Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/srlab/programs/samtools-1.20/samtools' Reference genome folder provided is /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ (absolute path is '/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/)' FastQ format assumed (by default) Attention: early reports suggested that high values of -p to have diminishing returns. Please test different values using a small subset of data for your hardware setting. Each Bowtie 2 instance is going to be run with 5 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-WGBS-alignment-SLURM_array-bismark'): /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.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 Output will be written into the directory: /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-WGBS-alignment-SLURM_array-bismark/ Summary of all aligner options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Running Bismark Parallel version. Number of parallel instances to be spawned: 5 Current working directory is: /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-WGBS-alignment-SLURM_array-bismark Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz and /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz and /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz and /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz and /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz and /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 9092285) Using the subset file >1D9_R1_001.fastp-trim.fq.gz.temp.3.gz< as new in-file 1 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 9092286) Using the subset file >1D9_R1_001.fastp-trim.fq.gz.temp.2.gz< as new in-file 1 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz for PID: 70250 and offset 5 (sequences written out: 9092285) Using the subset file >1D9_R1_001.fastp-trim.fq.gz.temp.5.gz< as new in-file 1 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 9092285) Using the subset file >1D9_R1_001.fastp-trim.fq.gz.temp.4.gz< as new in-file 1 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 9092286) Using the subset file >1D9_R1_001.fastp-trim.fq.gz.temp.1.gz< as new in-file 1 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 9092285) Using the subset file >1D9_R2_001.fastp-trim.fq.gz.temp.4.gz< as new in-file 2 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz to 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz to 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 9092286) Using the subset file >1D9_R2_001.fastp-trim.fq.gz.temp.1.gz< as new in-file 2 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz to 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz to 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 9092285) Using the subset file >1D9_R2_001.fastp-trim.fq.gz.temp.3.gz< as new in-file 2 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz to 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz to 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz for PID: 70250 and offset 5 (sequences written out: 9092285) Using the subset file >1D9_R2_001.fastp-trim.fq.gz.temp.5.gz< as new in-file 2 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz to 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz to 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 9092286) Using the subset file >1D9_R2_001.fastp-trim.fq.gz.temp.2.gz< as new in-file 2 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz to 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz to 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz (9092285 sequences in total) Writing a C -> T converted version of the input file 1D9_R2_001.fastp-trim.fq.gz.temp.4.gz to 1D9_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D9_R2_001.fastp-trim.fq.gz.temp.4.gz to 1D9_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz (9092285 sequences in total) Writing a C -> T converted version of the input file 1D9_R2_001.fastp-trim.fq.gz.temp.3.gz to 1D9_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D9_R2_001.fastp-trim.fq.gz.temp.3.gz to 1D9_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz (9092286 sequences in total) Writing a C -> T converted version of the input file 1D9_R2_001.fastp-trim.fq.gz.temp.1.gz to 1D9_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D9_R2_001.fastp-trim.fq.gz.temp.1.gz to 1D9_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz (9092286 sequences in total) Writing a C -> T converted version of the input file 1D9_R2_001.fastp-trim.fq.gz.temp.2.gz to 1D9_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D9_R2_001.fastp-trim.fq.gz.temp.2.gz to 1D9_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz (9092285 sequences in total) Writing a C -> T converted version of the input file 1D9_R2_001.fastp-trim.fq.gz.temp.5.gz to 1D9_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D9_R2_001.fastp-trim.fq.gz.temp.5.gz to 1D9_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1D9_R2_001.fastp-trim.fq.gz.temp.4.gz (9092285 sequences in total) Input files are 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ with the specified options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1D9_R2_001.fastp-trim.fq.gz.temp.3.gz (9092285 sequences in total) Input files are 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ with the specified options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:29905:1084_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TTATTTATTATTTATTTATAGATTTGTATAGGGGAGAGAATAATAGATGGGTTAATGTTTGAAATGTTAGTTTTTTAAATTTTTTATGGTGGTTATTTAATTTTTATTAATTTGTTTGATAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:29905:1084_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 ATTCTAATTTCTCTAAATAAAAAATTAATTTTTCTACATTTTATAAAATTAAATTAAAAAATTAAACCAAATAAAAAACTACATATCCTATTATTCTCTCCAAAAATTTAATTTTATCAAACAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:43355:1084_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TTTATGTTTTTTTTTTTTTTTTATAAAAAAAAAATAAAGAAATAAAAAAAATAAATAAATAAAAATTGGATTGTTATAAAATGGTGGGGGTTGTTATTTTAAAAAAAAAAAAAATTTTTTTAGTG III-IIIIIIIIIIIIIIIIII---IIIIIIIII-III-III-9IIIIIII-III-9II-IIIII-9-I9-9999-99999-9I-I99I9-99--99I9-9999-99999I9II-IIIIII-III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43355:1084_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 TTTTTTTTTTTTTTAAATCACAACCCCCACCATTTTATAACAATCCAATTTTTATTTATTTATTTTTTTTATTTATTTATTTTTTTTTTATAAAAAAAAAAAAAAAACACAAAAAAAACCTCACT IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII-III99IIIII-IIIII99-IIIIIIIIIIIIII-IIIIIIII99999IIIII-I-III9III9I9IIIII-I-IIII-II9I9-III- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:43355:1084_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TTTATATTTTTTTTTTTTTTTTACAAAAAAAAAACAAAAAAATAAAAAAAATAAATAAACAAAAATTAAATTATTATAAAATAATAAAAATTATTATTTCAAAAAAAAAAAAAATTTTTTTAATA III-IIIIIIIIIIIIIIIIII---IIIIIIIII-III-III-9IIIIIII-III-9II-IIIII-9-I9-9999-99999-9I-I99I9-99--99I9-9999-99999I9II-IIIIII-III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43355:1084_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 TTTTTTTTTTTTTTAAATTATAATTTTTATTATTTTATAATAATTTAATTTTTATTTATTTATTTTTTTTATTTATTTATTTTTTTTTTATAAAAAAAAAAAAAAAATATAAAAAAAATTTTATT IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII-III99IIIII-IIIII99-IIIIIIIIIIIIII-IIIIIIII99999IIIII-I-III9III9I9IIIII-I-IIII-II9I9-III- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:29905:1084_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TTATTTATTATTTATTTATAAATTTATATAAAAAAAAAAATAATAAATAAATTAATATTTAAAATATTAATTTTTTAAATTTTTTATAATAATTATTTAATTTTTATTAATTTATTTAATAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:29905:1084_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 ATTTTAATTTTTTTAAATAAAAAATTAATTTTTTTATATTTTATAAAATTAAATTAAAAAATTAAATTAAATAAAAAATTATATATTTTATTATTTTTTTTAAAAATTTAATTTTATTAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:43355:1084_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TTTATATTTTTTTTTTTTTTTTACAAAAAAAAAACAAAAAAATAAAAAAAATAAATAAACAAAAATTAAATTATTATAAAATAATAAAAATTATTATTTCAAAAAAAAAAAAAATTTTTTTAATA III-IIIIIIIIIIIIIIIIII---IIIIIIIII-III-III-9IIIIIII-III-9II-IIIII-9-I9-9999-99999-9I-I99I9-99--99I9-9999-99999I9II-IIIIII-III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43355:1084_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 TTTTTTTTTTTTTTAAATTATAATTTTTATTATTTTATAATAATTTAATTTTTATTTATTTATTTTTTTTATTTATTTATTTTTTTTTTATAAAAAAAAAAAAAAAATATAAAAAAAATTTTATT IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII-III99IIIII-IIIII99-IIIIIIIIIIIIII-IIIIIIII99999IIIII-I-III9III9I9IIIII-I-IIII-II9I9-III- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:29905:1084_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TTATTTATTATTTATTTATAAATTTATATAAAAAAAAAAATAATAAATAAATTAATATTTAAAATATTAATTTTTTAAATTTTTTATAATAATTATTTAATTTTTATTAATTTATTTAATAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:29905:1084_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 ATTTTAATTTTTTTAAATAAAAAATTAATTTTTTTATATTTTATAAAATTAAATTAAAAAATTAAATTAAATAAAAAATTATATATTTTATTATTTTTTTTAAAAATTTAATTTTATTAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:43355:1084_1:N:0:TACCTGCA+TGATGTCC/1 83 ptg000047l_GA_converted 3551514 0 11M1D59M1D55M = 3551527 139 CACTAAAAAAATTTTTTTTTTTTTTAAAATAACAACCCCCACCATTTTATAACAATCCAATTTTTATTTATTTATTTTTTTTATTTCTTTATTTTTTTTTTATAAAAAAAAAAAAAAAACATAAA III-IIIIII-II9I99999-9999-9I99--99-9I99I-I9-99999-9999-9I-9-IIIII-II9-III-IIIIIII9-III-III-IIIIIIIII---IIIIIIIIIIIIIIIIII-III AS:i:-64 XS:i:-68 XN:i:0 XM:i:8 XO:i:2 XG:i:2 NM:i:10 MD:Z:11^T14T4C6A32^T16A3T8A2A21C0 YS:i:-50 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:43355:1084_2:N:0:TACCTGCA+TGATGTCC/2 163 ptg000047l_GA_converted 3551527 0 58M1D67M = 3551514 -139 TTTTTTTTTTTTTTAAATCACAACCCCCACCATTTTATAACAATCCAATTTTTATTTATTTATTTTTTTTATTTATTTATTTTTTTTTTATAAAAAAAAAAAAAAAACACAAAAAAAACCTCACT IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII-III99IIIII-IIIII99-IIIIIIIIIIIIII-IIIIIIII99999IIIII-I-III9III9I9IIIII-I-IIII-II9I9-III- AS:i:-50 XS:i:-62 XN:i:0 XM:i:7 XO:i:1 XG:i:1 NM:i:8 MD:Z:25A32^T20T8A2A18T2C1C10 YS:i:-64 YT:Z:CP >>> Writing bisulfite mapping results to 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:29905:1084_1:N:0:TACCTGCA+TGATGTCC/1 83 ntLink_6_GA_converted 22813503 6 125M = 22813393 -235 ATTTTATCAAACAAATTAATAAAAATTAAATAACCACCATAAAAAATTTAAAAAACTAACATTTCAAACATTAACCCATCTATTATTCTCTCCCCTATACAAATCTATAAATAAATAATAAATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:29905:1084_2:N:0:TACCTGCA+TGATGTCC/2 163 ntLink_6_GA_converted 22813393 6 125M = 22813503 235 ATTCTAATTTCTCTAAATAAAAAATTAATTTTTCTACATTTTATAAAATTAAATTAAAAAATTAAACCAAATAAAAAACTACATATCCTATTATTCTCTCCAAAAATTTAATTTTATCAAACAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.3.gz Created C -> T as well as G -> A converted versions of the FastQ file 1D9_R2_001.fastp-trim.fq.gz.temp.1.gz (9092286 sequences in total) Input files are 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ with the specified options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1D9_R2_001.fastp-trim.fq.gz.temp.2.gz (9092286 sequences in total) Input files are 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ with the specified options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:50646:1070_1:N:0:TACCTGCA+TGATGTCC/1 99 ptg000016l_CT_converted 7561485 42 125M = 7561622 262 TAGTTGTTAGAGGGATGATTTGTGTGTTTTTTTTGGTTTGTTGTTTAGGTTGAGATAAGTTTGAATTTTTTGATGGAAATGTTGTAGTATTTAAGTTATTTGTGTTTTTAAATGTTGAATTTTTA IIIIIIIIII9I9II9-I9II9-IIIIIIIIII9IIIII99II-II-9IIII-I9II9IIIII9-IIIII9I-III9IIIIIIIIIIIIIIIIIII9IIIIIIIIIIII9II9IIIIIIIIII9I AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:43A81 YS:i:-12 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50646:1070_2:N:0:TACCTGCA+TGATGTCC/2 147 ptg000016l_CT_converted 7561622 42 125M = 7561485 -262 GAAATGTGGGATTTTTTTGTGTTTTTATTATTTTTTTGAGATAAGTTTTGTATTTTTTGGGTTAGTAGGTTGTAAATATTTTTAAATTTGTTATTATTTTGGTTTGAAAAATATGTATTTAAGTA IIII9-I9-9I9II9II99II9IIII--IIII-IIIIII9III9IIIIIIIIII9II9II9IIIIIIIIIII9I-IIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2T5T116 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:28174:1084_1:N:0:TACCTGCA+TGATGTCC/1 99 ptg000001l_CT_converted 9442728 16 125M = 9442707 -146 TTATAAGAATGGAAGTTTTAGATGTTGTTGTGTGATAAATTTTTAATAGGAGTTTTTTGGATGTTGTGTGTGATATAATTGTGAATAAAGTGGGAATAAATGGAGATTAAGTGAAGAAATATGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XS:i:-58 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:27G5A91 YS:i:-18 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:28174:1084_2:N:0:TACCTGCA+TGATGTCC/2 147 ptg000001l_CT_converted 9442707 16 125M = 9442728 146 TGTATGAAATGGTTATTTTATTTATAAGAATGGAAGTTTTAGATGTTGTTGTGTGATAAATTTTTAATAGGAGTTTTTTGGATGTTGTGTGTGATATAATTGTGAATAAAGTGGGAATAAATGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-52 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:8G39G5A70 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:28174:1084_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TTATAAAAATAAAAATTTTAAATATTATTATATAATAAATTTTTAATAAAAATTTTTTAAATATTATATATAATATAATTATAAATAAAATAAAAATAAATAAAAATTAAATAAAAAAATATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:28174:1084_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 TTTATTTATTTTTATTTTATTTATAATTATATTATATATAATATTTAAAAAATTTTTATTAAAAATTTATTATATAATAATATTTAAAATTTTTATTTTTATAAATAAAATAATTATTTTATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:50646:1070_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TAATTATTAAAAAAATAATTTATATATTTTTTTTAATTTATTACTTAAATTAAAATAAATTTAAATTTTTTAATAAAAATATTATAATATTTAAATTATTTATATTTTTAAATATTAAATTTTTA IIIIIIIIII9I9II9-I9II9-IIIIIIIIII9IIIII99II-II-9IIII-I9II9IIIII9-IIIII9I-III9IIIIIIIIIIIIIIIIIII9IIIIIIIIIIII9II9IIIIIIIIII9I YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50646:1070_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 TATTTAAATATATATTTTTTAAATTAAAATAATAATAAATTTAAAAATATTTATAATTTATTAATTTAAAAAATATAAAATTTATTTTAAAAAAATAATAAAAATATAAAAAAATTTTATATTTT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIII-I9IIIIIIIIIII9II9II9IIIIIIIIII9III9IIIIII-IIII--IIII9II99II9II9I9-9I-9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Created C -> T as well as G -> A converted versions of the FastQ file 1D9_R2_001.fastp-trim.fq.gz.temp.5.gz (9092285 sequences in total) Input files are 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ with the specified options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:50646:1070_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TAATTATTAAAAAAATAATTTATATATTTTTTTTAATTTATTACTTAAATTAAAATAAATTTAAATTTTTTAATAAAAATATTATAATATTTAAATTATTTATATTTTTAAATATTAAATTTTTA IIIIIIIIII9I9II9-I9II9-IIIIIIIIII9IIIII99II-II-9IIII-I9II9IIIII9-IIIII9I-III9IIIIIIIIIIIIIIIIIII9IIIIIIIIIIII9II9IIIIIIIIII9I YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50646:1070_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 TATTTAAATATATATTTTTTAAATTAAAATAATAATAAATTTAAAAATATTTATAATTTATTAATTTAAAAAATATAAAATTTATTTTAAAAAAATAATAAAAATATAAAAAAATTTTATATTTT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIII-I9IIIIIIIIIII9II9II9IIIIIIIIII9III9IIIIII-IIII--IIII9II99II9II9I9-9I-9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:28174:1084_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TTATAAAAATAAAAATTTTAAATATTATTATATAATAAATTTTTAATAAAAATTTTTTAAATATTATATATAATATAATTATAAATAAAATAAAAATAAATAAAAATTAAATAAAAAAATATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:28174:1084_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 TTTATTTATTTTTATTTTATTTATAATTATATTATATATAATATTTAAAAAATTTTTATTAAAAATTTATTATATAATAATATTTAAAATTTTTATTTTTATAAATAAAATAATTATTTTATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:44957:1084_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TATAGAATGTATGTGTTATTGTGATTTTTTTTATAATGTAAGTTATATAATGTTTTTTGTTGTGTGATTTTGGTTTAAGTTGTAGAGAAGGAGATTGAGGTTGGGTTTTAAATTTTTAATTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII-IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44957:1084_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 ACACAAACAACTCCTATCATTATTTAATTTATAAAAAAAAAAACCCCTACTCAATTAATTTTTATTTTTCTCATACAACTTAAAAATCACCCTTTCATCTATAACAAAAAATATCTACTTAATAC IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIII9II-IIIIIIIII-IIIIIIIIIII9III99IIII-IIIII9IIII-IIIIIII999-9IIIIII9I-I9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:44957:1084_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TATAAAATATATATATTATTATAATTTTTTTTATAATATAAATTATATAATATTTTTTATTATATAATTTTAATTTAAATTATAAAAAAAAAAATTAAAATTAAATTTTAAATTTTTAATTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII-IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44957:1084_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 ATATAAATAATTTTTATTATTATTTAATTTATAAAAAAAAAAATTTTTATTTAATTAATTTTTATTTTTTTTATATAATTTAAAAATTATTTTTTTATTTATAATAAAAAATATTTATTTAATAT IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIII9II-IIIIIIIII-IIIIIIIIIII9III99IIII-IIIII9IIII-IIIIIII999-9IIIIII9I-I9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:28174:1084_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TTATAAGAATGGAAGTTTTAGATGTTGTTGTGTGATAAATTTTTAATAGGAGTTTTTTGGATGTTGTGTGTGATATAATTGTGAATAAAGTGGGAATAAATGGAGATTAAGTGAAGAAATATGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:28174:1084_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 TCCATTTATTCCCACTTTATTCACAATTATATCACACACAACATCCAAAAAACTCCTATTAAAAATTTATCACACAACAACATCTAAAACTTCCATTCTTATAAATAAAATAACCATTTCATACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:50646:1070_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TAGTTGTTAGAGGGATGATTTGTGTGTTTTTTTTGGTTTGTTGTTTAGGTTGAGATAAGTTTGAATTTTTTGATGGAAATGTTGTAGTATTTAAGTTATTTGTGTTTTTAAATGTTGAATTTTTA IIIIIIIIII9I9II9-I9II9-IIIIIIIIII9IIIII99II-II-9IIII-I9II9IIIII9-IIIII9I-III9IIIIIIIIIIIIIIIIIII9IIIIIIIIIIII9II9IIIIIIIIII9I YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50646:1070_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 TACTTAAATACATATTTTTCAAACCAAAATAATAACAAATTTAAAAATATTTACAACCTACTAACCCAAAAAATACAAAACTTATCTCAAAAAAATAATAAAAACACAAAAAAATCCCACATTTC 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIII-I9IIIIIIIIIII9II9II9IIIIIIIIII9III9IIIIII-IIII--IIII9II99II9II9I9-9I-9IIII YT:Z:UP >>> Writing bisulfite mapping results to 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:44957:1084_1:N:0:TACCTGCA+TGATGTCC/1 77 * 0 0 * * 0 0 TATAAAATATATATATTATTATAATTTTTTTTATAATATAAATTATATAATATTTTTTATTATATAATTTTAATTTAAATTATAAAAAAAAAAATTAAAATTAAATTTTAAATTTTTAATTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII-IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44957:1084_2:N:0:TACCTGCA+TGATGTCC/2 141 * 0 0 * * 0 0 ATATAAATAATTTTTATTATTATTTAATTTATAAAAAAAAAAATTTTTATTTAATTAATTTTTATTTTTTTTATATAATTTAAAAATTATTTTTTTATTTATAATAAAAAATATTTATTTAATAT IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIII9II-IIIIIIIII-IIIIIIIIIII9III99IIII-IIIII9IIII-IIIIIII999-9IIIIII9I-I9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Reading in the sequence files 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:44957:1084_1:N:0:TACCTGCA+TGATGTCC/1 83 ntLink_6_GA_converted 16671225 42 125M = 16670956 -394 AAAAAATTAAAAATTTAAAACCCAACCTCAATCTCCTTCTCTACAACTTAAACCAAAATCACACAACAAAAAACATTATATAACTTACATTATAAAAAAAATCACAATAACACATACATTCTATA IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII-IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-14 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:44957:1084_2:N:0:TACCTGCA+TGATGTCC/2 163 ntLink_6_GA_converted 16670956 42 32M1D93M = 16671225 394 ACACAAACAACTCCTATCATTATTTAATTTATAAAAAAAAAAACCCCTACTCAATTAATTTTTATTTTTCTCATACAACTTAAAAATCACCCTTTCATCTATAACAAAAAATATCTACTTAATAC IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIII9II-IIIIIIIII-IIIIIIIIIII9III99IIII-IIIII9IIII-IIIIIII999-9IIIIII9I-I9IIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:32^A72T20 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.5.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1105:43088:27545_1:N:0:TACCTGCA+TGATGTCC ptg000015l 14997092 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1239:4941:23370_1:N:0:TACCTGCA+TGATGTCC ptg000025l 1 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1310:31500:13257_1:N:0:TACCTGCA+TGATGTCC ptg000092l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1363:32778:17879_1:N:0:TACCTGCA+TGATGTCC ptg000066l 66400 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1444:30043:7766_1:N:0:TACCTGCA+TGATGTCC ptg000015l 14997091 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1467:12418:20093_1:N:0:TACCTGCA+TGATGTCC ptg000054l 36030 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2288:22250:2653_1:N:0:TACCTGCA+TGATGTCC ptg000039l 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2374:24467:15764_1:N:0:TACCTGCA+TGATGTCC ptg000128l 1 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2418:5378:3647_1:N:0:TACCTGCA+TGATGTCC ptg000006l 3 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1152:18698:17375_1:N:0:TACCTGCA+TGATGTCC ptg000066l 66346 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1234:21490:20527_1:N:0:TACCTGCA+TGATGTCC ptg000066l 66355 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1476:19313:24323_1:N:0:TACCTGCA+TGATGTCC ptg000052l 52599 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2220:23464:23076_1:N:0:TACCTGCA+TGATGTCC ptg000080l 40109 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2408:23861:21802_1:N:0:TACCTGCA+TGATGTCC ptg000066l 66405 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far 9092286 reads; of these: 9092286 (100.00%) were paired; of these: 4027228 (44.29%) aligned concordantly 0 times 1694718 (18.64%) aligned concordantly exactly 1 time 3370340 (37.07%) aligned concordantly >1 times 55.71% overall alignment rate 9092286 reads; of these: 9092286 (100.00%) were paired; of these: 9062562 (99.67%) aligned concordantly 0 times 10538 (0.12%) aligned concordantly exactly 1 time 19186 (0.21%) aligned concordantly >1 times 0.33% overall alignment rate 9092286 reads; of these: 9092286 (100.00%) were paired; of these: 4021139 (44.23%) aligned concordantly 0 times 1696527 (18.66%) aligned concordantly exactly 1 time 3374620 (37.12%) aligned concordantly >1 times 55.77% overall alignment rate 9092286 reads; of these: 9092286 (100.00%) were paired; of these: 9063651 (99.69%) aligned concordantly 0 times 10386 (0.11%) aligned concordantly exactly 1 time 18249 (0.20%) aligned concordantly >1 times 0.31% overall alignment rate Processed 9092286 sequences in total Successfully deleted the temporary files 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1D9_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9092286 Final Cytosine Methylation Report ================================= Total number of C's analysed: 221338256 Total methylated C's in CpG context: 3035826 Total methylated C's in CHG context: 210663 Total methylated C's in CHH context: 929317 Total methylated C's in Unknown context: 6476 Total unmethylated C's in CpG context: 34210390 Total unmethylated C's in CHG context: 37860182 Total unmethylated C's in CHH context: 145091878 Total unmethylated C's in Unknown context: 311819 C methylated in CpG context: 8.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% 9092285 reads; of these: 9092285 (100.00%) were paired; of these: 9062582 (99.67%) aligned concordantly 0 times 10292 (0.11%) aligned concordantly exactly 1 time 19411 (0.21%) aligned concordantly >1 times 0.33% overall alignment rate 9092285 reads; of these: 9092285 (100.00%) were paired; of these: 9063329 (99.68%) aligned concordantly 0 times 10376 (0.11%) aligned concordantly exactly 1 time 18580 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 9092285 reads; of these: 9092285 (100.00%) were paired; of these: 4023228 (44.25%) aligned concordantly 0 times 1697990 (18.68%) aligned concordantly exactly 1 time 3371067 (37.08%) aligned concordantly >1 times 55.75% overall alignment rate 9092285 reads; of these: 9092285 (100.00%) were paired; of these: 4028584 (44.31%) aligned concordantly 0 times 1694992 (18.64%) aligned concordantly exactly 1 time 3368709 (37.05%) aligned concordantly >1 times 55.69% overall alignment rate Processed 9092285 sequences in total Successfully deleted the temporary files 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1D9_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9092285 Final Cytosine Methylation Report ================================= Total number of C's analysed: 221405238 Total methylated C's in CpG context: 3041767 Total methylated C's in CHG context: 210040 Total methylated C's in CHH context: 929655 Total methylated C's in Unknown context: 6763 Total unmethylated C's in CpG context: 34220841 Total unmethylated C's in CHG context: 37881536 Total unmethylated C's in CHH context: 145121399 Total unmethylated C's in Unknown context: 311083 C methylated in CpG context: 8.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% Processed 9000000 sequence pairs so far Processed 8000000 sequence pairs so far 9092285 reads; of these: 9092285 (100.00%) were paired; of these: 9063680 (99.69%) aligned concordantly 0 times 10351 (0.11%) aligned concordantly exactly 1 time 18254 (0.20%) aligned concordantly >1 times 0.31% overall alignment rate 9092285 reads; of these: 9092285 (100.00%) were paired; of these: 4023064 (44.25%) aligned concordantly 0 times 1698272 (18.68%) aligned concordantly exactly 1 time 3370949 (37.07%) aligned concordantly >1 times 55.75% overall alignment rate 9092285 reads; of these: 9092285 (100.00%) were paired; of these: 4028217 (44.30%) aligned concordantly 0 times 1697291 (18.67%) aligned concordantly exactly 1 time 3366777 (37.03%) aligned concordantly >1 times 55.70% overall alignment rate 9092285 reads; of these: 9092285 (100.00%) were paired; of these: 9062570 (99.67%) aligned concordantly 0 times 10439 (0.11%) aligned concordantly exactly 1 time 19276 (0.21%) aligned concordantly >1 times 0.33% overall alignment rate Processed 9092285 sequences in total Successfully deleted the temporary files 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1D9_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9092285 Final Cytosine Methylation Report ================================= Total number of C's analysed: 221521533 Total methylated C's in CpG context: 3039030 Total methylated C's in CHG context: 210582 Total methylated C's in CHH context: 926612 Total methylated C's in Unknown context: 6444 Total unmethylated C's in CpG context: 34258372 Total unmethylated C's in CHG context: 37907706 Total unmethylated C's in CHH context: 145179231 Total unmethylated C's in Unknown context: 311479 C methylated in CpG context: 8.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Processed 9000000 sequence pairs so far 9092286 reads; of these: 9092286 (100.00%) were paired; of these: 9063375 (99.68%) aligned concordantly 0 times 10413 (0.11%) aligned concordantly exactly 1 time 18498 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 9092286 reads; of these: 9092286 (100.00%) were paired; of these: 4026881 (44.29%) aligned concordantly 0 times 1696652 (18.66%) aligned concordantly exactly 1 time 3368753 (37.05%) aligned concordantly >1 times 55.71% overall alignment rate 9092286 reads; of these: 9092286 (100.00%) were paired; of these: 9062370 (99.67%) aligned concordantly 0 times 10576 (0.12%) aligned concordantly exactly 1 time 19340 (0.21%) aligned concordantly >1 times 0.33% overall alignment rate 9092286 reads; of these: 9092286 (100.00%) were paired; of these: 4024262 (44.26%) aligned concordantly 0 times 1694809 (18.64%) aligned concordantly exactly 1 time 3373215 (37.10%) aligned concordantly >1 times 55.74% overall alignment rate Processed 9092286 sequences in total Successfully deleted the temporary files 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1D9_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9092286 Final Cytosine Methylation Report ================================= Total number of C's analysed: 221477424 Total methylated C's in CpG context: 3040016 Total methylated C's in CHG context: 210466 Total methylated C's in CHH context: 922616 Total methylated C's in Unknown context: 6472 Total unmethylated C's in CpG context: 34244319 Total unmethylated C's in CHG context: 37891324 Total unmethylated C's in CHH context: 145168683 Total unmethylated C's in Unknown context: 313165 C methylated in CpG context: 8.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Processed 9000000 sequence pairs so far 9092285 reads; of these: 9092285 (100.00%) were paired; of these: 9063563 (99.68%) aligned concordantly 0 times 10393 (0.11%) aligned concordantly exactly 1 time 18329 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 9092285 reads; of these: 9092285 (100.00%) were paired; of these: 9062503 (99.67%) aligned concordantly 0 times 10619 (0.12%) aligned concordantly exactly 1 time 19163 (0.21%) aligned concordantly >1 times 0.33% overall alignment rate 9092285 reads; of these: 9092285 (100.00%) were paired; of these: 4024782 (44.27%) aligned concordantly 0 times 1698277 (18.68%) aligned concordantly exactly 1 time 3369226 (37.06%) aligned concordantly >1 times 55.73% overall alignment rate 9092285 reads; of these: 9092285 (100.00%) were paired; of these: 4031953 (44.34%) aligned concordantly 0 times 1696431 (18.66%) aligned concordantly exactly 1 time 3363901 (37.00%) aligned concordantly >1 times 55.66% overall alignment rate Processed 9092285 sequences in total Successfully deleted the temporary files 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1D9_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D9_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9092285 Final Cytosine Methylation Report ================================= Total number of C's analysed: 221386727 Total methylated C's in CpG context: 3032301 Total methylated C's in CHG context: 209900 Total methylated C's in CHH context: 923846 Total methylated C's in Unknown context: 6607 Total unmethylated C's in CpG context: 34219169 Total unmethylated C's in CHG context: 37871880 Total unmethylated C's in CHH context: 145129631 Total unmethylated C's in Unknown context: 311254 C methylated in CpG context: 8.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1D9_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-WGBS-alignment-SLURM_array-bismark/1D9_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_PE_report.txt into >>> /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-WGBS-alignment-SLURM_array-bismark/1D9_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1D9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D9_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 45461427 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1107129178 Total methylated C's in CpG context: 15188940 Total methylated C's in CHG context: 1051651 Total methylated C's in CHH context: 4632046 Total methylated C's in Unknown context: 32762 Total unmethylated C's in CpG context: 171153091 Total unmethylated C's in CHG context: 189412628 Total unmethylated C's in CHH context: 725690822 Total unmethylated C's in Unknown context: 1558800 C methylated in CpG context: 8.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% Deleting temporary report files... Bismark completed in 0d 5h 31m 39s ==================== Bismark run complete ====================