Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Processing sequences up to read no. 1000000 from the input file Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-27'): zr2096_10_s1_R1_val_1.fq.gz zr2096_10_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-04-27 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_10_s1_R1_val_1.fq.gz and zr2096_10_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000000 from zr2096_10_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_10_s1_R1_val_1.fq.gz to zr2096_10_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_10_s1_R1_val_1.fq.gz to zr2096_10_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_10_s1_R1_val_1.fq.gz (1000001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: zr2096_10_s1_R1_val_1.fq.gz: uncompress failed Processing reads up to sequence no. 1000000 from zr2096_10_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_10_s1_R2_val_2.fq.gz to zr2096_10_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_10_s1_R2_val_2.fq.gz to zr2096_10_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_10_s1_R2_val_2.fq.gz (1000001 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 /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_10_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_10_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:2:1101:1232:2155_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 ATTGTATTAATTATAAAAAATATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATTTATTATTAAAAATATTAAATA FFFFFFFFFBFFFFFFFFFFFFF#################################<>> Writing bisulfite mapping results to zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_10_s1_R1_val_1.fq.gz and zr2096_10_s1_R2_val_2.fq.gz 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 655733 (65.57%) aligned concordantly 0 times 127914 (12.79%) aligned concordantly exactly 1 time 216353 (21.64%) aligned concordantly >1 times 34.43% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 656097 (65.61%) aligned concordantly 0 times 127295 (12.73%) aligned concordantly exactly 1 time 216608 (21.66%) aligned concordantly >1 times 34.39% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 653826 (65.38%) aligned concordantly 0 times 128997 (12.90%) aligned concordantly exactly 1 time 217177 (21.72%) aligned concordantly >1 times 34.62% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 653718 (65.37%) aligned concordantly 0 times 129081 (12.91%) aligned concordantly exactly 1 time 217201 (21.72%) aligned concordantly >1 times 34.63% overall alignment rate Processed 1000000 sequence pairs so far Processed 1000000 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: 1000000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 14507114 Total methylated C's in CpG context: 1421648 Total methylated C's in CHG context: 83788 Total methylated C's in CHH context: 382029 Total methylated C's in Unknown context: 37110 Total unmethylated C's in CpG context: 604367 Total unmethylated C's in CHG context: 3125846 Total unmethylated C's in CHH context: 8889436 Total unmethylated C's in Unknown context: 164807 C methylated in CpG context: 70.2% C methylated in CHG context: 2.6% C methylated in CHH context: 4.1% C methylated in unknown context (CN or CHN): 18.4% Bismark completed in 0d 0h 10m 36s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: zr2096_10_s1_R1_val_1.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_10_s1_R2_val_2.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_10_s1_R2_val_2.fq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Processing sequences up to read no. 1000000 from the input file Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-27'): zr2096_1_s1_R1_val_1.fq.gz zr2096_1_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-04-27 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_1_s1_R1_val_1.fq.gz and zr2096_1_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000000 from zr2096_1_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_1_s1_R1_val_1.fq.gz to zr2096_1_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_1_s1_R1_val_1.fq.gz to zr2096_1_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_1_s1_R1_val_1.fq.gz (1000001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: zr2096_1_s1_R1_val_1.fq.gz: uncompress failed Processing reads up to sequence no. 1000000 from zr2096_1_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_1_s1_R2_val_2.fq.gz to zr2096_1_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_1_s1_R2_val_2.fq.gz to zr2096_1_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_1_s1_R2_val_2.fq.gz (1000001 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 /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_1_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_1_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1249:2156_1:N:0:CGATGT/1 99 NC_035784.1_CT_converted 257919 6 79M = 258023 184 GATTATTTGTTGTTTGTTGTTTGTTTGNNNNTNNNTNNGTTTGTTTGTTTGTTTGTTTGTTTGTAAATTTTTTATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFF####<###<##<<>> Writing bisulfite mapping results to zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_1_s1_R1_val_1.fq.gz and zr2096_1_s1_R2_val_2.fq.gz Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1104:3705:43673_1:N:0:CGATGT NC_035780.1 1 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 817311 (81.73%) aligned concordantly 0 times 65012 (6.50%) aligned concordantly exactly 1 time 117677 (11.77%) aligned concordantly >1 times 18.27% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 819345 (81.93%) aligned concordantly 0 times 64547 (6.45%) aligned concordantly exactly 1 time 116108 (11.61%) aligned concordantly >1 times 18.07% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 819081 (81.91%) aligned concordantly 0 times 64542 (6.45%) aligned concordantly exactly 1 time 116377 (11.64%) aligned concordantly >1 times 18.09% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 816839 (81.68%) aligned concordantly 0 times 64853 (6.49%) aligned concordantly exactly 1 time 118308 (11.83%) aligned concordantly >1 times 18.32% overall alignment rate Processed 1000000 sequence pairs so far Processed 1000000 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: 1000000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 7000478 Total methylated C's in CpG context: 585279 Total methylated C's in CHG context: 53657 Total methylated C's in CHH context: 541383 Total methylated C's in Unknown context: 54451 Total unmethylated C's in CpG context: 246829 Total unmethylated C's in CHG context: 1295385 Total unmethylated C's in CHH context: 4277945 Total unmethylated C's in Unknown context: 118630 C methylated in CpG context: 70.3% C methylated in CHG context: 4.0% C methylated in CHH context: 11.2% C methylated in unknown context (CN or CHN): 31.5% Bismark completed in 0d 0h 6m 39s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: zr2096_1_s1_R1_val_1.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_1_s1_R2_val_2.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_1_s1_R2_val_2.fq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Processing sequences up to read no. 1000000 from the input file Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-27'): zr2096_2_s1_R1_val_1.fq.gz zr2096_2_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-04-27 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_2_s1_R1_val_1.fq.gz and zr2096_2_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000000 from zr2096_2_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_2_s1_R1_val_1.fq.gz to zr2096_2_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_2_s1_R1_val_1.fq.gz to zr2096_2_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_2_s1_R1_val_1.fq.gz (1000001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: zr2096_2_s1_R1_val_1.fq.gz: uncompress failed Processing reads up to sequence no. 1000000 from zr2096_2_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_2_s1_R2_val_2.fq.gz to zr2096_2_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_2_s1_R2_val_2.fq.gz to zr2096_2_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_2_s1_R2_val_2.fq.gz (1000001 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 /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_2_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_2_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1148:2157_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 AAATTTATTATTTTAAAAATAAAAATTNNNNTNNNTTTTATTATTTTTTTTAATATTTTTTAATATAATTAAATAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFF####<###<<>> Writing bisulfite mapping results to zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_2_s1_R1_val_1.fq.gz and zr2096_2_s1_R2_val_2.fq.gz Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1101:20975:44723_1:N:0:TGACCA NC_035781.1 1 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 637193 (63.72%) aligned concordantly 0 times 126291 (12.63%) aligned concordantly exactly 1 time 236516 (23.65%) aligned concordantly >1 times 36.28% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 636608 (63.66%) aligned concordantly 0 times 126143 (12.61%) aligned concordantly exactly 1 ti11me0 000 00237249 00000(023.7 r 2er%aed)a sd;aligned c of these:onco s; of the se:r 10 dantl10000000y00 >1 time(s10000 (.00%100.)3 00were6.3%)4 paired; % of ovewere theparse:all alig i nmered; of these:nt r ate 638115 (63826 28 (3.863.821%)%) aligned concorda aligned concordantly 0 timesntly 0 times 125312442 (597 (1212.46.53%) ali%) alignedgne cod cncordantly oncexactordly 1 tantimely exactly 1 t 236543ime ( 223.37165%)75 alig(23.7ned2%) coalincordagned ntlcony >1 timecors dan36.19% tly >1 times ov36.18% erall ovealiralgnment l alignment rate rate Processed 1000000 sequence pairs so far Processed 1000000 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: 1000000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 12425132 Total methylated C's in CpG context: 1171780 Total methylated C's in CHG context: 75002 Total methylated C's in CHH context: 557179 Total methylated C's in Unknown context: 51768 Total unmethylated C's in CpG context: 462498 Total unmethylated C's in CHG context: 2635229 Total unmethylated C's in CHH context: 7523444 Total unmethylated C's in Unknown context: 169378 C methylated in CpG context: 71.7% C methylated in CHG context: 2.8% C methylated in CHH context: 6.9% C methylated in unknown context (CN or CHN): 23.4% Bismark completed in 0d 0h 9m 48s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: zr2096_2_s1_R1_val_1.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_2_s1_R2_val_2.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_2_s1_R2_val_2.fq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Processing sequences up to read no. 1000000 from the input file Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-27'): zr2096_3_s1_R1_val_1.fq.gz zr2096_3_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-04-27 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_3_s1_R1_val_1.fq.gz and zr2096_3_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000000 from zr2096_3_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_3_s1_R1_val_1.fq.gz to zr2096_3_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_3_s1_R1_val_1.fq.gz to zr2096_3_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_3_s1_R1_val_1.fq.gz (1000001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: zr2096_3_s1_R1_val_1.fq.gz: uncompress failed Processing reads up to sequence no. 1000000 from zr2096_3_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_3_s1_R2_val_2.fq.gz to zr2096_3_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_3_s1_R2_val_2.fq.gz to zr2096_3_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_3_s1_R2_val_2.fq.gz (1000001 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 /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_3_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_3_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1059:2153_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 TAATTTAAATAATTTTATATAAATNNNNNNNNNNNNNNNTATTTAAATTAAAAATTTAAATAAATTTTTTTAATTATTTA FFFFFFFFFFFFFFFFFFFFFFFF###############<<>> Writing bisulfite mapping results to zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_3_s1_R1_val_1.fq.gz and zr2096_3_s1_R2_val_2.fq.gz Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1104:2918:23440_1:N:0:ACAGTG NC_035780.1 2 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 637077 (63.71%) aligned concordantly 0 times 128026 (12.80%) aligned concordantly exactly 1 time 234897 (23.49%) aligned concordantly >1 times 36.29% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 637748 (63.77%) aligned concordantly 0 times 126797 (12.68%) aligned concordantly exactly 1 time 235455 (23.55%) aligned concordantly >1 times 36.23% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 637220 (63.72%) aligned concordantly 0 times 127285 (12.73%) aligned concordantly exactly 1 time 235495 (23.55%) aligned concordantly >1 times 36.28% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 637007 (63.70%) aligned concordantly 0 times 126860 (12.69%) aligned concordantly exactly 1 time 236133 (23.61%) aligned concordantly >1 times 36.30% overall alignment rate Processed 1000000 sequence pairs so far Processed 1000000 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: 1000000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 14440042 Total methylated C's in CpG context: 1612313 Total methylated C's in CHG context: 77322 Total methylated C's in CHH context: 361714 Total methylated C's in Unknown context: 36630 Total unmethylated C's in CpG context: 469203 Total unmethylated C's in CHG context: 3140194 Total unmethylated C's in CHH context: 8779296 Total unmethylated C's in Unknown context: 172384 C methylated in CpG context: 77.5% C methylated in CHG context: 2.4% C methylated in CHH context: 4.0% C methylated in unknown context (CN or CHN): 17.5% Bismark completed in 0d 0h 10m 19s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: zr2096_3_s1_R1_val_1.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_3_s1_R2_val_2.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_3_s1_R2_val_2.fq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Processing sequences up to read no. 1000000 from the input file Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-27'): zr2096_4_s1_R1_val_1.fq.gz zr2096_4_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-04-27 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_4_s1_R1_val_1.fq.gz and zr2096_4_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000000 from zr2096_4_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_4_s1_R1_val_1.fq.gz to zr2096_4_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_4_s1_R1_val_1.fq.gz to zr2096_4_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_4_s1_R1_val_1.fq.gz (1000001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: zr2096_4_s1_R1_val_1.fq.gz: uncompress failed Processing reads up to sequence no. 1000000 from zr2096_4_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_4_s1_R2_val_2.fq.gz to zr2096_4_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_4_s1_R2_val_2.fq.gz to zr2096_4_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_4_s1_R2_val_2.fq.gz (1000001 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 /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_4_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_4_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1343:2133_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 ATAGTGGTTGTTATGGAAATTAGNNNNNNNNNNNNNNNNNNNNNNNNNTGNANTNTTTTTATTAGAATTGTTAAGGTTT FFFFFFFFFFFFFFFFFFFFFFF#########################<<#<#/#<>> Writing bisulfite mapping results to zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_4_s1_R1_val_1.fq.gz and zr2096_4_s1_R2_val_2.fq.gz 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 612597 (61.26%) aligned concordantly 0 times 137835 (13.78%) aligned concordantly exactly 1 time 249568 (24.96%) aligned concordantly >1 times 38.74% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 613100 (61.31%) aligned concordantly 0 times 136995 (13.70%) aligned concordantly exactly 1 time 249905 (24.99%) aligned concordantly >1 times 38.691000000 reads; of these:1000 % 00 o10000 revea00dras;ll 0 ofa thelig(nmen100t .0rat0se%e: 1000000 (100.00%) were paired; of these: 618977 (61.90%) aligned concordantly 0 times 133983 (13.40%) aligned concordantly exactly 1 time 247040 (24.70%) aligned concordantly >1 times 38.10% overall alignment rate ) were paired; of these: 618972 (61.90%) aligned concordantly 0 times 134190 (13.42%) aligned concordantly exactly 1 time 246838 (24.68%) aligned concordantly >1 times 38.10% overall alignment rate Processed 1000000 sequence pairs so far Processed 1000000 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: 1000000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 13656928 Total methylated C's in CpG context: 1167119 Total methylated C's in CHG context: 68888 Total methylated C's in CHH context: 408851 Total methylated C's in Unknown context: 37082 Total unmethylated C's in CpG context: 579377 Total unmethylated C's in CHG context: 2907466 Total unmethylated C's in CHH context: 8525227 Total unmethylated C's in Unknown context: 172449 C methylated in CpG context: 66.8% C methylated in CHG context: 2.3% C methylated in CHH context: 4.6% C methylated in unknown context (CN or CHN): 17.7% Bismark completed in 0d 0h 10m 4s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: zr2096_4_s1_R1_val_1.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_4_s1_R2_val_2.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_4_s1_R2_val_2.fq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Processing sequences up to read no. 1000000 from the input file Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-27'): zr2096_5_s1_R1_val_1.fq.gz zr2096_5_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-04-27 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_5_s1_R1_val_1.fq.gz and zr2096_5_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000000 from zr2096_5_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_5_s1_R1_val_1.fq.gz to zr2096_5_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_5_s1_R1_val_1.fq.gz to zr2096_5_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_5_s1_R1_val_1.fq.gz (1000001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: zr2096_5_s1_R1_val_1.fq.gz: uncompress failed Processing reads up to sequence no. 1000000 from zr2096_5_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_5_s1_R2_val_2.fq.gz to zr2096_5_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_5_s1_R2_val_2.fq.gz to zr2096_5_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_5_s1_R2_val_2.fq.gz (1000001 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 /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_5_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_5_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1218:2142_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TTATTTAAATTTTATTATTTATANNNNNNNNNNNNNNNNNNATTNTTTTTATTATATATATAAAATTATTTTAAAATTAT FFFFFFFFFFFFFFFFFFFFFFF##################<<<#<>> Writing bisulfite mapping results to zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_5_s1_R1_val_1.fq.gz and zr2096_5_s1_R2_val_2.fq.gz 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 649525 (64.95%) aligned concordantly 0 times 130338 (13.03%) aligned concordantly exactly 1 time 220137 (22.01%) aligned concordantly >1 times 35.05% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 659823 (65.98%) aligned concordantly 0 times 124058 (12.41%) aligned concordantly exactly 1 time 216119 (21.61%) aligned concordantly >1 times 34.02% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 649909 (64.99%) aligned concordantly 0 times 130011 (13.00%) aligned concordantly exactly 1 time 220080 (22.01%) aligned concordantly >1 times 35.01% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 660038 (66.00%) aligned concordantly 0 times 124553 (12.46%) aligned concordantly exactly 1 time 215409 (21.54%) aligned concordantly >1 times 34.00% overall alignment rate Processed 1000000 sequence pairs so far Processed 1000000 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: 1000000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 13613606 Total methylated C's in CpG context: 1168935 Total methylated C's in CHG context: 74696 Total methylated C's in CHH context: 406740 Total methylated C's in Unknown context: 40389 Total unmethylated C's in CpG context: 543270 Total unmethylated C's in CHG context: 2814533 Total unmethylated C's in CHH context: 8605432 Total unmethylated C's in Unknown context: 174268 C methylated in CpG context: 68.3% C methylated in CHG context: 2.6% C methylated in CHH context: 4.5% C methylated in unknown context (CN or CHN): 18.8% Bismark completed in 0d 0h 9m 58s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: zr2096_5_s1_R1_val_1.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_5_s1_R2_val_2.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_5_s1_R2_val_2.fq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Processing sequences up to read no. 1000000 from the input file Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-27'): zr2096_6_s1_R1_val_1.fq.gz zr2096_6_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-04-27 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_6_s1_R1_val_1.fq.gz and zr2096_6_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000000 from zr2096_6_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_6_s1_R1_val_1.fq.gz to zr2096_6_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_6_s1_R1_val_1.fq.gz to zr2096_6_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_6_s1_R1_val_1.fq.gz (1000001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: zr2096_6_s1_R1_val_1.fq.gz: uncompress failed Processing reads up to sequence no. 1000000 from zr2096_6_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_6_s1_R2_val_2.fq.gz to zr2096_6_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_6_s1_R2_val_2.fq.gz to zr2096_6_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_6_s1_R2_val_2.fq.gz (1000001 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 /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_6_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_6_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1093:2134_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 TTAATTTTATTATTAAATAAAAANNNNNNNNNNNNNNNNNNNNNNANNTANANAAATATTAATTAAATATTTTTAAAATA FFFFFFFFFFFFFFFFFFFFFFF######################<##<<#<#<>> Writing bisulfite mapping results to zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_6_s1_R1_val_1.fq.gz and zr2096_6_s1_R2_val_2.fq.gz 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 607099 (60.71%) aligned concordantly 0 times 139607 (13.96%) aligned concordantly exactly 1 time 253294 (25.33%) aligned concordantly >1 times 39.29% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 606677 (60.67%) aligned concordantly 0 times 140422 (14.04%) aligned concordantly exactly 1 time 252901 (25.29%) aligned concordantly >1 times 39.33% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 622561 (62.26%) aligned concordantly 0 times 132304 (13.23%) aligned concordantly exactly 1 time 245135 (24.51%) aligned concordantly >1 times 37.74% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 623047 (62.30%) aligned concordantly 0 times 132273 (13.23%) aligned concordantly exactly 1 time 244680 (24.47%) aligned concordantly >1 times 37.70% overall alignment rate Processed 1000000 sequence pairs so far Processed 1000000 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: 1000000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 13938301 Total methylated C's in CpG context: 1349757 Total methylated C's in CHG context: 71272 Total methylated C's in CHH context: 402359 Total methylated C's in Unknown context: 39066 Total unmethylated C's in CpG context: 478109 Total unmethylated C's in CHG context: 2963255 Total unmethylated C's in CHH context: 8673549 Total unmethylated C's in Unknown context: 179065 C methylated in CpG context: 73.8% C methylated in CHG context: 2.3% C methylated in CHH context: 4.4% C methylated in unknown context (CN or CHN): 17.9% Bismark completed in 0d 0h 10m 13s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: zr2096_6_s1_R1_val_1.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_6_s1_R2_val_2.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_6_s1_R2_val_2.fq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Processing sequences up to read no. 1000000 from the input file Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-27'): zr2096_7_s1_R1_val_1.fq.gz zr2096_7_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-04-27 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_7_s1_R1_val_1.fq.gz and zr2096_7_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000000 from zr2096_7_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_7_s1_R1_val_1.fq.gz to zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_7_s1_R1_val_1.fq.gz to zr2096_7_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_7_s1_R1_val_1.fq.gz (1000001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: zr2096_7_s1_R1_val_1.fq.gz: uncompress failed Processing reads up to sequence no. 1000000 from zr2096_7_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_7_s1_R2_val_2.fq.gz to zr2096_7_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_7_s1_R2_val_2.fq.gz to zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_7_s1_R2_val_2.fq.gz (1000001 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 /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 TTATTATGATGAATTTAAATATTAATAATAAAATTTAAAAAAAATATAAATGTTAAATATTAAATTTTTTAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 141 * 0 0 * * 0 0 TTTTTAAAAAATTTAATATTTAACATTTATATTTTTTTTAAATTTTATTATTAATATTTAAATTCATCATAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFBBFFFFFFBBFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr2096_7_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_7_s1_R2_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 99 NC_035781.1_GA_converted 24539756 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,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 83 NC_035780.1_CT_converted 42548691 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,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 TTATTATGATGAATTTAAATATTAATAATAAAATTTAAAAAAAATATAAATGTTAAATATTAAATTTTTTAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 141 * 0 0 * * 0 0 TTTTTAAAAAATTTAATATTTAACATTTATATTTTTTTTAAATTTTATTATTAATATTTAAATTCATCATAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFBBFFFFFFBBFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_7_s1_R1_val_1.fq.gz and zr2096_7_s1_R2_val_2.fq.gz 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 670847 (67.08%) aligned concordantly 0 times 124517 (12.45%) aligned concordantly exactly 1 time 204636 (20.46%) aligned concordantly >1 times 32.92% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 667631 (66.76%) aligned concordantly 0 times 126358 (12.64%) aligned concordantly exactly 1 time 206011 (20.60%) aligned concordantly >1 times 33.24% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 670899 (67.09%) aligned concordantly 0 times 123995 (12.40%) aligned concordantly exactly 1 time 205106 (20.51%) aligned concordantly >1 times 32.91% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 667694 (66.77%) aligned concordantly 0 times 126378 (12.64%) aligned concordantly exactly 1 time 205928 (20.59%) aligned concordantly >1 times 33.23% overall alignment rate Processed 1000000 sequence pairs so far Processed 1000000 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: 1000000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 13806945 Total methylated C's in CpG context: 1263772 Total methylated C's in CHG context: 78374 Total methylated C's in CHH context: 384212 Total methylated C's in Unknown context: 36797 Total unmethylated C's in CpG context: 483667 Total unmethylated C's in CHG context: 2916755 Total unmethylated C's in CHH context: 8680165 Total unmethylated C's in Unknown context: 171742 C methylated in CpG context: 72.3% C methylated in CHG context: 2.6% C methylated in CHH context: 4.2% C methylated in unknown context (CN or CHN): 17.6% Bismark completed in 0d 0h 10m 2s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: zr2096_7_s1_R1_val_1.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_7_s1_R2_val_2.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_7_s1_R2_val_2.fq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Processing sequences up to read no. 1000000 from the input file Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-27'): zr2096_8_s1_R1_val_1.fq.gz zr2096_8_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-04-27 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_8_s1_R1_val_1.fq.gz and zr2096_8_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000000 from zr2096_8_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_8_s1_R1_val_1.fq.gz to zr2096_8_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_8_s1_R1_val_1.fq.gz to zr2096_8_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_8_s1_R1_val_1.fq.gz (1000001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: zr2096_8_s1_R1_val_1.fq.gz: uncompress failed Processing reads up to sequence no. 1000000 from zr2096_8_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_8_s1_R2_val_2.fq.gz to zr2096_8_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_8_s1_R2_val_2.fq.gz to zr2096_8_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_8_s1_R2_val_2.fq.gz (1000001 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 /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_8_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_8_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1281:2170_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 TTAAAAAATTTATTAAATTTATTATTATTTNTTATTTTTTATAAAAGAAAATAGAGAGAGAGAGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#<>> Writing bisulfite mapping results to zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_8_s1_R1_val_1.fq.gz and zr2096_8_s1_R2_val_2.fq.gz 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 687245 (68.72%) aligned concordantly 0 times 118201 (11.82%) aligned concordantly exactly 1 time 194554 (19.46%) aligned concordantly >1 times 31.28% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 689507 (68.95%) aligned concordantly 0 times 116468 (11.65%) aligned concordantly exactly 1 time 194025 (19.40%) aligned concordantly >1 times 31.05% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 690475 (69.05%) aligned concordantly 0 times 116121 (11.61%) aligned concordantly exactly 1 time 193404 (19.34%) aligned concordantly >1 times 30.95% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 686703 (68.67%) aligned concordantly 0 times 118970 (11.90%) aligned concordantly exactly 1 time 194327 (19.43%) aligned concordantly >1 times 31.33% overall alignment rate Processed 1000000 sequence pairs so far Processed 1000000 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: 1000000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 12325890 Total methylated C's in CpG context: 992024 Total methylated C's in CHG context: 72967 Total methylated C's in CHH context: 451622 Total methylated C's in Unknown context: 42077 Total unmethylated C's in CpG context: 486713 Total unmethylated C's in CHG context: 2574344 Total unmethylated C's in CHH context: 7748220 Total unmethylated C's in Unknown context: 161022 C methylated in CpG context: 67.1% C methylated in CHG context: 2.8% C methylated in CHH context: 5.5% C methylated in unknown context (CN or CHN): 20.7% Bismark completed in 0d 0h 9m 20s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: zr2096_8_s1_R1_val_1.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_8_s1_R2_val_2.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_8_s1_R2_val_2.fq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Processing sequences up to read no. 1000000 from the input file Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-27'): zr2096_9_s1_R1_val_1.fq.gz zr2096_9_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-04-27 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are zr2096_9_s1_R1_val_1.fq.gz and zr2096_9_s1_R2_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 1000000 from zr2096_9_s1_R1_val_1.fq.gz Writing a C -> T converted version of the input file zr2096_9_s1_R1_val_1.fq.gz to zr2096_9_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_9_s1_R1_val_1.fq.gz to zr2096_9_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_9_s1_R1_val_1.fq.gz (1000001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: zr2096_9_s1_R1_val_1.fq.gz: uncompress failed Processing reads up to sequence no. 1000000 from zr2096_9_s1_R2_val_2.fq.gz Writing a C -> T converted version of the input file zr2096_9_s1_R2_val_2.fq.gz to zr2096_9_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_9_s1_R2_val_2.fq.gz to zr2096_9_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_9_s1_R2_val_2.fq.gz (1000001 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 /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_9_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_9_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:2:1101:1135:2128_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 AAAATAATAAATAATAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN >> Writing bisulfite mapping results to zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files zr2096_9_s1_R1_val_1.fq.gz and zr2096_9_s1_R2_val_2.fq.gz 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 675888 (67.59%) aligned concordantly 0 times 119042 (11.90%) aligned concordantly exactly 1 time 205070 (20.51%) aligned concordantly >1 times 32.41% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 675441 (67.54%) aligned concordantly 0 times 118720 (11.87%) aligned concordantly exactly 1 time 205839 (20.58%) aligned concordantly >1 times 32.46% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 650875 (65.09%) aligned concordantly 0 times 130623 (13.06%) aligned concordantly exactly 1 time 218502 (21.85%) aligned concordantly >1 times 34.91% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 650877 (65.09%) aligned concordantly 0 times 129879 (12.99%) aligned concordantly exactly 1 time 219244 (21.92%) aligned concordantly >1 times 34.91% overall alignment rate Processed 1000000 sequence pairs so far Processed 1000000 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: 1000000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 14066922 Total methylated C's in CpG context: 1515913 Total methylated C's in CHG context: 87529 Total methylated C's in CHH context: 387857 Total methylated C's in Unknown context: 39698 Total unmethylated C's in CpG context: 453186 Total unmethylated C's in CHG context: 3021569 Total unmethylated C's in CHH context: 8600868 Total unmethylated C's in Unknown context: 175565 C methylated in CpG context: 77.0% C methylated in CHG context: 2.8% C methylated in CHH context: 4.3% C methylated in unknown context (CN or CHN): 18.4% Bismark completed in 0d 0h 10m 11s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: zr2096_9_s1_R1_val_1.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_9_s1_R2_val_2.fq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: zr2096_9_s1_R2_val_2.fq.gz: uncompress failed