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,-0.6 -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,-0.6 -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 10000 reads; of these: 10000 (100.00%) were paired; of these: 8119 (81.19%) aligned concordantly 0 times 870 (8.70%) aligned concordantly exactly 1 time 1011 (10.11%) aligned concordantly >1 times 18.81% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8008 (80.08%) aligned concordantly 0 times 960 (9.60%) aligned concordantly exactly 1 time 103210000 reads; of these: (10.32%) aligned concordantly >1 times 19.92% overall alignment rate 10000 (100.00%) were paired; of these: 8016 (80.16%) aligned concordantly 0 times 909 (9.09%) aligned concordantly exactly 1 time 1075 (10.75%) aligned concordantly >1 times 19.84% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8056 (80.56%) aligned concordantly 0 times 859 (8.59%) aligned concordantly exactly 1 time 1085 (10.85%) aligned concordantly >1 times 19.44% 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: 103183 Total methylated C's in CpG context: 10708 Total methylated C's in CHG context: 504 Total methylated C's in CHH context: 1507 Total methylated C's in Unknown context: 53 Total unmethylated C's in CpG context: 3919 Total unmethylated C's in CHG context: 23471 Total unmethylated C's in CHH context: 63074 Total unmethylated C's in Unknown context: 339 C methylated in CpG context: 73.2% C methylated in CHG context: 2.1% C methylated in CHH context: 2.3% C methylated in unknown context (CN or CHN): 13.5% Bismark completed in 0d 0h 0m 57s ==================== 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,-0.6 -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,-0.6 -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_035783.1_CT_converted 43673739 6 79M = 43673843 184 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: 9139 (91.39%) aligned concordantly 0 times 365 (3.65%) aligned concordantly exactly 1 time 496 (4.96%) aligned concordantly >1 times 8.61% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 9160 (91.60%) aligned concordantly 0 times 369 (3.69%) aligned concordantly exactly 1 time 471 (4.71%) aligned concordantly >1 times 8.40% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 9124 (91.24%) aligned concordantly 0 times 384 (3.84%) aligned concordantly exactly 1 time 492 (4.92%) aligned concordantly >1 times 8.76% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 9121 (91.21%) aligned concordantly 0 times 389 (3.89%) aligned concordantly exactly 1 time 490 (4.90%) aligned concordantly >1 times 8.79% 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: 41866 Total methylated C's in CpG context: 4226 Total methylated C's in CHG context: 155 Total methylated C's in CHH context: 752 Total methylated C's in Unknown context: 29 Total unmethylated C's in CpG context: 1418 Total unmethylated C's in CHG context: 9178 Total unmethylated C's in CHH context: 26137 Total unmethylated C's in Unknown context: 164 C methylated in CpG context: 74.9% C methylated in CHG context: 1.7% C methylated in CHH context: 2.8% C methylated in unknown context (CN or CHN): 15.0% Bismark completed in 0d 0h 0m 23s ==================== 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,-0.6 -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,-0.6 -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 (100.00%) were paired; of these: 8069 (80.69%) aligned concordantly 0 times 821 (8.21%) aligned concordantly exactly 1 time 1110 (11.10%) aligned concordantly >1 times 19.31% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8079 (80.79%) aligned concordantly 0 times 848 (8.48%) aligned concordantly exactly 1 time10000 reads; of these: 10000 (100.00%) were paired; of these: 8106 ( 1073 (10.73%) aligned concordantly >1 times 81.06%) aligned concordantly 0 times 789 (7.89%) aligned concordantly exactly 1 time 1105 (11.05%) aligned concordantly >1 times 18.94% overall alignment rate 19.21% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8069 (80.69%) aligned concordantly 0 times 830 (8.30%) aligned concordantly exactly 1 time 1101 (11.01%) aligned concordantly >1 times 19.31% 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: 83422 Total methylated C's in CpG context: 8583 Total methylated C's in CHG context: 405 Total methylated C's in CHH context: 1577 Total methylated C's in Unknown context: 48 Total unmethylated C's in CpG context: 3046 Total unmethylated C's in CHG context: 18954 Total unmethylated C's in CHH context: 50857 Total unmethylated C's in Unknown context: 281 C methylated in CpG context: 73.8% C methylated in CHG context: 2.1% C methylated in CHH context: 3.0% C methylated in unknown context (CN or CHN): 14.6% 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_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,-0.6 -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,-0.6 -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 100001000010000 reads; of these: reads; of these: reads; of these: 10000 ( 10000100.00 10000 (10000100.00 (%) were paired; of these: reads; of these:% ) were paired; of these: 100.007993%) were paired; of these: (7882 79.93 ( 78.82%%) aligned concordantly 0 times) aligned concordantly 0 times7960 ( 10000 (79.60975100.00 (%%) were paired; of these:) aligned concordantly 0 times882 (7944 ( 79.448.829.75%936) aligned concordantly exactly 1 time% () aligned concordantly exactly 1 time9.36% ) aligned concordantly exactly 1 time %1104) aligned concordantly 0 times ( 1143 (11.0492011.43%) aligned concordantly >1 times ( %1125) aligned concordantly >1 times9.20 (20.4021.18%% overall alignment rate%) aligned concordantly exactly 1 time overall alignment rate11.25 %) aligned concordantly >1 times 1136 (11.36%) aligned concordantly >1 times 20.56% overall alignment rate 20.07% 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: 104836 Total methylated C's in CpG context: 12516 Total methylated C's in CHG context: 451 Total methylated C's in CHH context: 1362 Total methylated C's in Unknown context: 64 Total unmethylated C's in CpG context: 2914 Total unmethylated C's in CHG context: 23280 Total unmethylated C's in CHH context: 64313 Total unmethylated C's in Unknown context: 374 C methylated in CpG context: 81.1% C methylated in CHG context: 1.9% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 14.6% 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_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,-0.6 -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,-0.6 -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 1000010000 reads; of these:1000010000 reads; of these: reads; of these: reads; of these: 100001000010000 ( ( ( 100.00 10000%100.00 () were paired; of these:100.00%) were paired; of these:100.00% %) were paired; of these:) were paired; of these: 7984 (7840801379.84 (7826%80.13 () aligned concordantly 0 times (78.40%) aligned concordantly 0 times78.26 %%) aligned concordantly 0 times ) aligned concordantly 0 times 948 876908 ( (8.768859.08 (%8.85) aligned concordantly exactly 1 time%) aligned concordantly exactly 1 time 1111 (11319.48%) aligned concordantly exactly 1 time (% ) aligned concordantly exactly 1 time 11.31 % () aligned concordantly >1 times 11.11 12521226 (20.16 (%12.2612.52%) aligned concordantly >1 times% ) aligned concordantly >1 times%) aligned concordantly >1 times21.74 overall alignment rate % overall alignment rate21.60 %19.87% 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: 93515 Total methylated C's in CpG context: 9018 Total methylated C's in CHG context: 388 Total methylated C's in CHH context: 1533 Total methylated C's in Unknown context: 68 Total unmethylated C's in CpG context: 3610 Total unmethylated C's in CHG context: 20708 Total unmethylated C's in CHH context: 58258 Total unmethylated C's in Unknown context: 371 C methylated in CpG context: 71.4% C methylated in CHG context: 1.8% C methylated in CHH context: 2.6% C methylated in unknown context (CN or CHN): 15.5% 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_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,-0.6 -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,-0.6 -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: 8151 (81.51%) aligned concordantly 0 times 856 (8.56%) aligned concordantly exactly 1 time 993 (9.93%) aligned concordantly >1 times 18.49% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8119 (81.19%) aligned concordantly 0 times 866 (8.66%) aligned concordantly exactly 1 time 1015 (10.15%) aligned concordantly >1 times 18.81% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8134 (81.34%) aligned concordantly 0 times 824 (8.24%) aligned concordantly exactly 1 time 1042 (10.42%) aligned concordantly >1 times 18.66% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8120 (81.20%) aligned concordantly 0 times 848 (8.48%) aligned concordantly exactly 1 time 1032 (10.32%) aligned concordantly >1 times 18.80% 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: 93919 Total methylated C's in CpG context: 8678 Total methylated C's in CHG context: 441 Total methylated C's in CHH context: 1393 Total methylated C's in Unknown context: 54 Total unmethylated C's in CpG context: 3408 Total unmethylated C's in CHG context: 20066 Total unmethylated C's in CHH context: 59933 Total unmethylated C's in Unknown context: 329 C methylated in CpG context: 71.8% C methylated in CHG context: 2.2% C methylated in CHH context: 2.3% 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_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,-0.6 -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,-0.6 -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 reads; of these: 10000 (100.00%) were paired; of these: 7778 (77.78%) aligned concordantly 0 times 1005 (10.05%) aligned concordantly exactly 1 time 1217 (12.17%) aligned concordantly >1 times 22.22% overall alignment rate 10000 (100.00%) were paired; of these: 7753 (77.53%) aligned concordantly 0 times 973 (9.73%) aligned concordantly exactly 1 time 1274 (12.74%) aligned concordantly >1 times 22.47% overall alignment rate 10000 reads; of these:10000 reads; of these: 10000 (10000 (100.00%100.00) were paired; of these: 8022 (%) were paired; of these:80.22%) aligned concordantly 0 times 896 ( 8.968006 (%80.06%) aligned concordantly exactly 1 time ) aligned concordantly 0 times 1082895 ( (10.82%) aligned concordantly >1 times 8.9519.78% overall alignment rate %) aligned concordantly exactly 1 time 1099 (10.99%) aligned concordantly >1 times 19.94% 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: 95740 Total methylated C's in CpG context: 10240 Total methylated C's in CHG context: 341 Total methylated C's in CHH context: 1247 Total methylated C's in Unknown context: 42 Total unmethylated C's in CpG context: 2888 Total unmethylated C's in CHG context: 21381 Total unmethylated C's in CHH context: 59643 Total unmethylated C's in Unknown context: 299 C methylated in CpG context: 78.0% C methylated in CHG context: 1.6% C methylated in CHH context: 2.0% C methylated in unknown context (CN or CHN): 12.3% Bismark completed in 0d 0h 0m 23s ==================== 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,-0.6 -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,-0.6 -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,-0.6 -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 30 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 30 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,-0.6 -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 30 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 30 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,-0.6 -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: 8190 (81.90%) aligned concordantly 0 times 831 (8.31%) aligned concordantly exactly 1 time 979 (9.79%) aligned concordantly >1 times 18.10% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8128 (81.28%) aligned concordantly 0 times 902 (9.02%) aligned concordantly exactly 1 time 970 (9.70%) aligned concordantly >1 times 18.72% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8173 (81.73%) aligned concordantly 0 times 861 (8.61%) aligned concordantly exactly 1 time 966 (9.66%) aligned concordantly >1 times 18.27% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8206 (82.06%) aligned concordantly 0 times 842 (8.42%) aligned concordantly exactly 1 time 952 (9.52%) aligned concordantly >1 times 17.94% 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: 94739 Total methylated C's in CpG context: 9100 Total methylated C's in CHG context: 455 Total methylated C's in CHH context: 1595 Total methylated C's in Unknown context: 39 Total unmethylated C's in CpG context: 2899 Total unmethylated C's in CHG context: 20800 Total unmethylated C's in CHH context: 59890 Total unmethylated C's in Unknown context: 333 C methylated in CpG context: 75.8% C methylated in CHG context: 2.1% C methylated in CHH context: 2.6% C methylated in unknown context (CN or CHN): 10.5% 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,-0.6 -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,-0.6 -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: 8273 (82.73%) aligned concordantly 0 times 805 (8.05%) aligned concordantly exactly 1 time 922 (9.22%) aligned concordantly >1 times 17.27% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8295 (82.95%) aligned concordantly 0 times 775 (7.75%) aligned concordantly exactly 1 time 930 (9.30%) aligned concordantly >1 times 17.05% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8275 (82.75%) aligned concordantly 0 times 775 (7.75%) aligned concordantly exactly 1 time 950 (9.50%) aligned concordantly >1 times 17.25% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8319 (83.19%) aligned concordantly 0 times 789 (7.89%) aligned concordantly exactly 1 time 892 (8.92%) aligned concordantly >1 times 16.81% 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: 84594 Total methylated C's in CpG context: 7626 Total methylated C's in CHG context: 359 Total methylated C's in CHH context: 1529 Total methylated C's in Unknown context: 56 Total unmethylated C's in CpG context: 3119 Total unmethylated C's in CHG context: 18757 Total unmethylated C's in CHH context: 53204 Total unmethylated C's in Unknown context: 282 C methylated in CpG context: 71.0% C methylated in CHG context: 1.9% C methylated in CHH context: 2.8% C methylated in unknown context (CN or CHN): 16.6% Bismark completed in 0d 0h 0m 23s ==================== 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,-0.6 -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,-0.6 -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: 8012 (80.12%) aligned concordantly 0 times 946 (9.46%) aligned concordantly exactly 1 time 1042 (10.42%) aligned concordantly >1 times 19.88% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8351 (83.51%) aligned concordantly 0 times 753 (7.53%) aligned concordantly exactly 1 time 896 (8.96%) aligned concordantly >1 times 16.49% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8296 (82.96%) aligned concordantly 0 times 787 (7.87%) aligned concordantly exactly 1 time 917 (9.17%) aligned concordantly >1 times 17.04% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8077 (80.77%) aligned concordantly 0 times 886 (8.86%) aligned concordantly exactly 1 time 1037 (10.37%) aligned concordantly >1 times 19.23% 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: 94223 Total methylated C's in CpG context: 11075 Total methylated C's in CHG context: 525 Total methylated C's in CHH context: 1471 Total methylated C's in Unknown context: 51 Total unmethylated C's in CpG context: 2709 Total unmethylated C's in CHG context: 20917 Total unmethylated C's in CHH context: 57526 Total unmethylated C's in Unknown context: 307 C methylated in CpG context: 80.3% C methylated in CHG context: 2.4% C methylated in CHH context: 2.5% C methylated in unknown context (CN or CHN): 14.2% Bismark completed in 0d 0h 0m 24s ==================== Bismark run complete ====================