.65% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7597 (75.97%) aligned concordantly 0 times 1024 (10.24%) aligned concordantly exactly 1 time 1379 (13.79%) aligned concordantly >1 times 24.03% overall alignment rate 10000 reads; of these:10000 reads; of these: 10000 ( 10000 (100.00100.00%) were paired; of these: 7625 (%) were paired; of these:76.25%) aligned concordantly 0 times 7622 (76.22%) aligned concordantly 0 times 997 (9.97%) aligned concordantly exactly 1 time 1378 ( 101113.78%) aligned concordantly >1 times 23.75% overall alignment rate (10.11%) aligned concordantly exactly 1 time 1367 (13.67%) aligned concordantly >1 times 23.78% overall alignment rate Processed 10000 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: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 116375 Total methylated C's in CpG context: 10734 Total methylated C's in CHG context: 576 Total methylated C's in CHH context: 2403 Total methylated C's in Unknown context: 150 Total unmethylated C's in CpG context: 3870 Total unmethylated C's in CHG context: 24960 Total unmethylated C's in CHH context: 73832 Total unmethylated C's in Unknown context: 917 C methylated in CpG context: 73.5% C methylated in CHG context: 2.3% C methylated in CHH context: 3.2% C methylated in unknown context (CN or CHN): 14.1% 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' [2.3.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/local/bin/samtools' Reference genome folder provided is /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ (absolute path is '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/)' Processing sequences up to read no. 10000 from the input file Input files to be analysed (in current folder '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing'): /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_8_s1_R1_val_1.fq.gz /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing Now reading in and storing sequence information of the genome specified in: /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_8_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_8_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 sequences in total) Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 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/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ with the specified options: -q --score-min L,0,-0.9 -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,-0.9 -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 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_8_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_8_s1_R2_val_2.fq.gz 10000 reads; of these: 10000 (100.00%) were paired; of these: 7742 (77.42%) aligned concordantly 0 times 966 (9.66%) aligned concordantly exactly 1 time 1292 (12.92%) aligned concordantly >1 times 22.58% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7774 (77.74%) aligned concordantly 0 times 923 (9.23%) aligned concordantly exactly 1 time 1303 (13.03%) aligned concordantly >1 times 22.26% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7722 (77.22%) aligned concordantly 0 times 990 (9.90%) aligned concordantly exactly 1 time 1288 (12.88%) aligned concordantly >1 times 22.78% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7700 (77.00%) aligned concordantly 0 times 952 (9.52%) aligned concordantly exactly 1 time 1348 (13.48%) aligned concordantly >1 times 23.00% overall alignment rate Processed 10000 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: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 102118 Total methylated C's in CpG context: 8829 Total methylated C's in CHG context: 480 Total methylated C's in CHH context: 2393 Total methylated C's in Unknown context: 155 Total unmethylated C's in CpG context: 3965 Total unmethylated C's in CHG context: 22117 Total unmethylated C's in CHH context: 64334 Total unmethylated C's in Unknown context: 735 C methylated in CpG context: 69.0% C methylated in CHG context: 2.1% C methylated in CHH context: 3.6% C methylated in unknown context (CN or CHN): 17.4% 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' [2.3.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/local/bin/samtools' Reference genome folder provided is /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ (absolute path is '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/)' Processing sequences up to read no. 10000 from the input file Input files to be analysed (in current folder '/Users/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing'): /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_9_s1_R1_val_1.fq.gz /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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/yaamini/Documents/project-virginica-oa/analyses/2018-10-03-Bismark-Parameter-Testing Now reading in and storing sequence information of the genome specified in: /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_9_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_9_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 sequences in total) Processing reads up to sequence no. 10000 from /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/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 (10001 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/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ with the specified options: -q --score-min L,0,-0.9 -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,-0.9 -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 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_9_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_9_s1_R2_val_2.fq.gz 10000 reads; of these: 10000 (100.00%) were paired; of these: 7464 (74.64%) aligned concordantly 0 times 1098 (10.98%) aligned concordantly exactly 1 time 1438 (14.38%) aligned concordantly >1 times 25.36% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7690 (76.90%) aligned concordantly 0 times 974 (9.74%) aligned concordantly exactly 1 time 1336 (13.36%) aligned concordantly >1 times 23.10% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7756 (77.56%) aligned concordantly 0 times 910 (9.10%) aligned concordantly exactly 1 time 1334 (13.34%) aligned concordantly >1 times 22.44% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7430 (74.30%) aligned concordantly 0 times 1124 (11.24%) aligned concordantly exactly 1 time 1446 (14.46%) aligned concordantly >1 times 25.70% overall alignment rate Processed 10000 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: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 116613 Total methylated C's in CpG context: 13168 Total methylated C's in CHG context: 691 Total methylated C's in CHH context: 2440 Total methylated C's in Unknown context: 152 Total unmethylated C's in CpG context: 3625 Total unmethylated C's in CHG context: 25419 Total unmethylated C's in CHH context: 71270 Total unmethylated C's in Unknown context: 842 C methylated in CpG context: 78.4% C methylated in CHG context: 2.6% C methylated in CHH context: 3.3% C methylated in unknown context (CN or CHN): 15.3% Bismark completed in 0d 0h 0m 26s ==================== Bismark run complete ====================