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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): /Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/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/18-04-29 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 /Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_10_s1_R2_val_2.fq.gz Input files are in FastQ format 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 (17448883 sequences in total) 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 (17448883 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 /Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_10_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far 1174488874488833 read reads; of these: s; of these: 17 448883 (174488100.0803 (%)100.00 were %) were paired; of pairethese: d; of these:1 1356748114 (89857 (65.09%) aligned concordantly 0 times 2277521 (65.85%) al13.ign05ed concordantly 0 time%)s aligned2211257 ( 12.67%) aligned concorconcordantly exactlydan 1 timetly e xactly 1 time 37 34776814614 (21.86%) aligned concordantly >1 9times (21.4 834.91% overall alignment rate%) aligned concordantly >1 times 34.15% overall alignment rate 17448883 reads; of these: 17448883 (100.00%) were paired; of these: 11494275 (65.87%) aligned concordantly 0 times 2202634 (12.62%) aligned concordantly exactly 1 time 3751974 (21.50%) aligned concordantly >1 times 34.13% overall alignment rate 17448883 reads; of these: 17448883 (100.00%) were paired; of these: 11364137 (65.13%) aligned concordantly 0 times 2265077 (12.98%) aligned concordantly exactly 1 time 3819669 (21.89%) aligned concordantly >1 times 34.87% overall alignment rate Processed 17448883 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: 17448883 Final Cytosine Methylation Report ================================= Total number of C's analysed: 252303007 Total methylated C's in CpG context: 24797899 Total methylated C's in CHG context: 1458878 Total methylated C's in CHH context: 6698414 Total methylated C's in Unknown context: 649565 Total unmethylated C's in CpG context: 10526009 Total unmethylated C's in CHG context: 54477988 Total unmethylated C's in CHH context: 154343819 Total unmethylated C's in Unknown context: 2848039 C methylated in CpG context: 70.2% C methylated in CHG context: 2.6% C methylated in CHH context: 4.2% C methylated in unknown context (CN or CHN): 18.6% Bismark completed in 0d 3h 9m 45s ==================== Bismark run complete ==================== 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): /Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/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/18-04-29 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 /Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_1_s1_R2_val_2.fq.gz Input files are in FastQ format 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 (28603346 sequences in total) 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 (28603346 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 /Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/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 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far 28603346286 2r8e602ads;033348606 3 o3346f r re4ea6thesds; ads; eof t:r hofee theseasd2:8 e60:33s ;46 2( o 8f16003328 046.0 (0100.0%t)h060 %) we3e346se wrere e: p pairea (28di6;r 10e03346od f th0.es0;(e o:1f0 0 thes %e0 :.00)2 3423we03r934e555% paired51) w (; of5 tere pai(red; of these: hese: 23381207 ( 23380237 (81.65%) aligned8 conco81.rdant18l7y 0 t.4im1.74%8%) e4asligned c %) ali gno ed1n) aligc8ned cc5oo6rdantly 0 tim8one3nco5 (rc6.ds49o ardann% ) tta lli ly 0 ygn 0 titmeesdi concm o1186re8ds 51a nt7 589ly exactly7 11856 2 t3(im68.849 (e6 % ) aligned7 co 339(.0n48%9966 (co.5rd)11 aalign1nte.8%)6 aldy e %lcignoxaed concordcn)ctorlya alida ngnn1te dtltime c oncyl o 3338025 y e(exactrx1dl1aa.nc6ty7l 1 %ty >time1 t) alil y mes i gn3361ed ti1c13on8.3225c% me overal( l ordant1a1.l lign75me %ynt r ) a3>1 timat3ee sl6i9 g1875.1n16% overaled concordanl alignmently t ra>1 ttei( me1s 1.78%) aligned concordant18.26ly >1 times 18.26% overall alignment rate % overall alignment rate Processed 28603346 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: 28603346 Final Cytosine Methylation Report ================================= Total number of C's analysed: 200758561 Total methylated C's in CpG context: 16775795 Total methylated C's in CHG context: 1545637 Total methylated C's in CHH context: 15604110 Total methylated C's in Unknown context: 1572866 Total unmethylated C's in CpG context: 7091116 Total unmethylated C's in CHG context: 37129696 Total unmethylated C's in CHH context: 122612207 Total unmethylated C's in Unknown context: 3387885 C methylated in CpG context: 70.3% C methylated in CHG context: 4.0% C methylated in CHH context: 11.3% C methylated in unknown context (CN or CHN): 31.7% Bismark completed in 0d 3h 28m 53s ==================== Bismark run complete ==================== 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): /Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/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/18-04-29 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 /Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_2_s1_R2_val_2.fq.gz Input files are in FastQ format 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 (30325606 sequences in total) 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 (30325606 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 /Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/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 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1210:4310:17386_1:N:0:TGACCA NC_035780.1 1 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1316:4047:74652_1:N:0:TGACCA NC_007175.2 17170 Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far 330325606 reads; of these: 30325606 (100.00%) were paired; of these: 19323983 (63.72%) aligned concordantly 0 times 3832182 (12.64%) 0aligned concordantly exactly 1 time 7169441 (23.64%) aligned concordantly >1 times 36.28% overall alignment rate 325606 reads; of these: 30325606 (100.00%) were paired; of these: 19332051 (63.75%) aligned concordantly 0 times 3840894 (12.67%) aligned concordantly exactly 1 time 7152661 (23.59%) aligned concordantly >1 times 36.25% overall alignment rate 30325606 reads; of these: 30325606 (100.00%) were paired; of these: 19382354 (63.91%) aligned concordantly 0 times 3781139 (12.47%) aligned concordantly exactly 1 time 7162113 (23.62%) aligned concordantly >1 times 36.09% overall alignment rate 30325606 reads; of these: 30325606 (100.00%) were paired; of these: 19387689 (63.93%) aligned concordantly 0 times 3786203 (12.49%) aligned concordantly exactly 1 time 7151714 (23.58%) aligned concordantly >1 times 36.07% overall alignment rate Processed 30325606 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: 30325606 Final Cytosine Methylation Report ================================= Total number of C's analysed: 375896419 Total methylated C's in CpG context: 35550304 Total methylated C's in CHG context: 2282737 Total methylated C's in CHH context: 16987048 Total methylated C's in Unknown context: 1561533 Total unmethylated C's in CpG context: 13991251 Total unmethylated C's in CHG context: 79870209 Total unmethylated C's in CHH context: 227214870 Total unmethylated C's in Unknown context: 5108826 C methylated in CpG context: 71.8% C methylated in CHG context: 2.8% C methylated in CHH context: 7.0% C methylated in unknown context (CN or CHN): 23.4% Bismark completed in 0d 5h 7m 17s ==================== Bismark run complete ==================== 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): /Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/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/18-04-29 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 /Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_3_s1_R2_val_2.fq.gz Input files are in FastQ format 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 (29548753 sequences in total) 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 (29548753 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 /Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/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 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2209:16034:32588_1:N:0:ACAGTG NC_007175.2 2 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far 29548753 reads; of these: 29548753 (100.00%) were paired; of these: 18861166 (63.83%) aligned concordantly 0 times 3732382 (12.63%) aligned concordantly exactly 1 time 6955205 (23.54%) aligned concordantly >1 times 36.17% overall alignment rate 29548753 reads; of these: 29548753 (100.00%) were paired; of these: 18778548 (63.55%) aligned concordantly 0 times 3781038 (12.80%) aligned concordantly exactly 1 time 6989167 (23.65%) aligned concordantly >1 times 36.45% overall alignment rate 29548753 reads; of these: 29548753 (100.00%) were paired; of these: 18846751 (63.78%) aligned concordantly 0 times 3755828 (12.71%) aligned concordantly exactly 1 time 6946174 (23.51%) aligned concordantly >1 times 36.22% overall alignment rate 29548753 reads; of these: 29548753 (100.00%) were paired; of these: 18789249 (63.59%) aligned concordantly 0 times 3757098 (12.71%) aligned concordantly exactly 1 time 7002406 (23.70%) aligned concordantly >1 times 36.41% overall alignment rate Processed 29548753 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: 29548753 Final Cytosine Methylation Report ================================= Total number of C's analysed: 424899469 Total methylated C's in CpG context: 47524867 Total methylated C's in CHG context: 2298043 Total methylated C's in CHH context: 10743678 Total methylated C's in Unknown context: 1088927 Total unmethylated C's in CpG context: 13919758 Total unmethylated C's in CHG context: 92489635 Total unmethylated C's in CHH context: 257923488 Total unmethylated C's in Unknown context: 5034580 C methylated in CpG context: 77.3% C methylated in CHG context: 2.4% C methylated in CHH context: 4.0% C methylated in unknown context (CN or CHN): 17.8% Bismark completed in 0d 4h 55m 57s ==================== Bismark run complete ==================== 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): /Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/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/18-04-29 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 /Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_4_s1_R2_val_2.fq.gz Input files are in FastQ format 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 (23970516 sequences in total) 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 (23970516 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 /Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_4_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2114:3090:6243_1:N:0:GCCAAT NC_007175.2 17180 Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2206:10235:74664_1:N:0:GCCAAT NC_007175.2 17189 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far 239705123970516 reads; of these:6 23 reads; of these:970516 ( 100.00%) were paired; of these: 14841949 ( 23970516 (61.92%) al100.00igned concordantly 0 tim%es) were paired; of 321these: 3245 (13.40%) aligned concordantly exactly 1 time 5915322 (24.68%) aligned concordantly >1 times 38.08% o v14846937 (erall61. alignment rate 94%) aligned concordantly 0 ti23970516mes re a ds; of these:32028 1 23970516 (1 (13.100.00%) were paired; of these: 14656563 (3661.14%) aligned c%) aligned concordantly exactly 1 time oncordan592076tly8 ( 0 times 24. 70330%) aligned concordantly >1 times 0138.06% over50all alignment rate (13.77%) aligned concordantly exactly 1 time 6013803 (25.09%) aligned concordantly >1 times 38.86% overall alignment rate 23970516 reads; of these: 23970516 (100.00%) were paired; of these: 14648886 (61.11%) aligned concordantly 0 times 3318130 (13.84%) aligned concordantly exactly 1 time 6003500 (25.05%) aligned concordantly >1 times 38.89% overall alignment rate Processed 23970516 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: 23970516 Final Cytosine Methylation Report ================================= Total number of C's analysed: 327201316 Total methylated C's in CpG context: 28026421 Total methylated C's in CHG context: 1662436 Total methylated C's in CHH context: 9876129 Total methylated C's in Unknown context: 887156 Total unmethylated C's in CpG context: 13940071 Total unmethylated C's in CHG context: 69726438 Total unmethylated C's in CHH context: 203969821 Total unmethylated C's in Unknown context: 4128531 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 3h 55m 40s ==================== Bismark run complete ==================== 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): /Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/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/18-04-29 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 /Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_5_s1_R2_val_2.fq.gz Input files are in FastQ format 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 (31503281 sequences in total) 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 (31503281 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 /Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_5_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1204:19985:42416_1:N:0:CAGATC NC_007175.2 1 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1310:9844:19111_1:N:0:CAGATC NC_007175.2 17197 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2109:17502:89766_1:N:0:CAGATC NC_007175.2 17173 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2116:16897:28912_1:N:0:CAGATC NC_035780.1 1 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2311:18572:58643_1:N:0:CAGATC NC_007175.2 17189 Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far 31503281 reads; of these: 31503281 (100.00%) were paired; of these: 20448241 (64.91%) aligned concordantly 0 times 4092438 (12.99%) aligned concordantly exactly 1 time 6962602 (22.10%) aligned concordantly >1 times 35.09% overall alignment rate 31503281 reads; of these: 31503281 (100.00%) were paired; of these: 20454049 (64.93%) aligned concordantly 0 times 4100113 (13.01%) aligned concordantly exactly 1 time 6949119 (22.06%) aligned concordantly >1 times 35.07% overall alignment rate 31503281 reads; of these: 31503281 (100.00%) were paired; of these: 20804982 (66.04%) aligned concordantly 0 times 3911943 (12.42%) aligned concordantly exactly 1 time 6786356 (21.54%) aligned concordantly >1 times 33.96% overall alignment rate 31503281 reads; of these: 31503281 (100.00%) were paired; of these: 20820413 (66.09%) aligned concordantly 0 times 3908348 (12.41%) aligned concordantly exactly 1 time 6774520 (21.50%) aligned concordantly >1 times 33.91% overall alignment rate Processed 31503281 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: 31503281 Final Cytosine Methylation Report ================================= Total number of C's analysed: 427057721 Total methylated C's in CpG context: 36699636 Total methylated C's in CHG context: 2370188 Total methylated C's in CHH context: 12902291 Total methylated C's in Unknown context: 1275308 Total unmethylated C's in CpG context: 17105060 Total unmethylated C's in CHG context: 88534839 Total unmethylated C's in CHH context: 269445707 Total unmethylated C's in Unknown context: 5454992 C methylated in CpG context: 68.2% C methylated in CHG context: 2.6% C methylated in CHH context: 4.6% C methylated in unknown context (CN or CHN): 18.9% Bismark completed in 0d 5h 6m 43s ==================== Bismark run complete ==================== 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): /Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/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/18-04-29 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 /Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_6_s1_R2_val_2.fq.gz Input files are in FastQ format 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 (23909493 sequences in total) 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 (23909493 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 /Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_6_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1201:7258:96604_1:N:0:CTTGTA NC_035780.1 1 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far 232239094933 r92e90949ads; o0394f 39t903 hes9re4ead93s rr:e; of the a ds; 2ofeads39094se:; 923t390 (9493h (eo1s100.0ef0:%) th were paired; of these: 00.00 1e4494se:% 223 )9094 49 wer 3 (e p1 (2a10i6030r.e.069d20%;90 )of these:4%) wer ae 9 3l (i pa i1rgne4ed9115 d70con7cor; of9d 0a( tn6ht.002ese.38l%y%) al)ig0 t:n eid m 1449 ew8sco11n er3 ( e 60co.64pa r33605di7ant%0r)l y(ed; 14.0 0of t6 ti%a) alhmesel ig si genn: e 31521d con 9ce2 o (d r1conc149127dora9nd2tantl3ly. (y 6 018 tiexm2esa% c. tly 1 ) t3 a il7m%)3ie 3a4g 8l n605468ed ig5289 ne d((c25.31on2%)c alcoignordeantdly nc4 eo.0nxcorc1o%ardantc)tdlly y al >ig1 n1tea dnt imestime l39 c.y on c0 tiorm3d85ea8%n sto4lv1ey r al5el axactll2 i2gnmey (nt r2 1 a43te1621 ti.43%) a19lme i g ned60627 9con1c ( o25.36(%r1da3).23%ntly > ali)1gn taligneed d ccioomesnc nco37.62% overdaralnolr alignmedantly n>1t timt ly rate es ex3actly9. 1 36time 58% 3458o2 (24.40ve%) aligned concordantly >1 times rall3 alignment rate 7.63% overall alignment rate Processed 23909493 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: 23909493 Final Cytosine Methylation Report ================================= Total number of C's analysed: 332065337 Total methylated C's in CpG context: 32090090 Total methylated C's in CHG context: 1709783 Total methylated C's in CHH context: 9696641 Total methylated C's in Unknown context: 935583 Total unmethylated C's in CpG context: 11442690 Total unmethylated C's in CHG context: 70560142 Total unmethylated C's in CHH context: 206565991 Total unmethylated C's in Unknown context: 4259145 C methylated in CpG context: 73.7% C methylated in CHG context: 2.4% C methylated in CHH context: 4.5% C methylated in unknown context (CN or CHN): 18.0% Bismark completed in 0d 3h 59m 15s ==================== Bismark run complete ==================== 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): /Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/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/18-04-29 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 /Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_7_s1_R2_val_2.fq.gz Input files are in FastQ format 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 (29273635 sequences in total) 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 (29273635 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 /Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_7_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1316:19155:63509_1:N:0:ATCACG NC_007175.2 17169 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2209:9828:53780_1:N:0:ATCACG NC_007175.2 17175 Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2211:12726:18562_1:N:0:ATCACG NC_007175.2 17178 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2215:3758:74065_1:N:0:ATCACG NC_007175.2 17183 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2309:5099:43290_1:N:0:ATCACG NC_035788.1 1 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2310:2897:70225_1:N:0:ATCACG NC_007175.2 17178 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far 22292739229276373356 reads; o63f t3he595 r2re7easd3eads; o:f th 6ese 35: rs; ofe 2a9 2ds; tohfe tsehes2e927:7:36353 ( 6 35129290 20(273635 (.7100100%) 3635 (wer10e.00.0000%0.)%) were paipr ewad00;%i) of werreed ere; tophpaefise:ai rt rehed; o ed ;f 196919 of tthhe7ese:se:9 se: ( 11954 1969551709 (46 (9534907 (67.66.7666732%) 7.a.2lig%n7)e ald8 %5ig%cned )onc oraligned dcanc)to ncooncrdly 0 aliotimegnedrdanta colsnyntl y 0 0cort i mes d 37 t36a0ni35mes7t10 5l ( 12.65%83 y53 ( )0 6alig11times2 .n3 e3 52d50% () 369110a5l i 1gnedc(2.341 c2o.61%) ncoro%ali)dgna alinngntely ecxado erddcao ccntly extnaloycc t1 tlyime 1 timonrde 5coan9 rda622nt8 3tl ly exa(c2t y603 lyexa05c.158 t31l tyi7% 1(m 20te.ime)6 2 al %i) gna li gned ceo6d con0n cco 4r d 1o58a5ntr9ld64 y( >2ant081ly >1 t.1643%6) im(estim aes32lign ed 2.7233.0.32%9co7 %no ovvecr%)oerra alall adl lilgnedig aalignmeconntcor dnrnmeatenat r tntlalyty >e >1 time1 tis me32.s 733.25% overall3% overall alignment rate alignment rate Processed 29273635 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: 29273635 Final Cytosine Methylation Report ================================= Total number of C's analysed: 401391964 Total methylated C's in CpG context: 36887057 Total methylated C's in CHG context: 2314187 Total methylated C's in CHH context: 11264648 Total methylated C's in Unknown context: 1069033 Total unmethylated C's in CpG context: 14089338 Total unmethylated C's in CHG context: 84945133 Total unmethylated C's in CHH context: 251891601 Total unmethylated C's in Unknown context: 4972076 C methylated in CpG context: 72.4% C methylated in CHG context: 2.7% C methylated in CHH context: 4.3% C methylated in unknown context (CN or CHN): 17.7% Bismark completed in 0d 4h 47m 19s ==================== Bismark run complete ==================== 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): /Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/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/18-04-29 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 /Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_8_s1_R2_val_2.fq.gz Input files are in FastQ format 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 (29483218 sequences in total) 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 (29483218 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 /Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_8_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1105:1822:7304_1:N:0:TTAGGC NC_007175.2 17173 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1112:2054:25809_1:Y:0:TTAGGC NC_007175.2 17197 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1205:19006:29835_1:N:0:TTAGGC NC_007175.2 17173 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1208:16282:90212_1:N:0:TTAGGC NC_007175.2 1 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1301:18980:18166_1:Y:0:TTAGGC NC_007175.2 17175 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1304:9180:4925_1:N:0:TTAGGC NC_007175.2 17172 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1311:7196:8646_1:N:0:TTAGGC NC_007175.2 1 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2112:7223:18290_1:N:0:TTAGGC NC_007175.2 17197 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2209:16412:85480_1:N:0:TTAGGC NC_007175.2 17173 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2303:6577:56043_1:N:0:TTAGGC NC_007175.2 17170 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2315:4342:46624_1:N:0:TTAGGC NC_007175.2 17187 Processed 29000000 sequence pairs so far 29483218 reads; of these: 29483218 (100.00%) were paired; of these: 20226493 (68.60%) aligned concordantly 0 times 3503231 (11.88%) aligned concordantly exactly 1 time 5753494 (19.51%) aligned concordantly >1 times 31.40% overall alignment rate 29483218 reads; of these: 29483218 (100.00%) were paired; of these: 20209918 (68.55%) aligned concordantly 0 times 3511077 (11.91%) aligned concordantly exactly 1 time 5762223 (19.54%) aligned concor29dan48321tly >1 times8 31.45% overall alignment ratereads; of these: 29483218 (100.00%) were paired; of these: 20396723 (69.18%) aligned concordantly 0 times 3400391 (11.53%) aligned concordantly exactly 1 time 5686104 (19.29%) aligned concordantly >1 times 30.82% overall alignment rate 29483218 reads; of these: 29483218 (100.00%) were paired; of these: 20371543 (69.10%) aligned concordantly 0 times 3414484 (11.58%) aligned concordantly exactly 1 time 5697191 (19.32%) aligned concordantly >1 times 30.90% overall alignment rate Processed 29483218 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: 29483218 Final Cytosine Methylation Report ================================= Total number of C's analysed: 362392795 Total methylated C's in CpG context: 29294128 Total methylated C's in CHG context: 2164397 Total methylated C's in CHH context: 13260103 Total methylated C's in Unknown context: 1218115 Total unmethylated C's in CpG context: 14337861 Total unmethylated C's in CHG context: 75732890 Total unmethylated C's in CHH context: 227603416 Total unmethylated C's in Unknown context: 4698419 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): 20.6% Bismark completed in 0d 4h 27m 30s ==================== Bismark run complete ==================== 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): /Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/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/18-04-29 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 /Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_9_s1_R2_val_2.fq.gz Input files are in FastQ format 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 (31847541 sequences in total) 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 (31847541 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 /Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_9_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:2:1215:9101:87373_1:N:0:ACTTGA NC_007175.2 17190 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:2:1313:3789:2859_1:N:0:ACTTGA NC_007175.2 17190 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:2:2207:4799:56169_1:N:0:ACTTGA NC_007175.2 17167 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:2:2213:18183:81000_1:N:0:ACTTGA NC_007175.2 17188 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:2:2312:18012:97005_1:N:0:ACTTGA NC_007175.2 17168 Processed 31000000 sequence pairs so far 31847541 31847541 reads; of these:re a 31847541 (ds; o1f these:00.00%) were paired; of these: 3184 73 5124811584143 184r7541 (eads;108 o f thes4(e:67.777541% r 0e a) d .00318a%li)sg ;4 of these:wned7 ere p 5con4a 1co ir31e (rdad100n84;.00 ot%7)f54l1 twh ee(re pa1yi se0:r e d0; t 0.00 %20692of 97ti)he6 weres e: ( p6m ae4i s20r 6e.d 891 89 ;373894 o%864) a fl(i 64.9g(1tned concorda41nhetse:l %) al .y 7i4%) gnea d2 159cloncordaign 1936tly 0 n0et it(ime67.8mesd s0 % )c 4 o1 a nl8 9c43i1o2rg6ned2 d24c2 o3(a n(ntly ec13ord.11a35%.07) alignnxtace%t) adl yll y 0c tio1ni tgmneiemcode concordantlryds eanx tly a e xa cc tly 1375t5 ly 1 620t 5 i5(met241i m41e49 . 7 69969%2(93724)02. a 64l2i9(%21.31)g96%ne d a)( aligned c2lconon1iccorda.9ordnagnt1t%ly >1)l ny a tligneexactlidy ed cm oe1cnco tso i35.02rdamn%ce o nt o650vrld0ery a4la0>01 n til( atmlies2 0gl.yn4 35m>.106e1%n timest roverall a la%32.i) ali23teg%n gedo concvone rdantment lrall aratey >lignment rat1 timese 32.20% overall alignment rate Processed 31847541 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: 31847541 Final Cytosine Methylation Report ================================= Total number of C's analysed: 446271830 Total methylated C's in CpG context: 48190808 Total methylated C's in CHG context: 2774831 Total methylated C's in CHH context: 12251657 Total methylated C's in Unknown context: 1258835 Total unmethylated C's in CpG context: 14405999 Total unmethylated C's in CHG context: 95964094 Total unmethylated C's in CHH context: 272684441 Total unmethylated C's in Unknown context: 5548505 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): 18.5% Bismark completed in 0d 5h 3m 0s ==================== Bismark run complete ==================== 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! 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/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-29'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify!