Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 28 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/0626_1311'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_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) Summary of all aligner options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/0626_1311 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-103_S27_L005_R1_001_val_1.fq.gz to EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-103_S27_L005_R1_001_val_1.fq.gz to EPI-103_S27_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-103_S27_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-103_S27_L005_R2_001_val_2.fq.gz to EPI-103_S27_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-103_S27_L005_R2_001_val_2.fq.gz to EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-103_S27_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1512:1956_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 NGTTTATATGTATGTATTATATTTGTGTAGGTATTGTATTTGATAAGGAT #<<>> Writing bisulfite mapping results to EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 97821 (97.82%) aligned concordantly 0 times 622 (0.62%) aligned concordantly exactly 1 time 1557 (1.56%) aligned concordantly >1 times 2.18% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 97814 (97.81%) aligned concordantly 0 times 633 (0.63%) aligned concordantly exactly 1 time 1553 (1.55%) aligned concordantly >1 times 2.19% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64324 (64.32%) aligned concordantly 0 times 16514 (16.51%) aligned concordantly exactly 1 time 19162 (19.16%) aligned concordantly >1 times 35.68% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64308 (64.31%) aligned concordantly 0 times 16711 (16.71%) aligned concordantly exactly 1 time 18981 (18.98%) aligned concordantly >1 times 35.69% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-103_S27_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-103_S27_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1452797 Total methylated C's in CpG context: 46768 Total methylated C's in CHG context: 6688 Total methylated C's in CHH context: 35838 Total methylated C's in Unknown context: 427 Total unmethylated C's in CpG context: 152252 Total unmethylated C's in CHG context: 292234 Total unmethylated C's in CHH context: 919017 Total unmethylated C's in Unknown context: 3138 C methylated in CpG context: 23.5% C methylated in CHG context: 2.2% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 12.0% Bismark completed in 0d 2h 31m 25s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-104_S28_L005_R1_001_val_1.fq.gz to EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-104_S28_L005_R1_001_val_1.fq.gz to EPI-104_S28_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-104_S28_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-104_S28_L005_R2_001_val_2.fq.gz to EPI-104_S28_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-104_S28_L005_R2_001_val_2.fq.gz to EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-104_S28_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1112:1988_1:N:0:CGATGT/1 99 PGA_scaffold5__109_contigs__length_67248332_CT_converted 17340906 1 101M = 17341304 497 NGGTGGTAGTTATTAAGTATGTATATGTATTAAAAATTGAAATGAAAAATTATTTTATTAGTTTTTGAAATATTTTGGTATTATATTTAGAGGTGTTTGTG #<>> Writing bisulfite mapping results to EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 96906 (96.91%) aligned concordantly 0 times 868 (0.87%) aligned concordantly exactly 1 time 2226 (2.23%) aligned concordantly >1 times 3.09% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 96938 (96.94%) aligned concordantly 0 times 816 (0.82%) aligned concordantly exactly 1 time 2246 (2.25%) aligned concordantly >1 times 3.06% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 63185 (63.19%) aligned concordantly 0 times 16869 (16.87%) aligned concordantly exactly 1 time 19946 (19.95%) aligned concordantly >1 times 36.81% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 63146 (63.15%) aligned concordantly 0 times 16870 (16.87%) aligned concordantly exactly 1 time 19984 (19.98%) aligned concordantly >1 times 36.85% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-104_S28_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-104_S28_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1432969 Total methylated C's in CpG context: 51586 Total methylated C's in CHG context: 7144 Total methylated C's in CHH context: 42020 Total methylated C's in Unknown context: 485 Total unmethylated C's in CpG context: 136387 Total unmethylated C's in CHG context: 284339 Total unmethylated C's in CHH context: 911493 Total unmethylated C's in Unknown context: 3198 C methylated in CpG context: 27.4% C methylated in CHG context: 2.5% C methylated in CHH context: 4.4% C methylated in unknown context (CN or CHN): 13.2% Bismark completed in 0d 4h 59m 23s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-111_S29_L005_R1_001_val_1.fq.gz to EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-111_S29_L005_R1_001_val_1.fq.gz to EPI-111_S29_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-111_S29_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-111_S29_L005_R2_001_val_2.fq.gz to EPI-111_S29_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-111_S29_L005_R2_001_val_2.fq.gz to EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-111_S29_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1222:1965_1:N:0:TTAGGC/1 99 PGA_scaffold2__36_contigs__length_69596280_CT_converted 52423574 6 101M = 52423755 280 NTGATGAGTGATTTATAATGTTTTGTAGGTTTATTAAAAGATTGTGTTTGTGTTTGTAATTTTTTTGATATATTGTTAATTAAAGTTGGGATGGTTGGATT #<>> Writing bisulfite mapping results to EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 97086 (97.09%) aligned concordantly 0 times 896 (0.90%) aligned concordantly exactly 1 time 2018 (2.02%) aligned concordantly >1 times 2.91% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 97053 (97.05%) aligned concordantly 0 times 944 (0.94%) aligned concordantly exactly 1 time 2003 (2.00%) aligned concordantly >1 times 2.95% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 62947 (62.95%) aligned concordantly 0 times 17074 (17.07%) aligned concordantly exactly 1 time 19979 (19.98%) aligned concordantly >1 times 37.05% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 62928 (62.93%) aligned concordantly 0 times 17190 (17.19%) aligned concordantly exactly 1 time 19882 (19.88%) aligned concordantly >1 times 37.07% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-111_S29_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-111_S29_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1422622 Total methylated C's in CpG context: 48507 Total methylated C's in CHG context: 7359 Total methylated C's in CHH context: 36057 Total methylated C's in Unknown context: 463 Total unmethylated C's in CpG context: 146646 Total unmethylated C's in CHG context: 281287 Total unmethylated C's in CHH context: 902766 Total unmethylated C's in Unknown context: 3057 C methylated in CpG context: 24.9% C methylated in CHG context: 2.5% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 13.2% Bismark completed in 0d 7h 24m 20s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-113_S30_L005_R1_001_val_1.fq.gz to EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-113_S30_L005_R1_001_val_1.fq.gz to EPI-113_S30_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-113_S30_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-113_S30_L005_R2_001_val_2.fq.gz to EPI-113_S30_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-113_S30_L005_R2_001_val_2.fq.gz to EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-113_S30_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1442:1956_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 NTAGTATTTTTATTAGAAGAATTAGAAATATTAGTAATAGTAAATTATTAGGTAGTGATAATATTGTAAATGAGTAATTAAAGTATTTATTATATGTGATG #>> Writing bisulfite mapping results to EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 97227 (97.23%) aligned concordantly 0 times 829 (0.83%) aligned concordantly exactly 1 time 1944 (1.94%) aligned concordantly >1 times 2.77% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 97220 (97.22%) aligned concordantly 0 times 857 (0.86%) aligned concordantly exactly 1 time 1923 (1.92%) aligned concordantly >1 times 2.78% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64657 (64.66%) aligned concordantly 0 times 16784 (16.78%) aligned concordantly exactly 1 time 18559 (18.56%) aligned concordantly >1 times 35.34% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64595 (64.59%) aligned concordantly 0 times 16707 (16.71%) aligned concordantly exactly 1 time 18698 (18.70%) aligned concordantly >1 times 35.41% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-113_S30_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-113_S30_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1403354 Total methylated C's in CpG context: 46955 Total methylated C's in CHG context: 6874 Total methylated C's in CHH context: 35540 Total methylated C's in Unknown context: 434 Total unmethylated C's in CpG context: 144123 Total unmethylated C's in CHG context: 277989 Total unmethylated C's in CHH context: 891873 Total unmethylated C's in Unknown context: 3257 C methylated in CpG context: 24.6% C methylated in CHG context: 2.4% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 11.8% Bismark completed in 0d 9h 48m 0s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-119_S31_L005_R1_001_val_1.fq.gz to EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-119_S31_L005_R1_001_val_1.fq.gz to EPI-119_S31_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-119_S31_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-119_S31_L005_R2_001_val_2.fq.gz to EPI-119_S31_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-119_S31_L005_R2_001_val_2.fq.gz to EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-119_S31_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1132:1973_1:N:0:ACAGTG/1 99 PGA_scaffold12__71_contigs__length_50438331_CT_converted 4017483 2 93M = 4017483 -93 NTGGTGAAAATTTTGAAAATTGTTTAATAATGGTGTAAAATATTAATTTATATATTATTTTAGTAATTAGGGTGAAATATTTTGAAAGTAAGA #<>> Writing bisulfite mapping results to EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 97403 (97.40%) aligned concordantly 0 times 737 (0.74%) aligned concordantly exactly 1 time 1860 (1.86%) aligned concordantly >1 times 2.60% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 66297 (66.30%) aligned concordantly 0 times 16041 (16.04%) aligned concordantly exactly 1 time 17662 (17.66%) aligned concordantly >1 times 33.70% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65668 (65.67%) aligned concordantly 0 times 16396 (16.40%) aligned concordantly exactly 1 time 17936 (17.94%) aligned concordantly >1 times 34.33% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 97360 (97.36%) aligned concordantly 0 times 770 (0.77%) aligned concordantly exactly 1 time 1870 (1.87%) aligned concordantly >1 times 2.64% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-119_S31_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-119_S31_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1376795 Total methylated C's in CpG context: 43381 Total methylated C's in CHG context: 6798 Total methylated C's in CHH context: 33605 Total methylated C's in Unknown context: 408 Total unmethylated C's in CpG context: 155884 Total unmethylated C's in CHG context: 275311 Total unmethylated C's in CHH context: 861816 Total unmethylated C's in Unknown context: 2896 C methylated in CpG context: 21.8% C methylated in CHG context: 2.4% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 12.3% Bismark completed in 0d 12h 7m 11s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-120_S32_L005_R1_001_val_1.fq.gz to EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-120_S32_L005_R1_001_val_1.fq.gz to EPI-120_S32_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-120_S32_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-120_S32_L005_R2_001_val_2.fq.gz to EPI-120_S32_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-120_S32_L005_R2_001_val_2.fq.gz to EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-120_S32_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1140:1995_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 NGTATTTGGTTATATTTTAATATTAAATTTTGATTAAAATAGTTGTTGAAAATTGATTAGTATTATTTAGGAAGTATAGAAGTGTTAATATAAAGTTAATT #<>> Writing bisulfite mapping results to EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 97384 (97.38%) aligned concordantly 0 times 788 (0.79%) aligned concordantly exactly 1 time 1828 (1.83%) aligned concordantly >1 times 2.62% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 97363 (97.36%) aligned concordantly 0 times 768 (0.77%) aligned concordantly exactly 1 time 1869 (1.87%) aligned concordantly >1 times 2.64% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 62861 (62.86%) aligned concordantly 0 times 17582 (17.58%) aligned concordantly exactly 1 time 19557 (19.56%) aligned concordantly >1 times 37.14% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 63371 (63.37%) aligned concordantly 0 times 17085 (17.09%) aligned concordantly exactly 1 time 19544 (19.54%) aligned concordantly >1 times 36.63% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-120_S32_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-120_S32_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1451901 Total methylated C's in CpG context: 48860 Total methylated C's in CHG context: 7255 Total methylated C's in CHH context: 35386 Total methylated C's in Unknown context: 393 Total unmethylated C's in CpG context: 148228 Total unmethylated C's in CHG context: 288741 Total unmethylated C's in CHH context: 923431 Total unmethylated C's in Unknown context: 3104 C methylated in CpG context: 24.8% C methylated in CHG context: 2.5% C methylated in CHH context: 3.7% C methylated in unknown context (CN or CHN): 11.2% Bismark completed in 0d 14h 35m 35s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-127_S33_L005_R1_001_val_1.fq.gz to EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-127_S33_L005_R1_001_val_1.fq.gz to EPI-127_S33_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-127_S33_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-127_S33_L005_R2_001_val_2.fq.gz to EPI-127_S33_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-127_S33_L005_R2_001_val_2.fq.gz to EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-127_S33_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1259:1963_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 NTATTTATTTTTATATATTATTAAAAATTTATATTTTTATTATTAAAAATATAAATTTATATATTATTAATAATTTATTTTTATATTTTATTAATAAT #<>> Writing bisulfite mapping results to EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 97489 (97.49%) aligned concordantly 0 times 733 (0.73%) aligned concordantly exactly 1 time 1778 (1.78%) aligned concordantly >1 times 2.51% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 97493 (97.49%) aligned concordantly 0 times 656 (0.66%) aligned concordantly exactly 1 time 1851 (1.85%) aligned concordantly >1 times 2.51% overall alignment rate 100000 reads; of these: 100000 (100000100.00 reads; of these:% ) were paired; of these: 100000 (64330 (64.33%) aligned concordantly 0 times 16773100.00 (%16.77) were paired; of these:% ) aligned concordantly exactly 1 time 63903 (1889763.90 (%18.90) aligned concordantly 0 times% ) aligned concordantly >1 times 1690335.67 (%16.90 overall alignment rate% ) aligned concordantly exactly 1 time 19194 (19.19%) aligned concordantly >1 times 36.10% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-127_S33_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-127_S33_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1438388 Total methylated C's in CpG context: 49666 Total methylated C's in CHG context: 7185 Total methylated C's in CHH context: 36215 Total methylated C's in Unknown context: 447 Total unmethylated C's in CpG context: 148192 Total unmethylated C's in CHG context: 286858 Total unmethylated C's in CHH context: 910272 Total unmethylated C's in Unknown context: 3056 C methylated in CpG context: 25.1% C methylated in CHG context: 2.4% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 12.8% Bismark completed in 0d 17h 0m 54s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-128_S34_L005_R1_001_val_1.fq.gz to EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-128_S34_L005_R1_001_val_1.fq.gz to EPI-128_S34_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-128_S34_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-128_S34_L005_R2_001_val_2.fq.gz to EPI-128_S34_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-128_S34_L005_R2_001_val_2.fq.gz to EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-128_S34_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1617:1971_1:N:0:ACTTGA/1 99 PGA_scaffold7__69_contigs__length_43120122_CT_converted 39044038 2 98M = 39044221 281 NGAGATTATTTAATATAGATATGTGTTTAAGGTTTTGGTAGATATTGTTAATTATGATTATTGAGGTTATTTAATATAGATATGTTTTAAAGGTTTGG #<<>> Writing bisulfite mapping results to EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 97242 (97.24%) aligned concordantly 0 times 827 (0.83%) aligned concordantly exactly 1 time 1931 (1.93%) aligned concordantly >1 times 2.76% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 97210 (97.21%) aligned concordantly 0 times 852 (0.85%) aligned concordantly exactly 1 time 1938 (1.94%) aligned concordantly >1 times 2.79% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64119 (64.12%) aligned concordantly 0 times 17001 (17.00%) aligned concordantly exactly 1 time 18880 (18.88%) aligned concordantly >1 times 35.88% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 63801 (63.80%) aligned concordantly 0 times 17036 (17.04%) aligned concordantly exactly 1 time 19163 (19.16%) aligned concordantly >1 times 36.20% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-128_S34_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-128_S34_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1420514 Total methylated C's in CpG context: 49009 Total methylated C's in CHG context: 7303 Total methylated C's in CHH context: 31447 Total methylated C's in Unknown context: 369 Total unmethylated C's in CpG context: 146686 Total unmethylated C's in CHG context: 282255 Total unmethylated C's in CHH context: 903814 Total unmethylated C's in Unknown context: 3058 C methylated in CpG context: 25.0% C methylated in CHG context: 2.5% C methylated in CHH context: 3.4% C methylated in unknown context (CN or CHN): 10.8% Bismark completed in 0d 19h 22m 6s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-135_S35_L005_R1_001_val_1.fq.gz to EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-135_S35_L005_R1_001_val_1.fq.gz to EPI-135_S35_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-135_S35_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-135_S35_L005_R2_001_val_2.fq.gz to EPI-135_S35_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-135_S35_L005_R2_001_val_2.fq.gz to EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-135_S35_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1469:1995_1:N:0:GATCAG/1 99 PGA_scaffold9__45_contigs__length_38581958_CT_converted 24563066 1 97M = 24563072 104 NTGTATTTGTTATATTTTTAAAATAAATTAAAATTTTAATTATTTGTTTATTTTGTTTTTTTGGAATTTTGAGTGTATATGTATTATATAATTTATT #<>> Writing bisulfite mapping results to EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 95642 (95.64%) aligned concordantly 0 times 1268 (1.27%) aligned concordantly exactly 1 time 3090 (3.09%) aligned concordantly >1 times 4.36% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 95635 (95.64%) aligned concordantly 0 times 1244 (1.24%) aligned concordantly exactly 1 time 3121 (3.12%) aligned concordantly >1 times 4.37% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 63074 (63.07%) aligned concordantly 0 times 16689 (16.69%) aligned concordantly exactly 1 time 20237 (20.24%) aligned concordantly >1 times 36.93% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 63405 (63.41%) aligned concordantly 0 times 16671 (16.67%) aligned concordantly exactly 1 time 19924 (19.92%) aligned concordantly >1 times 36.59% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-135_S35_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-135_S35_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1349942 Total methylated C's in CpG context: 48334 Total methylated C's in CHG context: 7736 Total methylated C's in CHH context: 39216 Total methylated C's in Unknown context: 509 Total unmethylated C's in CpG context: 137052 Total unmethylated C's in CHG context: 268288 Total unmethylated C's in CHH context: 849316 Total unmethylated C's in Unknown context: 2950 C methylated in CpG context: 26.1% C methylated in CHG context: 2.8% C methylated in CHH context: 4.4% C methylated in unknown context (CN or CHN): 14.7% Bismark completed in 0d 21h 37m 45s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-136_S36_L005_R1_001_val_1.fq.gz to EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-136_S36_L005_R1_001_val_1.fq.gz to EPI-136_S36_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-136_S36_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-136_S36_L005_R2_001_val_2.fq.gz to EPI-136_S36_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-136_S36_L005_R2_001_val_2.fq.gz to EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-136_S36_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1242:1980_1:N:0:TAGCTT/1 99 PGA_scaffold11__79_contigs__length_51449921_CT_converted 30489349 0 100M = 30489366 109 NATGGTTGGATTATTTTATAGTTAAAATATTATGAGGTGTATTGATTGTTTTATTTTGAGATGTTGTGTAGATATTGTTTTAATGGGGTGTAGTGTTTTT #<>> Writing bisulfite mapping results to EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 10000096702 reads; of these: ( 96.70 %100000) aligned concordantly 0 times ( 1032 (1.03%) aligned concordantly exactly 1 time100.00 % ) were paired; of these:2266 ( 2.2796844% () aligned concordantly >1 times96.84 %3.30) aligned concordantly 0 times% overall alignment rate 954 (0.95%) aligned concordantly exactly 1 time 2202 (2.20%) aligned concordantly >1 times 3.16% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 63458 (63.46%) aligned concordantly 0 times 16307 (16.31%) aligned concordantly exactly 1 time 20235 (20.23%) aligned concordantly >1 times 36.54% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 63352 (63.35%) aligned concordantly 0 times 16615 (16.61%) aligned concordantly exactly 1 time 20033 (20.03%) aligned concordantly >1 times 36.65% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-136_S36_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-136_S36_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1358832 Total methylated C's in CpG context: 45450 Total methylated C's in CHG context: 7070 Total methylated C's in CHH context: 33845 Total methylated C's in Unknown context: 494 Total unmethylated C's in CpG context: 141733 Total unmethylated C's in CHG context: 271660 Total unmethylated C's in CHH context: 859074 Total unmethylated C's in Unknown context: 3000 C methylated in CpG context: 24.3% C methylated in CHG context: 2.5% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 14.1% Bismark completed in 0d 23h 51m 54s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-143_S37_L005_R1_001_val_1.fq.gz to EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-143_S37_L005_R1_001_val_1.fq.gz to EPI-143_S37_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-143_S37_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-143_S37_L005_R2_001_val_2.fq.gz to EPI-143_S37_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-143_S37_L005_R2_001_val_2.fq.gz to EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-143_S37_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1205:1956_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 NGAAGGAAAATGAATTGATAGTATTATAAGGTTTAAATTTGTTATTATTTTTATAATTTGTATTATTTTTATTATTATGTTATATTTTTATAAATAAATTT #<>> Writing bisulfite mapping results to EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 97332 (97.33%) aligned concordantly 0 times 782 (0.78%) aligned concordantly exactly 1 time 1886 (1.89%) aligned concordantly >1 times 2.67% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 97315 (97.31%) aligned concordantly 0 times 777 (0.78%) aligned concordantly exactly 1 time 1908 (1.91%) aligned concordantly >1 times 2.69% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64650 (64.65%) aligned concordantly 0 times 16476 (16.48%) aligned concordantly exactly 1 time 18874 (18.87%) aligned concordantly >1 times 35.35% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64749 (64.75%) aligned concordantly 0 times 16487 (16.49%) aligned concordantly exactly 1 time 18764 (18.76%) aligned concordantly >1 times 35.25% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-143_S37_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-143_S37_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1381007 Total methylated C's in CpG context: 49547 Total methylated C's in CHG context: 6872 Total methylated C's in CHH context: 35045 Total methylated C's in Unknown context: 427 Total unmethylated C's in CpG context: 137979 Total unmethylated C's in CHG context: 275631 Total unmethylated C's in CHH context: 875933 Total unmethylated C's in Unknown context: 2877 C methylated in CpG context: 26.4% C methylated in CHG context: 2.4% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 12.9% Bismark completed in 1d 2h 11m 53s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-145_S38_L005_R1_001_val_1.fq.gz to EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-145_S38_L005_R1_001_val_1.fq.gz to EPI-145_S38_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-145_S38_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-145_S38_L005_R2_001_val_2.fq.gz to EPI-145_S38_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-145_S38_L005_R2_001_val_2.fq.gz to EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-145_S38_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1386:1965_1:N:0:CTTGTA/1 99 PGA_scaffold1__77_contigs__length_89643857_CT_converted 61447290 40 97M = 61447296 105 NTGGGTAAGTAAAGATATAATATTGTAAGTATTATTATGTATATAAGTTTTATATTTTTTTTTTGAGGGTTGAAGTGTTATTATTTTGATATATATT #<>> Writing bisulfite mapping results to EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 97245 (97.25%) aligned concordantly 0 times 787 (0.79%) aligned concordantly exactly 1 time 1968 (1.97%) aligned concordantly >1 times 2.75% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 97269 (97.27%) aligned concordantly 0 times 791 (0.79%) aligned concordantly exactly 1 time 1940 (1.94%) aligned concordantly >1 times 2.73% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64249 (64.25%) aligned concordantly 0 times 16964 (16.96%) aligned concordantly exactly 1 time 18787 (18.79%) aligned concordantly >1 times 35.75% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64763 (64.76%) aligned concordantly 0 times 16516 (16.52%) aligned concordantly exactly 1 time 18721 (18.72%) aligned concordantly >1 times 35.24% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-145_S38_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-145_S38_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1398966 Total methylated C's in CpG context: 48723 Total methylated C's in CHG context: 7205 Total methylated C's in CHH context: 36788 Total methylated C's in Unknown context: 430 Total unmethylated C's in CpG context: 143551 Total unmethylated C's in CHG context: 276654 Total unmethylated C's in CHH context: 886045 Total unmethylated C's in Unknown context: 2982 C methylated in CpG context: 25.3% C methylated in CHG context: 2.5% C methylated in CHH context: 4.0% C methylated in unknown context (CN or CHN): 12.6% Bismark completed in 1d 4h 35m 8s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-151_S2_L002_R1_001_val_1.fq.gz to EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-151_S2_L002_R1_001_val_1.fq.gz to EPI-151_S2_L002_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-151_S2_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-151_S2_L002_R2_001_val_2.fq.gz to EPI-151_S2_L002_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-151_S2_L002_R2_001_val_2.fq.gz to EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-151_S2_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-151_S2_L002_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-151_S2_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1928:2248_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 TAGTAGAGGTTTATATGTATTTATGTTTGGTTAGAAAAGGTTTATATGTATTTATGTTTGGTTAGTAGAGGTTTATATGTATTTATGTTTGGTTA BBBBBFFBFFBBFBBBBFFF/B/FBBF>> Writing bisulfite mapping results to EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 96459 (96.46%) aligned concordantly 0 times 914 (0.91%) aligned concordantly exactly 1 time 2627 (2.63%) aligned concordantly >1 times 3.54% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 96510 (96.51%) aligned concordantly 0 times 918 (0.92%) aligned concordantly exactly 1 time 2572 (2.57%) aligned concordantly >1 times 3.49% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 66759 (66.76%) aligned concordantly 0 times 14629 (14.63%) aligned concordantly exactly 1 time 18612 (18.61%) aligned concordantly >1 times 33.24% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 67114 (67.11%) aligned concordantly 0 times 14437 (14.44%) aligned concordantly exactly 1 time 18449 (18.45%) aligned concordantly >1 times 32.89% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-151_S2_L002_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-151_S2_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1280490 Total methylated C's in CpG context: 51142 Total methylated C's in CHG context: 6347 Total methylated C's in CHH context: 50412 Total methylated C's in Unknown context: 534 Total unmethylated C's in CpG context: 126971 Total unmethylated C's in CHG context: 263380 Total unmethylated C's in CHH context: 782238 Total unmethylated C's in Unknown context: 2967 C methylated in CpG context: 28.7% C methylated in CHG context: 2.4% C methylated in CHH context: 6.1% C methylated in unknown context (CN or CHN): 15.3% Bismark completed in 1d 6h 42m 54s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-152_S3_L002_R1_001_val_1.fq.gz to EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-152_S3_L002_R1_001_val_1.fq.gz to EPI-152_S3_L002_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-152_S3_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-152_S3_L002_R2_001_val_2.fq.gz to EPI-152_S3_L002_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-152_S3_L002_R2_001_val_2.fq.gz to EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-152_S3_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-152_S3_L002_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-152_S3_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1155:2233_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 AATGGNTATGAAAATGTAATAAAGGAAGAGATATGAAAATGTAATAAAGGAANATTTATGANAATGTATTGTGGGAAGTGATATGAAAATGTAATATG BBBBB#B>> Writing bisulfite mapping results to EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 96758 (96.76%) aligned concordantly 0 times 847 (0.85%) aligned concordantly exactly 1 time 2395 (2.40%) aligned concordantly >1 times 3.24% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 96708 (96.71%) aligned concordantly 0 times 899 (0.90%) aligned concordantly exactly 1 time 2393 (2.39%) aligned concordantly >1 times 3.29% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 67487 (67.49%) aligned concordantly 0 times 14495 (14.49%) aligned concordantly exactly 1 time 18018 (18.02%) aligned concordantly >1 times 32.51% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 67757 (67.76%) aligned concordantly 0 times 14341 (14.34%) aligned concordantly exactly 1 time 17902 (17.90%) aligned concordantly >1 times 32.24% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-152_S3_L002_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-152_S3_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1258945 Total methylated C's in CpG context: 49975 Total methylated C's in CHG context: 6498 Total methylated C's in CHH context: 45498 Total methylated C's in Unknown context: 527 Total unmethylated C's in CpG context: 118253 Total unmethylated C's in CHG context: 253146 Total unmethylated C's in CHH context: 785575 Total unmethylated C's in Unknown context: 2825 C methylated in CpG context: 29.7% C methylated in CHG context: 2.5% C methylated in CHH context: 5.5% C methylated in unknown context (CN or CHN): 15.7% Bismark completed in 1d 8h 53m 21s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-153_S4_L002_R1_001_val_1.fq.gz to EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-153_S4_L002_R1_001_val_1.fq.gz to EPI-153_S4_L002_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-153_S4_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-153_S4_L002_R2_001_val_2.fq.gz to EPI-153_S4_L002_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-153_S4_L002_R2_001_val_2.fq.gz to EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-153_S4_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-153_S4_L002_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-153_S4_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1785:2231_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 TGTTGNGATATATAATTGAAAATTGTTGAAAGTGTTATTAAATATAATGTAATAATAAATGATAAAGGGATGTAATGTTGTATATTAATTATTAT BBBBB#BBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:2:2207:1785:2231_2:N:0:TTAGGC/2 141 * 0 0 * * 0 0 ATANNNNNNNNNNNNNNNNNNNNNNNNNNNNTNNNATTTATTATTACATTATATTTAATAACACTTTCAACAATTTTCAATTATATATCACAACA BBB############################B###BB<>> Writing bisulfite mapping results to EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 95668 (95.67%) aligned concordantly 0 times 1189 (1.19%) aligned concordantly exactly 1 time 3143 (3.14%) aligned concordantly >1 times 4.33% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 95731 (95.73%) aligned concordantly 0 times 1102 (1.10%) aligned concordantly exactly 1 time 3167 (3.17%) aligned concordantly >1 times 4.27% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 66384 (66.38%) aligned concordantly 0 times 14784 (14.78%) aligned concordantly exactly 1 time 18832 (18.83%) aligned concordantly >1 times 33.62% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 67104 (67.10%) aligned concordantly 0 times 14414 (14.41%) aligned concordantly exactly 1 time 18482 (18.48%) aligned concordantly >1 times 32.90% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-153_S4_L002_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-153_S4_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1259492 Total methylated C's in CpG context: 46766 Total methylated C's in CHG context: 6696 Total methylated C's in CHH context: 54175 Total methylated C's in Unknown context: 634 Total unmethylated C's in CpG context: 127922 Total unmethylated C's in CHG context: 257823 Total unmethylated C's in CHH context: 766110 Total unmethylated C's in Unknown context: 2801 C methylated in CpG context: 26.8% C methylated in CHG context: 2.5% C methylated in CHH context: 6.6% C methylated in unknown context (CN or CHN): 18.5% Bismark completed in 1d 10h 58m 54s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-154_S5_L002_R1_001_val_1.fq.gz to EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-154_S5_L002_R1_001_val_1.fq.gz to EPI-154_S5_L002_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-154_S5_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-154_S5_L002_R2_001_val_2.fq.gz to EPI-154_S5_L002_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-154_S5_L002_R2_001_val_2.fq.gz to EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-154_S5_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-154_S5_L002_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-154_S5_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:2191:2242_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 ATGTANATTAAGAGTTAAATTATGTAGATGTAGATTAAAAGTTAAATTATGTATAGGTAGATTAAGAGTTAAATTAAGTAGATGTAGATTAAGAGTTTAAT BBBBB#>> Writing bisulfite mapping results to EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 96651 (96.65%) aligned concordantly 0 times 951 (0.95%) aligned concordantly exactly 1 time 2398 (2.40%) aligned concordantly >1 times 3.35% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 69325 (69.33%) aligned concordantly 0 times 13666 (13.67%) aligned concordantly exactly 1 time 17009 (17.01%) aligned concordantly >1 times 30.68% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 69011 (69.01%) aligned concordantly 0 times 13645 (13.64%) aligned concordantly exactly 1 time 17344 (17.34%) aligned concordantly >1 times 30.99% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 96596 (96.60%) aligned concordantly 0 times 969 (0.97%) aligned concordantly exactly 1 time 2435 (2.44%) aligned concordantly >1 times 3.40% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-154_S5_L002_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-154_S5_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1187602 Total methylated C's in CpG context: 45245 Total methylated C's in CHG context: 5749 Total methylated C's in CHH context: 46056 Total methylated C's in Unknown context: 597 Total unmethylated C's in CpG context: 113591 Total unmethylated C's in CHG context: 240273 Total unmethylated C's in CHH context: 736688 Total unmethylated C's in Unknown context: 2664 C methylated in CpG context: 28.5% C methylated in CHG context: 2.3% C methylated in CHH context: 5.9% C methylated in unknown context (CN or CHN): 18.3% Bismark completed in 1d 13h 5m 43s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-159_S6_L002_R1_001_val_1.fq.gz to EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-159_S6_L002_R1_001_val_1.fq.gz to EPI-159_S6_L002_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-159_S6_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-159_S6_L002_R2_001_val_2.fq.gz to EPI-159_S6_L002_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-159_S6_L002_R2_001_val_2.fq.gz to EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-159_S6_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-159_S6_L002_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-159_S6_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1469:2230_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 GGTTANTGAAGTGTATATAGTTATATTGTAAATTAATGGTTGAGTGAGTTTTNTTTTTTATTAGGTAATATTTTAAGGGAATGGTTGTTTGTAAATATTGG BBBBB#BBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFF#<>> Writing bisulfite mapping results to EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 95795 (95.80%) aligned concordantly 0 times 1167 (1.17%) aligned concordantly exactly 1 time 3038 (3.04%) aligned concordantly >1 times 4.21% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 95720 (95.72%) aligned concordantly 0 times 1200 (1.20%) aligned concordantly exactly 1 time 3080 (3.08%) aligned concordantly >1 times 4.28% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65882 (65.88%) aligned concordantly 0 times 15036 (15.04%) aligned concordantly exactly 1 time 19082 (19.08%) aligned concordantly >1 times 34.12% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65556 (65.56%) aligned concordantly 0 times 15340 (15.34%) aligned concordantly exactly 1 time 19104 (19.10%) aligned concordantly >1 times 34.44% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-159_S6_L002_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-159_S6_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1328729 Total methylated C's in CpG context: 51781 Total methylated C's in CHG context: 7253 Total methylated C's in CHH context: 52915 Total methylated C's in Unknown context: 761 Total unmethylated C's in CpG context: 126344 Total unmethylated C's in CHG context: 268067 Total unmethylated C's in CHH context: 822369 Total unmethylated C's in Unknown context: 2993 C methylated in CpG context: 29.1% C methylated in CHG context: 2.6% C methylated in CHH context: 6.0% C methylated in unknown context (CN or CHN): 20.3% Bismark completed in 1d 15h 25m 45s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-160_S7_L002_R1_001_val_1.fq.gz to EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-160_S7_L002_R1_001_val_1.fq.gz to EPI-160_S7_L002_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-160_S7_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-160_S7_L002_R2_001_val_2.fq.gz to EPI-160_S7_L002_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-160_S7_L002_R2_001_val_2.fq.gz to EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-160_S7_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-160_S7_L002_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-160_S7_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1522:2231_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 GTATGNGTAATTAGGTGATTTTTTTTGATTTGATGTAGTTAGTGGATTGGGAATTGGTAA BBBBB#BBBFFBFFFFFFFFFFFFFFB/>> Writing bisulfite mapping results to EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 94634 (94.63%) aligned concordantly 0 times 1468 (1.47%) aligned concordantly exactly 1 time 3898 (3.90%) aligned concordantly >1 times 5.37% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 94679 (94.68%) aligned concordantly 0 times 1399 (1.40%) aligned concordantly exactly 1 time 3922 (3.92%) aligned concordantly >1 times 5.32% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 66831 (66.83%) aligned concordantly 0 times 14164 (14.16%) aligned concordantly exactly 1 time 19005 (19.00%) aligned concordantly >1 times 33.17% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 67331 (67.33%) aligned concordantly 0 times 14028 (14.03%) aligned concordantly exactly 1 time 18641 (18.64%) aligned concordantly >1 times 32.67% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-160_S7_L002_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-160_S7_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1160580 Total methylated C's in CpG context: 43784 Total methylated C's in CHG context: 6484 Total methylated C's in CHH context: 46612 Total methylated C's in Unknown context: 579 Total unmethylated C's in CpG context: 116615 Total unmethylated C's in CHG context: 236254 Total unmethylated C's in CHH context: 710831 Total unmethylated C's in Unknown context: 2732 C methylated in CpG context: 27.3% C methylated in CHG context: 2.7% C methylated in CHH context: 6.2% C methylated in unknown context (CN or CHN): 17.5% Bismark completed in 1d 17h 26m 39s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-161_S8_L002_R1_001_val_1.fq.gz to EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-161_S8_L002_R1_001_val_1.fq.gz to EPI-161_S8_L002_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-161_S8_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-161_S8_L002_R2_001_val_2.fq.gz to EPI-161_S8_L002_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-161_S8_L002_R2_001_val_2.fq.gz to EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-161_S8_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-161_S8_L002_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-161_S8_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:2010:2229_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TGATANGTAGTATATGGTGTATGATATAGTA BBBBB#>> Writing bisulfite mapping results to EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 95520 (95.52%) aligned concordantly 0 times 1263 (1.26%) aligned concordantly exactly 1 time 3217 (3.22%) aligned concordantly >1 times 4.48% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 95570 (95.57%) aligned concordantly 0 times 1256 (1.26%) aligned concordantly exactly 1 time 3174 (3.17%) aligned concordantly >1 times 4.43% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 70232 (70.23%) aligned concordantly 0 times 12834 (12.83%) aligned concordantly exactly 1 time 16934 (16.93%) aligned concordantly >1 times 29.77% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 70444 (70.44%) aligned concordantly 0 times 12931 (12.93%) aligned concordantly exactly 1 time 16625 (16.62%) aligned concordantly >1 times 29.56% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-161_S8_L002_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-161_S8_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1076985 Total methylated C's in CpG context: 37941 Total methylated C's in CHG context: 5651 Total methylated C's in CHH context: 42826 Total methylated C's in Unknown context: 606 Total unmethylated C's in CpG context: 107393 Total unmethylated C's in CHG context: 216779 Total unmethylated C's in CHH context: 666395 Total unmethylated C's in Unknown context: 2495 C methylated in CpG context: 26.1% C methylated in CHG context: 2.5% C methylated in CHH context: 6.0% C methylated in unknown context (CN or CHN): 19.5% Bismark completed in 1d 19h 20m 34s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-162_S9_L002_R1_001_val_1.fq.gz to EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-162_S9_L002_R1_001_val_1.fq.gz to EPI-162_S9_L002_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-162_S9_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-162_S9_L002_R2_001_val_2.fq.gz to EPI-162_S9_L002_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-162_S9_L002_R2_001_val_2.fq.gz to EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-162_S9_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-162_S9_L002_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-162_S9_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1238:2233_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 TGTTANTTATTTTAAAATTTGTTGATAAATTGTTTATTTTTAGGATAGTTTTTTTAGATATTGTTTTTTTTTGGTTTGAAAGGGTTATGAATAGTTTTTTT BBBBB#>> Writing bisulfite mapping results to EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 94704 (94.70%) aligned concordantly 0 times 1406 (1.41%) aligned concordantly exactly 1 time 3890 (3.89%) aligned concordantly >1 times 5.30% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 94725 (94.72%) aligned concordantly 0 times 1419 (1.42%) aligned concordantly exactly 1 time 3856 (3.86%) aligned concordantly >1 times 5.28% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 68848 (68.85%) aligned concordantly 0 times 13102 (13.10%) aligned concordantly exactly 1 time 18050 (18.05%) aligned concordantly >1 times 31.15% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 68419 (68.42%) aligned concordantly 0 times 13166 (13.17%) aligned concordantly exactly 1 time 18415 (18.41%) aligned concordantly >1 times 31.58% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-162_S9_L002_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-162_S9_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1090879 Total methylated C's in CpG context: 38872 Total methylated C's in CHG context: 5795 Total methylated C's in CHH context: 45688 Total methylated C's in Unknown context: 678 Total unmethylated C's in CpG context: 108363 Total unmethylated C's in CHG context: 222063 Total unmethylated C's in CHH context: 670098 Total unmethylated C's in Unknown context: 2505 C methylated in CpG context: 26.4% C methylated in CHG context: 2.5% C methylated in CHH context: 6.4% C methylated in unknown context (CN or CHN): 21.3% Bismark completed in 1d 21h 20m 44s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-167_S10_L002_R1_001_val_1.fq.gz to EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-167_S10_L002_R1_001_val_1.fq.gz to EPI-167_S10_L002_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-167_S10_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-167_S10_L002_R2_001_val_2.fq.gz to EPI-167_S10_L002_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-167_S10_L002_R2_001_val_2.fq.gz to EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-167_S10_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-167_S10_L002_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-167_S10_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1666:2232_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 TTGAANTTGTTGATTTATATGGGGATATGAATAATAAGTTTAATATTTAAGATGGAGAAGAAATAAGTGTAGAATTTTGGATAAAGGATAATTAAGTTAAT BBBBB#BBFFFFFF>> Writing bisulfite mapping results to EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 97239 (97.24%) aligned concordantly 0 times 795 (0.80%) aligned concordantly exactly 1 time 1966 (1.97%) aligned concordantly >1 times 2.76% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 97233 (97.23%) aligned concordantly 0 times 826 (0.83%) aligned concordantly exactly 1 time 1941 (1.94%) aligned concordantly >1 times 2.77% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65801 (65.80%) aligned concordantly 0 times 15372 (15.37%) aligned concordantly exactly 1 time 18827 (18.83%) aligned concordantly >1 times 34.20% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65397 (65.40%) aligned concordantly 0 times 15621 (15.62%) aligned concordantly exactly 1 time 18982 (18.98%) aligned concordantly >1 times 34.60% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-167_S10_L002_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-167_S10_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1380393 Total methylated C's in CpG context: 50036 Total methylated C's in CHG context: 8693 Total methylated C's in CHH context: 53232 Total methylated C's in Unknown context: 567 Total unmethylated C's in CpG context: 132885 Total unmethylated C's in CHG context: 279697 Total unmethylated C's in CHH context: 855850 Total unmethylated C's in Unknown context: 3088 C methylated in CpG context: 27.4% C methylated in CHG context: 3.0% C methylated in CHH context: 5.9% C methylated in unknown context (CN or CHN): 15.5% Bismark completed in 1d 23h 45m 13s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-168_S11_L002_R1_001_val_1.fq.gz to EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-168_S11_L002_R1_001_val_1.fq.gz to EPI-168_S11_L002_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-168_S11_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-168_S11_L002_R2_001_val_2.fq.gz to EPI-168_S11_L002_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-168_S11_L002_R2_001_val_2.fq.gz to EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-168_S11_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-168_S11_L002_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-168_S11_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1424:2239_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 GTGATNTATAATGTATTATTGAAAGTTAATAGTTTATTTAAGTTTTTGGTATTTTTTGATTTAGGTTTAATTATTTTGTTATGTGGGTTTGTGATTTG BBBBB#B>> Writing bisulfite mapping results to EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 96781 (96.78%) aligned concordantly 0 times 886 (0.89%) aligned concordantly exactly 1 time 2333 (2.33%) aligned concordantly >1 times 3.22% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 96719 (96.72%) aligned concordantly 0 times 899 (0.90%) aligned concordantly exactly 1 time 2382 (2.38%) aligned concordantly >1 times 3.28% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 67845 (67.84%) aligned concordantly 0 times 14173 (14.17%) aligned concordantly exactly 1 time 17982 (17.98%) aligned concordantly >1 times 32.16% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 67364 (67.36%) aligned concordantly 0 times 14282 (14.28%) aligned concordantly exactly 1 time 18354 (18.35%) aligned concordantly >1 times 32.64% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-168_S11_L002_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-168_S11_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1288250 Total methylated C's in CpG context: 47707 Total methylated C's in CHG context: 6030 Total methylated C's in CHH context: 50534 Total methylated C's in Unknown context: 615 Total unmethylated C's in CpG context: 130095 Total unmethylated C's in CHG context: 266530 Total unmethylated C's in CHH context: 787354 Total unmethylated C's in Unknown context: 2798 C methylated in CpG context: 26.8% C methylated in CHG context: 2.2% C methylated in CHH context: 6.0% C methylated in unknown context (CN or CHN): 18.0% Bismark completed in 2d 2h 0m 25s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-169_S12_L002_R1_001_val_1.fq.gz to EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-169_S12_L002_R1_001_val_1.fq.gz to EPI-169_S12_L002_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-169_S12_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-169_S12_L002_R2_001_val_2.fq.gz to EPI-169_S12_L002_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-169_S12_L002_R2_001_val_2.fq.gz to EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-169_S12_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-169_S12_L002_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-169_S12_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1452:2231_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 TGGTANGAGGTTGTGTGATTAGTATAAAGGTGTTTAGAGTTATTAAGTGGATTGGATTGGAGTTTGGATTGGTTTTGTATTAATAAAAGTGTTTTTTTTGT BBBBB#<>> Writing bisulfite mapping results to EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 94314 (94.31%) aligned concordantly 0 times 1416 (1.42%) aligned concordantly exactly 1 time 4270 (4.27%) aligned concordantly >1 times 5.69% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 94353 (94.35%) aligned concordantly 0 times 1422 (1.42%) aligned concordantly exactly 1 time 4225 (4.22%) aligned concordantly >1 times 5.65% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 66311 (66.31%) aligned concordantly 0 times 14236 (14.24%) aligned concordantly exactly 1 time 19453 (19.45%) aligned concordantly >1 times 33.69% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65864 (65.86%) aligned concordantly 0 times 14400 (14.40%) aligned concordantly exactly 1 time 19736 (19.74%) aligned concordantly >1 times 34.14% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-169_S12_L002_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-169_S12_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1210712 Total methylated C's in CpG context: 45834 Total methylated C's in CHG context: 6782 Total methylated C's in CHH context: 54452 Total methylated C's in Unknown context: 731 Total unmethylated C's in CpG context: 121772 Total unmethylated C's in CHG context: 247802 Total unmethylated C's in CHH context: 734070 Total unmethylated C's in Unknown context: 2695 C methylated in CpG context: 27.3% C methylated in CHG context: 2.7% C methylated in CHH context: 6.9% C methylated in unknown context (CN or CHN): 21.3% Bismark completed in 2d 4h 8m 37s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-170_S13_L002_R1_001_val_1.fq.gz to EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-170_S13_L002_R1_001_val_1.fq.gz to EPI-170_S13_L002_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-170_S13_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-170_S13_L002_R2_001_val_2.fq.gz to EPI-170_S13_L002_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-170_S13_L002_R2_001_val_2.fq.gz to EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-170_S13_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-170_S13_L002_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-170_S13_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:2244:2228_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 TTGTTNAGTTTGTTTAAGTTATTTTGATTTGTTAAAAAATATGGTAG BBBBB#<>> Writing bisulfite mapping results to EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 94706 (94.71%) aligned concordantly 0 times 1428 (1.43%) aligned concordantly exactly 1 time 3866 (3.87%) aligned concordantly >1 times 5.29% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 94706 (94.71%) aligned concordantly 0 times 1417 (1.42%) aligned concordantly exactly 1 time 3877 (3.88%) aligned concordantly >1 times 5.29% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 68652 (68.65%) aligned concordantly 0 times 13474 (13.47%) aligned concordantly exactly 1 time 17874 (17.87%) aligned concordantly >1 times 31.35% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 68273 (68.27%) aligned concordantly 0 times 13450 (13.45%) aligned concordantly exactly 1 time 18277 (18.28%) aligned concordantly >1 times 31.73% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-170_S13_L002_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-170_S13_L002_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1096629 Total methylated C's in CpG context: 38504 Total methylated C's in CHG context: 5942 Total methylated C's in CHH context: 42344 Total methylated C's in Unknown context: 587 Total unmethylated C's in CpG context: 113366 Total unmethylated C's in CHG context: 223121 Total unmethylated C's in CHH context: 673352 Total unmethylated C's in Unknown context: 2413 C methylated in CpG context: 25.4% C methylated in CHG context: 2.6% C methylated in CHH context: 5.9% C methylated in unknown context (CN or CHN): 19.6% Bismark completed in 2d 6h 2m 3s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-175_S14_L003_R1_001_val_1.fq.gz to EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-175_S14_L003_R1_001_val_1.fq.gz to EPI-175_S14_L003_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-175_S14_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-175_S14_L003_R2_001_val_2.fq.gz to EPI-175_S14_L003_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-175_S14_L003_R2_001_val_2.fq.gz to EPI-175_S14_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-175_S14_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-175_S14_L003_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-175_S14_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-175_S14_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-175_S14_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:1436:2247_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 AAGAANATGTGTTTGTATGTTGGAAGTTTGTTTAGTGTGG BBBBB#>> Writing bisulfite mapping results to EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 96547 (96.55%) aligned concordantly 0 times 973 (0.97%) aligned concordantly exactly 1 time 2480 (2.48%) aligned concordantly >1 times 3.45% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 96502 (96.50%) aligned concordantly 0 times 942 (0.94%) aligned concordantly exactly 1 time 2556 (2.56%) aligned concordantly >1 times 3.50% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 66042 (66.04%) aligned concordantly 0 times 14798 (14.80%) aligned concordantly exactly 1 time 19160 (19.16%) aligned concordantly >1 times 33.96% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 66165 (66.17%) aligned concordantly 0 times 14864 (14.86%) aligned concordantly exactly 1 time 18971 (18.97%) aligned concordantly >1 times 33.84% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-175_S14_L003_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-175_S14_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-175_S14_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1299008 Total methylated C's in CpG context: 48249 Total methylated C's in CHG context: 6347 Total methylated C's in CHH context: 50137 Total methylated C's in Unknown context: 552 Total unmethylated C's in CpG context: 129776 Total unmethylated C's in CHG context: 262940 Total unmethylated C's in CHH context: 801559 Total unmethylated C's in Unknown context: 2862 C methylated in CpG context: 27.1% C methylated in CHG context: 2.4% C methylated in CHH context: 5.9% C methylated in unknown context (CN or CHN): 16.2% Bismark completed in 2d 8h 16m 11s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-176_S15_L003_R1_001_val_1.fq.gz to EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-176_S15_L003_R1_001_val_1.fq.gz to EPI-176_S15_L003_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-176_S15_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-176_S15_L003_R2_001_val_2.fq.gz to EPI-176_S15_L003_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-176_S15_L003_R2_001_val_2.fq.gz to EPI-176_S15_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-176_S15_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-176_S15_L003_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-176_S15_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-176_S15_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-176_S15_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4405:2246_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 TGTGGNGTAGATGAAGATGTTTGATATGTTGTAGAATATGTAGTTGTAGAGTGTTATTGTGAAGGTGATGTATGTTGTTATTATTGAGAG BBBBB#B>> Writing bisulfite mapping results to EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 96998 (97.00%) aligned concordantly 0 times 943 (0.94%) aligned concordantly exactly 1 time 2059 (2.06%) aligned concordantly >1 times 3.00% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 97034 (97.03%) aligned concordantly 0 times 909 (0.91%) aligned concordantly exactly 1 time 2057 (2.06%) aligned concordantly >1 times 2.97% overall alignment rate 100000 reads; of these: 100000 (100000100.00 reads; of these:% ) were paired; of these: 100000 (69019 (69.02%) aligned concordantly 0 times 100.0013948% () were paired; of these:13.95 % ) aligned concordantly exactly 1 time68752 ( 68.7517033% () aligned concordantly 0 times17.03 % ) aligned concordantly >1 times14081 (30.9814.08%% overall alignment rate) aligned concordantly exactly 1 time 17167 (17.17%) aligned concordantly >1 times 31.25% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-176_S15_L003_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-176_S15_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-176_S15_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1182642 Total methylated C's in CpG context: 42228 Total methylated C's in CHG context: 5395 Total methylated C's in CHH context: 32535 Total methylated C's in Unknown context: 408 Total unmethylated C's in CpG context: 125051 Total unmethylated C's in CHG context: 238162 Total unmethylated C's in CHH context: 739271 Total unmethylated C's in Unknown context: 2546 C methylated in CpG context: 25.2% C methylated in CHG context: 2.2% C methylated in CHH context: 4.2% C methylated in unknown context (CN or CHN): 13.8% Bismark completed in 2d 10h 20m 15s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-181_S16_L003_R1_001_val_1.fq.gz to EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-181_S16_L003_R1_001_val_1.fq.gz to EPI-181_S16_L003_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-181_S16_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-181_S16_L003_R2_001_val_2.fq.gz to EPI-181_S16_L003_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-181_S16_L003_R2_001_val_2.fq.gz to EPI-181_S16_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-181_S16_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-181_S16_L003_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-181_S16_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-181_S16_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-181_S16_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:3117:2249_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 GTTAGNGTTTAAAATATATGTATATTGAATATGTAGTAATTATATAGATAAAGTTTTATTGGTTATAAAATAGGGATGTTTTTAGTTTTGTTGAGTAT BBBBB#>> Writing bisulfite mapping results to EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 96929 (96.93%) aligned concordantly 0 times 844 (0.84%) aligned concordantly exactly 1 time 2227 (2.23%) aligned concordantly >1 times 3.07% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 96956 (96.96%) aligned concordantly 0 times 859 (0.86%) aligned concordantly exactly 1 time 2185 (2.19%) aligned concordantly >1 times 3.04% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 67500 (67.50%) aligned concordantly 0 times 14519 (14.52%) aligned concordantly exactly 1 time 17981 (17.98%) aligned concordantly >1 times 32.50% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 68019 (68.02%) aligned concordantly 0 times 14374 (14.37%) aligned concordantly exactly 1 time 17607 (17.61%) aligned concordantly >1 times 31.98% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-181_S16_L003_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-181_S16_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-181_S16_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1285492 Total methylated C's in CpG context: 49369 Total methylated C's in CHG context: 6583 Total methylated C's in CHH context: 42294 Total methylated C's in Unknown context: 553 Total unmethylated C's in CpG context: 129234 Total unmethylated C's in CHG context: 262943 Total unmethylated C's in CHH context: 795069 Total unmethylated C's in Unknown context: 2891 C methylated in CpG context: 27.6% C methylated in CHG context: 2.4% C methylated in CHH context: 5.1% C methylated in unknown context (CN or CHN): 16.1% Bismark completed in 2d 12h 29m 8s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-182_S17_L003_R1_001_val_1.fq.gz to EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-182_S17_L003_R1_001_val_1.fq.gz to EPI-182_S17_L003_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-182_S17_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-182_S17_L003_R2_001_val_2.fq.gz to EPI-182_S17_L003_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-182_S17_L003_R2_001_val_2.fq.gz to EPI-182_S17_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-182_S17_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-182_S17_L003_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-182_S17_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-182_S17_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-182_S17_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:2786:2250_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 TGATTNTATTATGGAAATATTGTTTAGTTTAGTAGAAATATTTTTTGGAGTTGTTGTGA BBBBB#<>> Writing bisulfite mapping results to EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 96920 (96.92%) aligned concordantly 0 times 931 (0.93%) aligned concordantly exactly 1 time 2149 (2.15%) aligned concordantly >1 times 3.08% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 96953 (96.95%) aligned concordantly 0 times 924 (0.92%) aligned concordantly exactly 1 time 2123 (2.12%) aligned concordantly >1 times 3.05% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65678 (65.68%) aligned concordantly 0 times 15118 (15.12%) aligned concordantly exactly 1 time 19204 (19.20%) aligned concordantly >1 times 34.32% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65889 (65.89%) aligned concordantly 0 times 15305 (15.30%) aligned concordantly exactly 1 time 18806 (18.81%) aligned concordantly >1 times 34.11% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-182_S17_L003_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-182_S17_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-182_S17_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1331400 Total methylated C's in CpG context: 47146 Total methylated C's in CHG context: 6629 Total methylated C's in CHH context: 40870 Total methylated C's in Unknown context: 532 Total unmethylated C's in CpG context: 130388 Total unmethylated C's in CHG context: 268941 Total unmethylated C's in CHH context: 837426 Total unmethylated C's in Unknown context: 3114 C methylated in CpG context: 26.6% C methylated in CHG context: 2.4% C methylated in CHH context: 4.7% C methylated in unknown context (CN or CHN): 14.6% Bismark completed in 2d 14h 48m 28s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-184_S18_L003_R1_001_val_1.fq.gz to EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-184_S18_L003_R1_001_val_1.fq.gz to EPI-184_S18_L003_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-184_S18_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-184_S18_L003_R2_001_val_2.fq.gz to EPI-184_S18_L003_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-184_S18_L003_R2_001_val_2.fq.gz to EPI-184_S18_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-184_S18_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-184_S18_L003_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-184_S18_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-184_S18_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-184_S18_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:2159:2247_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 GAATANGGAAATGGGTAGGATGTAGGTTATAAAGGAAATTGGGTTAATAATGTGAATAGAGAAATGGGTAGGAGGTAGGTTATAAAGGAAATTGGGT BBBBB#B>> Writing bisulfite mapping results to EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 95679 (95.68100000% reads; of these:) aligned concordantly 0 times 1000001254 ( (1.25%) aligned concordantly exactly 1 time 3067 (100.003.07%%) were paired; of these:) aligned concordantly >1 times 4.3295690% ( overall alignment rate95.69 %) aligned concordantly 0 times 1269 (1.27%) aligned concordantly exactly 1 time 3041 (3.04%) aligned concordantly >1 times 4.31% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65307 (65.31%) aligned concordantly 0 times 14644 (14.64%) aligned concordantly exactly 1 time 20049 (20.05%) aligned concordantly >1 times 34.69% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65411 (65.41%) aligned concordantly 0 times 14982 (14.98%) aligned concordantly exactly 1 time 19607 (19.61%) aligned concordantly >1 times 34.59% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-184_S18_L003_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-184_S18_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-184_S18_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1283864 Total methylated C's in CpG context: 48464 Total methylated C's in CHG context: 6495 Total methylated C's in CHH context: 46806 Total methylated C's in Unknown context: 595 Total unmethylated C's in CpG context: 126521 Total unmethylated C's in CHG context: 264415 Total unmethylated C's in CHH context: 791163 Total unmethylated C's in Unknown context: 2996 C methylated in CpG context: 27.7% C methylated in CHG context: 2.4% C methylated in CHH context: 5.6% C methylated in unknown context (CN or CHN): 16.6% Bismark completed in 2d 17h 6m 34s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-185_S19_L003_R1_001_val_1.fq.gz to EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-185_S19_L003_R1_001_val_1.fq.gz to EPI-185_S19_L003_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-185_S19_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-185_S19_L003_R2_001_val_2.fq.gz to EPI-185_S19_L003_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-185_S19_L003_R2_001_val_2.fq.gz to EPI-185_S19_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-185_S19_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-185_S19_L003_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-185_S19_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-185_S19_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-185_S19_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4218:2247_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 GGGGANGGAGAGTTATAGGTAGTTGTAGTGGATATGTTGTGGGATTGAGGATGTTGTGTTGTGTTTTATGGTTTTGGGTTGTTGTTGTAGAGTTGAATTTG BBBBB#B>> Writing bisulfite mapping results to EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 95351 (95.35%) aligned concordantly 0 times 1364 (1.36%) aligned concordantly exactly 1 time 3285 (3.29%) aligned concordantly >1 times 4.65% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 69332 (69.33%) aligned concordantly 0 times 13328 (13.33%) aligned concordantly exactly 1 time 17340 (17.34%) aligned concordantly >1 times 30.67% overall alignment rate100000 reads; of these: 100000 (100.00%) were paired; of these: 95312 (95.31%) aligned concordantly 0 times 1343 (1.34%) aligned concordantly exactly 1 time 3345 (3.35%) aligned concordantly >1 times 4.69% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 68973 (68.97%) aligned concordantly 0 times 13413 (13.41%) aligned concordantly exactly 1 time 17614 (17.61%) aligned concordantly >1 times 31.03% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-185_S19_L003_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-185_S19_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-185_S19_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1211193 Total methylated C's in CpG context: 43601 Total methylated C's in CHG context: 6566 Total methylated C's in CHH context: 53458 Total methylated C's in Unknown context: 788 Total unmethylated C's in CpG context: 125087 Total unmethylated C's in CHG context: 251433 Total unmethylated C's in CHH context: 731048 Total unmethylated C's in Unknown context: 2645 C methylated in CpG context: 25.8% C methylated in CHG context: 2.5% C methylated in CHH context: 6.8% C methylated in unknown context (CN or CHN): 23.0% Bismark completed in 2d 19h 15m 29s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-187_S20_L003_R1_001_val_1.fq.gz to EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-187_S20_L003_R1_001_val_1.fq.gz to EPI-187_S20_L003_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-187_S20_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-187_S20_L003_R2_001_val_2.fq.gz to EPI-187_S20_L003_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-187_S20_L003_R2_001_val_2.fq.gz to EPI-187_S20_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-187_S20_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-187_S20_L003_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-187_S20_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-187_S20_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-187_S20_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:5270:2246_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TAATANATAATTATTTTAGATAATAAGGTTGGAAAAATTGTTGAAATATGGGTTTATTTTTTGTTTTATTGTTTGTAAATTTAGTGTTGAGTTATTGT BBBBB#BBBFFFFFFFFBFFFFFFBBFFF>> Writing bisulfite mapping results to EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 96059 (96.06%) aligned concordantly 0 times 1096 (1.10%) aligned concordantly exactly 1 time 2845 (2.85%) aligned concordantly >1 times 3.94% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64592 (64.59%) aligned concordantly 0 times 15610 (15.61%) aligned concordantly exactly 1 time 19798 (19.80%) aligned concordantly >1 times 35.41% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 95979 (95.98%) aligned concordantly 0 times 1112 (1.11%) aligned concordantly exactly 1 time 2909 (2.91%) aligned concordantly >1 times 4.02% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65080 (65.08%) aligned concordantly 0 times 15582 (15.58%) aligned concordantly exactly 1 time 19338 (19.34%) aligned concordantly >1 times 34.92% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-187_S20_L003_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-187_S20_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-187_S20_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1347498 Total methylated C's in CpG context: 56000 Total methylated C's in CHG context: 7287 Total methylated C's in CHH context: 48471 Total methylated C's in Unknown context: 687 Total unmethylated C's in CpG context: 129714 Total unmethylated C's in CHG context: 277021 Total unmethylated C's in CHH context: 829005 Total unmethylated C's in Unknown context: 2994 C methylated in CpG context: 30.2% C methylated in CHG context: 2.6% C methylated in CHH context: 5.5% C methylated in unknown context (CN or CHN): 18.7% Bismark completed in 2d 21h 35m 32s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-188_S21_L003_R1_001_val_1.fq.gz to EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-188_S21_L003_R1_001_val_1.fq.gz to EPI-188_S21_L003_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-188_S21_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-188_S21_L003_R2_001_val_2.fq.gz to EPI-188_S21_L003_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-188_S21_L003_R2_001_val_2.fq.gz to EPI-188_S21_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-188_S21_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-188_S21_L003_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-188_S21_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-188_S21_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-188_S21_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:6853:2249_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 AGTTGNGGGTAAGAGAGAGTTTTTTTGGAAAATTTTGATATTTTAAAAGTTAAATAATGTATTATAGTAAGTTTTATAGTGTATGAGGGG BBBBB#>> Writing bisulfite mapping results to EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 93194 (93.19%) aligned concordantly 0 times 1804 (1.80%) aligned concordantly exactly 1 time 5002 (5.00%) aligned concordantly >1 times 6.81% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 93093 (93.09%) aligned concordantly 0 times 1829 (1.83%) aligned concordantly exactly 1 time 5078 (5.08%) aligned concordantly >1 times 6.91% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65477 (65.48%) aligned concordantly 0 times 14666 (14.67%) aligned concordantly exactly 1 time 19857 (19.86%) aligned concordantly >1 times 34.52% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65509 (65.51%) aligned concordantly 0 times 14451 (14.45%) aligned concordantly exactly 1 time 20040 (20.04%) aligned concordantly >1 times 34.49% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-188_S21_L003_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-188_S21_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-188_S21_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1138212 Total methylated C's in CpG context: 41493 Total methylated C's in CHG context: 6520 Total methylated C's in CHH context: 42401 Total methylated C's in Unknown context: 699 Total unmethylated C's in CpG context: 117465 Total unmethylated C's in CHG context: 229470 Total unmethylated C's in CHH context: 700863 Total unmethylated C's in Unknown context: 2554 C methylated in CpG context: 26.1% C methylated in CHG context: 2.8% C methylated in CHH context: 5.7% C methylated in unknown context (CN or CHN): 21.5% Bismark completed in 2d 23h 36m 0s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-193_S22_L003_R1_001_val_1.fq.gz to EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-193_S22_L003_R1_001_val_1.fq.gz to EPI-193_S22_L003_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-193_S22_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-193_S22_L003_R2_001_val_2.fq.gz to EPI-193_S22_L003_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-193_S22_L003_R2_001_val_2.fq.gz to EPI-193_S22_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-193_S22_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-193_S22_L003_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-193_S22_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-193_S22_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-193_S22_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:3001:2249_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 ATTGTNTATAATTTTGGTATAGTTTTATGTAGTTGGGGATATTTAGGGATATTGTATATAATTTTGGTATAGTTTTGTAAAGTTAGGGATATTTAGGG /B/BB#//>> Writing bisulfite mapping results to EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 93783 (93.78%) aligned concordantly 0 times 1680 (1.68%) aligned concordantly exactly 1 time 4537 (4.54%) aligned concordantly >1 times 6.22% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 93749 (93.75%) aligned concordantly 0 times 1716 (1.72%) aligned concordantly exactly 1 time 4535 (4.54%) aligned concordantly >1 times 6.25% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64681 (64.68%) aligned concordantly 0 times 15057 (15.06%) aligned concordantly exactly 1 time 20262 (20.26%) aligned concordantly >1 times 35.32% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65049 (65.05%) aligned concordantly 0 times 14966 (14.97%) aligned concordantly exactly 1 time 19985 (19.98%) aligned concordantly >1 times 34.95% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-193_S22_L003_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-193_S22_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-193_S22_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1184436 Total methylated C's in CpG context: 46818 Total methylated C's in CHG context: 6259 Total methylated C's in CHH context: 47129 Total methylated C's in Unknown context: 663 Total unmethylated C's in CpG context: 116014 Total unmethylated C's in CHG context: 239367 Total unmethylated C's in CHH context: 728849 Total unmethylated C's in Unknown context: 2718 C methylated in CpG context: 28.8% C methylated in CHG context: 2.5% C methylated in CHH context: 6.1% C methylated in unknown context (CN or CHN): 19.6% Bismark completed in 3d 1h 42m 48s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-194_S23_L003_R1_001_val_1.fq.gz to EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-194_S23_L003_R1_001_val_1.fq.gz to EPI-194_S23_L003_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-194_S23_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-194_S23_L003_R2_001_val_2.fq.gz to EPI-194_S23_L003_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-194_S23_L003_R2_001_val_2.fq.gz to EPI-194_S23_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-194_S23_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-194_S23_L003_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-194_S23_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-194_S23_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-194_S23_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4438:2247_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 TTAGTNATTAAGGGGTTGTGTGTTTGAATTTTTTGTTTGGTAATAGTTTTTGTGATGATTGATATATGATATTGTGTTTTATTATTATTTGTTTTTTA BBBBB#BBB>> Writing bisulfite mapping results to EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 96743 (96.74%) aligned concordantly 0 times 898 (0.90%) aligned concordantly exactly 1 time 2359 (2.36%) aligned concordantly >1 times 3.26% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 96782 (96.78%) aligned concordantly 0 times 883 (0.88%) aligned concordantly exactly 1 time 2335 (2.33%) aligned concordantly >1 times 3.22% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65424 (65.42%) aligned concordantly 0 times 15505 (15.51%) aligned concordantly exactly 1 time 19071 (19.07%) aligned concordantly >1 times 34.58% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65811 (65.81%) aligned concordantly 0 times 15486 (15.49%) aligned concordantly exactly 1 time 18703 (18.70%) aligned concordantly >1 times 34.19% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-194_S23_L003_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-194_S23_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-194_S23_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1371773 Total methylated C's in CpG context: 56309 Total methylated C's in CHG context: 6811 Total methylated C's in CHH context: 50466 Total methylated C's in Unknown context: 530 Total unmethylated C's in CpG context: 128701 Total unmethylated C's in CHG context: 279332 Total unmethylated C's in CHH context: 850154 Total unmethylated C's in Unknown context: 2960 C methylated in CpG context: 30.4% C methylated in CHG context: 2.4% C methylated in CHH context: 5.6% C methylated in unknown context (CN or CHN): 15.2% Bismark completed in 3d 4h 3m 45s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-199_S24_L003_R1_001_val_1.fq.gz to EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-199_S24_L003_R1_001_val_1.fq.gz to EPI-199_S24_L003_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-199_S24_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-199_S24_L003_R2_001_val_2.fq.gz to EPI-199_S24_L003_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-199_S24_L003_R2_001_val_2.fq.gz to EPI-199_S24_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-199_S24_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-199_S24_L003_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-199_S24_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-199_S24_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-199_S24_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:3720:2249_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 ATTAGNTTTTTATATTTAAGGAGATTGAGAGATATATTGTGAATTTTGAAAGAAAATTGAAAGAGGTTATTGAAGAAAGAGGTATGTG BBBBB#BB>> Writing bisulfite mapping results to EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 93640 (93.64%) aligned concordantly 0 times 1735 (1.74%) aligned concordantly exactly 1 time 4625 (4.62%) aligned concordantly >1 times 6.36% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 93708 (93.71%) aligned concordantly 0 times 1642 (1.64%) aligned concordantly exactly 1 time 4650 (4.65%) aligned concordantly >1 times 6.29% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 66246 (66.25%) aligned concordantly 0 times 14390 (14.39%) aligned concordantly exactly 1 time 19364 (19.36%) aligned concordantly >1 times 33.75% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 66745 (66.75%) aligned concordantly 0 times 14342 (14.34%) aligned concordantly exactly 1 time 18913 (18.91%) aligned concordantly >1 times 33.26% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-199_S24_L003_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-199_S24_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-199_S24_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1207297 Total methylated C's in CpG context: 51102 Total methylated C's in CHG context: 6936 Total methylated C's in CHH context: 57304 Total methylated C's in Unknown context: 889 Total unmethylated C's in CpG context: 114819 Total unmethylated C's in CHG context: 244162 Total unmethylated C's in CHH context: 732974 Total unmethylated C's in Unknown context: 2878 C methylated in CpG context: 30.8% C methylated in CHG context: 2.8% C methylated in CHH context: 7.3% C methylated in unknown context (CN or CHN): 23.6% Bismark completed in 3d 6h 14m 31s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-200_S25_L003_R1_001_val_1.fq.gz to EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-200_S25_L003_R1_001_val_1.fq.gz to EPI-200_S25_L003_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-200_S25_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-200_S25_L003_R2_001_val_2.fq.gz to EPI-200_S25_L003_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-200_S25_L003_R2_001_val_2.fq.gz to EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-200_S25_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4688:2247_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 GTATGNTGTTTATGTGTTTTAGAGGTGGAGTATTGGATTAATGATAA BBBBB#BBFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:3:1107:4688:2247_2:N:0:CTTGTA/2 141 * 0 0 * * 0 0 TTANCANNNNNNNNNNNNNNNNNCTNTNNNNNACATAAACACCATAC BBB#BB#################B<#B#####BBBFFFFFFFFFFFF YT:Z:UP YF:Z:NS Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EPI-200_S25_L003_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4688:2247_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 ATACANTATTTATATATTTTAAAAATAAAATATTAAATTAACAATAA BBBBB#BBFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:3:1107:4688:2247_2:N:0:CTTGTA/2 141 * 0 0 * * 0 0 TTANTGNNNNNNNNNNNNNNNNNTTNTNNNNNATATAAATATTGTAT BBB#BB#################B<#B#####BBBFFFFFFFFFFFF YT:Z:UP YF:Z:NS Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EPI-200_S25_L003_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4688:2247_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 ATACANTATTTATATATTTTAAAAATAAAATATTAAATTAACAATAA BBBBB#BBFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:3:1107:4688:2247_2:N:0:CTTGTA/2 141 * 0 0 * * 0 0 TTANTGNNNNNNNNNNNNNNNNNTTNTNNNNNATATAAATATTGTAT BBB#BB#################B<#B#####BBBFFFFFFFFFFFF YT:Z:UP YF:Z:NS Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4688:2247_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 GTATGNTGTTTATGTGTTTTAGAGGTGGAGTATTGGATTAATGATAA BBBBB#BBFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:3:1107:4688:2247_2:N:0:CTTGTA/2 141 * 0 0 * * 0 0 TTANCANNNNNNNNNNNNNNNNNCTNTNNNNNACATAAACACCATAC BBB#BB#################B<#B#####BBBFFFFFFFFFFFF YT:Z:UP YF:Z:NS >>> Writing bisulfite mapping results to EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 93319 (93.32%) aligned concordantly 0 times 1736 (1.74%) aligned concordantly exactly 1 time 4945 (4.95%) aligned concordantly >1 times 6.68% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 93259 (93.26%) aligned concordantly 0 times 1844 (1.84%) aligned concordantly exactly 1 time 4897 (4.90%) aligned concordantly >1 times 6.74% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 63531 (63.53%) aligned concordantly 0 times 15248 (15.25%) aligned concordantly exactly 1 time 21221 (21.22%) aligned concordantly >1 times 36.47% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 63273 (63.27%) aligned concordantly 0 times 15310 (15.31%) aligned concordantly exactly 1 time 21417 (21.42%) aligned concordantly >1 times 36.73% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-200_S25_L003_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-200_S25_L003_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1220982 Total methylated C's in CpG context: 50023 Total methylated C's in CHG context: 6998 Total methylated C's in CHH context: 51803 Total methylated C's in Unknown context: 697 Total unmethylated C's in CpG context: 114797 Total unmethylated C's in CHG context: 247337 Total unmethylated C's in CHH context: 750024 Total unmethylated C's in Unknown context: 2932 C methylated in CpG context: 30.4% C methylated in CHG context: 2.8% C methylated in CHH context: 6.5% C methylated in unknown context (CN or CHN): 19.2% Bismark completed in 3d 8h 27m 8s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-205_S26_L004_R1_001_val_1.fq.gz to EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-205_S26_L004_R1_001_val_1.fq.gz to EPI-205_S26_L004_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-205_S26_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-205_S26_L004_R2_001_val_2.fq.gz to EPI-205_S26_L004_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-205_S26_L004_R2_001_val_2.fq.gz to EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-205_S26_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-205_S26_L004_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-205_S26_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1391:2218_1:N:0:ATCACG/1 99 PGA_scaffold15__101_contigs__length_47938513_CT_converted 19003108 1 45M = 19003108 -45 GATGTAGGTTGTGGTTGATGGAGAAATATTGGAAGTAGTATTTGT BBBBB/FFFFFFFFFFFFFFFFFFFF>> Writing bisulfite mapping results to EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 91079 (91.08%) aligned concordantly 0 times 2130 (2.13%) aligned concordantly exactly 1 time 6791 (6.79%) aligned concordantly >1 times 8.92% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65431 (65.43%) aligned concordantly 0 times 14304 (14.30%) aligned concordantly exactly 1 time 20265 (20.27%) aligned concordantly >1 times 34.57% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 91117 (91.12%) aligned concordantly 0 times 2129 (2.13%) aligned concordantly exactly 1 time 6754 (6.75%) aligned concordantly >1 times 8.88% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65712 (65.71%) aligned concordantly 0 times 14271 (14.27%) aligned concordantly exactly 1 time 20017 (20.02%) aligned concordantly >1 times 34.29% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-205_S26_L004_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-205_S26_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1097117 Total methylated C's in CpG context: 45280 Total methylated C's in CHG context: 6524 Total methylated C's in CHH context: 51112 Total methylated C's in Unknown context: 748 Total unmethylated C's in CpG context: 111878 Total unmethylated C's in CHG context: 221485 Total unmethylated C's in CHH context: 660838 Total unmethylated C's in Unknown context: 2527 C methylated in CpG context: 28.8% C methylated in CHG context: 2.9% C methylated in CHH context: 7.2% C methylated in unknown context (CN or CHN): 22.8% Bismark completed in 3d 10h 19m 3s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-206_S27_L004_R1_001_val_1.fq.gz to EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-206_S27_L004_R1_001_val_1.fq.gz to EPI-206_S27_L004_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-206_S27_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-206_S27_L004_R2_001_val_2.fq.gz to EPI-206_S27_L004_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-206_S27_L004_R2_001_val_2.fq.gz to EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-206_S27_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-206_S27_L004_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-206_S27_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1645:2233_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 TTATATGAGGTGGTGGTTATATTTTGATTTAATTTGAGGTTTTTTTTATTAATATGATTGG BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF>> Writing bisulfite mapping results to EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 91942 (91.94%) aligned concordantly 0 times 1969 (1.97%) aligned concordantly exactly 1 time 6089 (6.09%) aligned concordantly >1 times 8.06% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 91904 (91.90%) aligned concordantly 0 times 2009 (2.01%) aligned concordantly exactly 1 time 6087 (6.09%) aligned concordantly >1 times 8.10% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 63291 (63.29%) aligned concordantly 0 times 15309 (15.31%) aligned concordantly exactly 1 time 21400 (21.40%) aligned concordantly >1 times 36.71% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 62945 (62.95%) aligned concordantly 0 times 15303 (15.30%) aligned concordantly exactly 1 time 21752 (21.75%) aligned concordantly >1 times 37.05% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-206_S27_L004_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-206_S27_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1251141 Total methylated C's in CpG context: 50142 Total methylated C's in CHG context: 7138 Total methylated C's in CHH context: 52714 Total methylated C's in Unknown context: 752 Total unmethylated C's in CpG context: 127409 Total unmethylated C's in CHG context: 259611 Total unmethylated C's in CHH context: 754127 Total unmethylated C's in Unknown context: 2750 C methylated in CpG context: 28.2% C methylated in CHG context: 2.7% C methylated in CHH context: 6.5% C methylated in unknown context (CN or CHN): 21.5% Bismark completed in 3d 12h 27m 56s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-208_S28_L004_R1_001_val_1.fq.gz to EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-208_S28_L004_R1_001_val_1.fq.gz to EPI-208_S28_L004_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-208_S28_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-208_S28_L004_R2_001_val_2.fq.gz to EPI-208_S28_L004_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-208_S28_L004_R2_001_val_2.fq.gz to EPI-208_S28_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-208_S28_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-208_S28_L004_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-208_S28_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-208_S28_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-208_S28_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1156:2191_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 ATGTTTTATTTTTTAGANATAATAGGTTAANNNTNTNNNNTGTAGTATTTAGNGGTTNGNNNGGAAGAGTATATGTTTGAATTTTAGTTATTTAGGTATTT BBBBBFF>> Writing bisulfite mapping results to EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 91549 (91.55%) aligned concordantly 0 times 2154 (2.15%) aligned concordantly exactly 1 time 6297 (6.30%) aligned concordantly >1 times 8.45% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 91490 (91.49%) aligned concordantly 0 times 2137 (2.14%) aligned concordantly exactly 1 time 6373 (6.37%) aligned concordantly >1 times 8.51% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64852 (64.85%) aligned concordantly 0 times 13775 (13.78%) aligned concordantly exactly 1 time 21373 (21.37%) aligned concordantly >1 times 35.15% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64707 (64.71%) aligned concordantly 0 times 14195 (14.20%) aligned concordantly exactly 1 time 21098 (21.10%) aligned concordantly >1 times 35.29% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-208_S28_L004_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-208_S28_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-208_S28_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1115719 Total methylated C's in CpG context: 39515 Total methylated C's in CHG context: 6616 Total methylated C's in CHH context: 44418 Total methylated C's in Unknown context: 668 Total unmethylated C's in CpG context: 114348 Total unmethylated C's in CHG context: 231412 Total unmethylated C's in CHH context: 679410 Total unmethylated C's in Unknown context: 2805 C methylated in CpG context: 25.7% C methylated in CHG context: 2.8% C methylated in CHH context: 6.1% C methylated in unknown context (CN or CHN): 19.2% Bismark completed in 3d 14h 26m 20s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-209_S29_L004_R1_001_val_1.fq.gz to EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-209_S29_L004_R1_001_val_1.fq.gz to EPI-209_S29_L004_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-209_S29_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-209_S29_L004_R2_001_val_2.fq.gz to EPI-209_S29_L004_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-209_S29_L004_R2_001_val_2.fq.gz to EPI-209_S29_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-209_S29_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-209_S29_L004_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-209_S29_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-209_S29_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-209_S29_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1317:2220_1:N:0:TGACCA/1 99 PGA_scaffold10__49_contigs__length_53961475_CT_converted 32311949 42 87M = 32311949 -87 TAAAGGTATTGGATTAGTTATTGTTGTATGAGTAAAGAATGTATATAATAAATATGATTTTAAATAGTTTTAGTTGATATATTAGGT BB>> Writing bisulfite mapping results to EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 95166 (95.17%) aligned concordantly 0 times 1339 (1.34%) aligned concordantly exactly 1 time 3495 (3.50%) aligned concordantly >1 times 4.83% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64291 (64.29%) aligned concordantly 0 times 15289 (15.29%) aligned concordantly exactly 1 time 20420 (20.42%) aligned concordantly >1 times 35.71% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64651 (64.65%) aligned concordantly 0 times 15336 (15.34%) aligned concordantly exactly 1 time 20013 (20.01%) aligned concordantly >1 times 35.35% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 95135 (95.14%) aligned concordantly 0 times 1302 (1.30%) aligned concordantly exactly 1 time 3563 (3.56%) aligned concordantly >1 times 4.87% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-209_S29_L004_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-209_S29_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-209_S29_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1290862 Total methylated C's in CpG context: 51956 Total methylated C's in CHG context: 6869 Total methylated C's in CHH context: 47541 Total methylated C's in Unknown context: 503 Total unmethylated C's in CpG context: 132069 Total unmethylated C's in CHG context: 265339 Total unmethylated C's in CHH context: 787088 Total unmethylated C's in Unknown context: 2975 C methylated in CpG context: 28.2% C methylated in CHG context: 2.5% C methylated in CHH context: 5.7% C methylated in unknown context (CN or CHN): 14.5% Bismark completed in 3d 16h 37m 56s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-214_S30_L004_R1_001_val_1.fq.gz to EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-214_S30_L004_R1_001_val_1.fq.gz to EPI-214_S30_L004_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-214_S30_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-214_S30_L004_R2_001_val_2.fq.gz to EPI-214_S30_L004_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-214_S30_L004_R2_001_val_2.fq.gz to EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-214_S30_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-214_S30_L004_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-214_S30_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1228:2242_1:N:0:ACAGTG/1 99 PGA_scaffold9__45_contigs__length_38581958_CT_converted 16210783 1 41M = 16210783 -41 TAAGATGTATTTTTATAGTATAATGAAGTATATTTATTTTT BBBBBFFFFFFFFFFFFFFFFBBFFBFFFFFFFFFBFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:41 YS:i:0 YT:Z:CP D00743:144:CAAWNANXX:4:2315:1228:2242_2:N:0:ACAGTG/2 147 PGA_scaffold9__45_contigs__length_38581958_CT_converted 16210783 1 41M = 16210783 -41 TAAGATGTATTTTTATAGTATAATGAAGTATATTTATTTTT FFFFFFFFFFFFFFFFFFBFFFFFFFFFFF>> Writing bisulfite mapping results to EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 95824 (95.82%) aligned concordantly 0 times 1173 (1.17%) aligned concordantly exactly 1 time 3003 (3.00%) aligned concordantly >1 times 4.18% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 95808 (95.81%) aligned concordantly 0 times 1147 (1.15%) aligned concordantly exactly 1 time 3045 (3.04%) aligned concordantly >1 times 4.19% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 66263 (66.26%) aligned concordantly 0 times 14937 (14.94%) aligned concordantly exactly 1 time 18800 (18.80%) aligned concordantly >1 times 33.74% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 66119 (66.12%) aligned concordantly 0 times 14732 (14.73%) aligned concordantly exactly 1 time 19149 (19.15%) aligned concordantly >1 times 33.88% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-214_S30_L004_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-214_S30_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1257148 Total methylated C's in CpG context: 46335 Total methylated C's in CHG context: 6389 Total methylated C's in CHH context: 43971 Total methylated C's in Unknown context: 592 Total unmethylated C's in CpG context: 126604 Total unmethylated C's in CHG context: 255163 Total unmethylated C's in CHH context: 778686 Total unmethylated C's in Unknown context: 2965 C methylated in CpG context: 26.8% C methylated in CHG context: 2.4% C methylated in CHH context: 5.3% C methylated in unknown context (CN or CHN): 16.6% Bismark completed in 3d 18h 50m 29s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-215_S31_L004_R1_001_val_1.fq.gz to EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-215_S31_L004_R1_001_val_1.fq.gz to EPI-215_S31_L004_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-215_S31_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-215_S31_L004_R2_001_val_2.fq.gz to EPI-215_S31_L004_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-215_S31_L004_R2_001_val_2.fq.gz to EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-215_S31_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-215_S31_L004_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-215_S31_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1539:2240_1:N:0:GCCAAT/1 99 PGA_scaffold13__52_contigs__length_44396874_CT_converted 10986848 1 101M = 10986886 137 ATGGTAGTAGAGTGTTGGATTAATATTGGGGTTTGTATGTTTGAGTGTATGGTTTAGTAGTAGAGTGTTGGATTAATATTGGGGGTTGTATGTTTGAGTGT BBBBBFF>> Writing bisulfite mapping results to EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 93127 (93.13%) aligned concordantly 0 times 1797 (1.80%) aligned concordantly exactly 1 time 5076 (5.08%) aligned concordantly >1 times 6.87% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 93076 (93.08%) aligned concordantly 0 times 1760 (1.76%) aligned concordantly exactly 1 time 5164 (5.16%) aligned concordantly >1 times 6.92% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 63291 (63.29%) aligned concordantly 0 times 15618 (15.62%) aligned concordantly exactly 1 time 21091 (21.09%) aligned concordantly >1 times 36.71% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 62712 (62.71%) aligned concordantly 0 times 15777 (15.78%) aligned concordantly exactly 1 time 21511 (21.51%) aligned concordantly >1 times 37.29% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-215_S31_L004_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-215_S31_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1267261 Total methylated C's in CpG context: 55024 Total methylated C's in CHG context: 7467 Total methylated C's in CHH context: 51124 Total methylated C's in Unknown context: 726 Total unmethylated C's in CpG context: 119794 Total unmethylated C's in CHG context: 257247 Total unmethylated C's in CHH context: 776605 Total unmethylated C's in Unknown context: 2910 C methylated in CpG context: 31.5% C methylated in CHG context: 2.8% C methylated in CHH context: 6.2% C methylated in unknown context (CN or CHN): 20.0% Bismark completed in 3d 21h 0m 18s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-220_S32_L004_R1_001_val_1.fq.gz to EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-220_S32_L004_R1_001_val_1.fq.gz to EPI-220_S32_L004_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-220_S32_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-220_S32_L004_R2_001_val_2.fq.gz to EPI-220_S32_L004_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-220_S32_L004_R2_001_val_2.fq.gz to EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-220_S32_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-220_S32_L004_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-220_S32_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1490:2220_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TTTTTTGGTTGTTGTATGGTGTTGTTGTATAGTGTTGTGGTGTTGTTGTATGGTGTTGGTATATGGTGTTGTGGTGTTATGTATGGTGTTGTGGTGTTGGT BBBBBFFFFFFBFFFFFFF/BFFFFFBF/FFFFFFFFFFFBF>> Writing bisulfite mapping results to EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 95117 (95.12%) aligned concordantly 0 times 1441 (1.44%) aligned concordantly exactly 1 time 3442 (3.44%) aligned concordantly >1 times 4.88% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 95245 (95.25%) aligned concordantly 0 times 1368 (1.37%) aligned concordantly exactly 1 time 3387 (3.39%) aligned concordantly >1 times 4.75% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65057 (65.06%) aligned concordantly 0 times 15050 (15.05%) aligned concordantly exactly 1 time 19893 (19.89%) aligned concordantly >1 times 34.94% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65432 (65.43%) aligned concordantly 0 times 15004 (15.00%) aligned concordantly exactly 1 time 19564 (19.56%) aligned concordantly >1 times 34.57% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-220_S32_L004_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-220_S32_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1288026 Total methylated C's in CpG context: 50434 Total methylated C's in CHG context: 7171 Total methylated C's in CHH context: 49935 Total methylated C's in Unknown context: 695 Total unmethylated C's in CpG context: 126689 Total unmethylated C's in CHG context: 262459 Total unmethylated C's in CHH context: 791338 Total unmethylated C's in Unknown context: 2982 C methylated in CpG context: 28.5% C methylated in CHG context: 2.7% C methylated in CHH context: 5.9% C methylated in unknown context (CN or CHN): 18.9% Bismark completed in 3d 23h 12m 34s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-221_S33_L004_R1_001_val_1.fq.gz to EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-221_S33_L004_R1_001_val_1.fq.gz to EPI-221_S33_L004_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-221_S33_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-221_S33_L004_R2_001_val_2.fq.gz to EPI-221_S33_L004_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-221_S33_L004_R2_001_val_2.fq.gz to EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-221_S33_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-221_S33_L004_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-221_S33_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1412:2190_1:N:0:ACTTGA/1 99 PGA_scaffold13__52_contigs__length_44396874_CT_converted 41856358 2 98M = 41856393 133 ATTTTNTGTTTTATGTTTTATTTTTATTTTAGTGTTTGAAAAAATTTTGGAGAAAGGTAGATATTTTTTAGTGGTTGTAAAAAATATAAGTTGGATTG BBBBB#BBBBFFFFFFFFFFFFFFFFFFFFFBF7FFFFF>> Writing bisulfite mapping results to EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 92670 (92.67%) aligned concordantly 0 times 2002 (2.00%) aligned concordantly exactly 1 time 5328 (5.33%) aligned concordantly >1 times 7.33% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 92772 (92.77%) aligned concordantly 0 times 1947 (1.95%) aligned concordantly exactly 1 time 5281 (5.28%) aligned concordantly >1 times 7.23% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 63252 (63.25%) aligned concordantly 0 times 15488 (15.49%) aligned concordantly exactly 1 time 21260 (21.26%) aligned concordantly >1 times 36.75% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 62718 (62.72%) aligned concordantly 0 times 15583 (15.58%) aligned concordantly exactly 1 time 21699 (21.70%) aligned concordantly >1 times 37.28% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-221_S33_L004_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-221_S33_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1257487 Total methylated C's in CpG context: 51006 Total methylated C's in CHG context: 7464 Total methylated C's in CHH context: 49314 Total methylated C's in Unknown context: 707 Total unmethylated C's in CpG context: 121319 Total unmethylated C's in CHG context: 256081 Total unmethylated C's in CHH context: 772303 Total unmethylated C's in Unknown context: 2928 C methylated in CpG context: 29.6% C methylated in CHG context: 2.8% C methylated in CHH context: 6.0% C methylated in unknown context (CN or CHN): 19.4% Bismark completed in 4d 1h 25m 56s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-226_S34_L004_R1_001_val_1.fq.gz to EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-226_S34_L004_R1_001_val_1.fq.gz to EPI-226_S34_L004_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-226_S34_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-226_S34_L004_R2_001_val_2.fq.gz to EPI-226_S34_L004_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-226_S34_L004_R2_001_val_2.fq.gz to EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-226_S34_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-226_S34_L004_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-226_S34_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1168:2235_1:N:0:GATCAG/1 99 PGA_scaffold9__45_contigs__length_38581958_CT_converted 21134968 1 84M = 21134968 -84 TTATATTATATTTTATANTGTGTAAAGTTGTNGTTAAGTGATTTATATTTGTNGTATTTTNNTTGTTATTGTTTATATAGTGGG BBBBBFFFFFFFFFFBF#BB>> Writing bisulfite mapping results to EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 95794 (95.79%) aligned concordantly 0 times 1168 (1.17%) aligned concordantly exactly 1 time 3038 (3.04%) aligned concordantly >1 times 4.21% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 95817 (95.82%) aligned concordantly 0 times 1152 (1.15%) aligned concordantly exactly 1 time 3031 (3.03%) aligned concordantly >1 times 4.18% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65660 (65.66%) aligned concordantly 0 times 15159 (15.16%) aligned concordantly exactly 1 time 19181 (19.18%) aligned concordantly >1 times 34.34% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65034 (65.03%) aligned concordantly 0 times 15329 (15.33%) aligned concordantly exactly 1 time 19637 (19.64%) aligned concordantly >1 times 34.97% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-226_S34_L004_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-226_S34_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1345209 Total methylated C's in CpG context: 54864 Total methylated C's in CHG context: 7262 Total methylated C's in CHH context: 53779 Total methylated C's in Unknown context: 739 Total unmethylated C's in CpG context: 128231 Total unmethylated C's in CHG context: 272857 Total unmethylated C's in CHH context: 828216 Total unmethylated C's in Unknown context: 3090 C methylated in CpG context: 30.0% C methylated in CHG context: 2.6% C methylated in CHH context: 6.1% C methylated in unknown context (CN or CHN): 19.3% Bismark completed in 4d 3h 42m 23s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-227_S35_L004_R1_001_val_1.fq.gz to EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-227_S35_L004_R1_001_val_1.fq.gz to EPI-227_S35_L004_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-227_S35_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-227_S35_L004_R2_001_val_2.fq.gz to EPI-227_S35_L004_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-227_S35_L004_R2_001_val_2.fq.gz to EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-227_S35_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-227_S35_L004_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-227_S35_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1203:2205_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 TTTGTTTTTTTTTATATATAAATTATTAATTAAATAATTTAATTTTGTAAAANTTGTAAAANTATATAAATATTTATGTATTATTTTAATATTTTATAGTT BBBBB>> Writing bisulfite mapping results to EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 94484 (94.48%) aligned concordantly 0 times 1558 (1.56%) aligned concordantly exactly 1 time 3958 (3.96%) aligned concordantly >1 times 5.52% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 94495 (94.50%) aligned concordantly 0 times 1511 (1.51%) aligned concordantly exactly 1 time 3994 (3.99%) aligned concordantly >1 times 5.50% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 63458 (63.46%) aligned concordantly 0 times 15691 (15.69%) aligned concordantly exactly 1 time 20851 (20.85%) aligned concordantly >1 times 36.54% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 62964 (62.96%) aligned concordantly 0 times 15935 (15.94%) aligned concordantly exactly 1 time 21101 (21.10%) aligned concordantly >1 times 37.04% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-227_S35_L004_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-227_S35_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1329207 Total methylated C's in CpG context: 53928 Total methylated C's in CHG context: 7314 Total methylated C's in CHH context: 51209 Total methylated C's in Unknown context: 647 Total unmethylated C's in CpG context: 126519 Total unmethylated C's in CHG context: 269265 Total unmethylated C's in CHH context: 820972 Total unmethylated C's in Unknown context: 2980 C methylated in CpG context: 29.9% C methylated in CHG context: 2.6% C methylated in CHH context: 5.9% C methylated in unknown context (CN or CHN): 17.8% Bismark completed in 4d 6h 1m 40s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-229_S36_L004_R1_001_val_1.fq.gz to EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-229_S36_L004_R1_001_val_1.fq.gz to EPI-229_S36_L004_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-229_S36_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-229_S36_L004_R2_001_val_2.fq.gz to EPI-229_S36_L004_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-229_S36_L004_R2_001_val_2.fq.gz to EPI-229_S36_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-229_S36_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-229_S36_L004_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-229_S36_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-229_S36_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-229_S36_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1979:2198_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 TGTATAGTATAGTTTAGTGTTGTGGTTAGTTTTAATATAGAAATATTAATTTTAATTTAATGTGATGTATTTAGAAAGTTTTAGAAAGTTTGTGGTAG B/BBBFFFF>> Writing bisulfite mapping results to EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 94739 (94.74%) aligned concordantly 0 times 1445 (1.45%) aligned concordantly exactly 1 time 3816 (3.82%) aligned concordantly >1 times 5.26% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 94668 (94.67%) aligned concordantly 0 times 1473 (1.47%) aligned concordantly exactly 1 time 3859 (3.86%) aligned concordantly >1 times 5.33% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65463 (65.46%) aligned concordantly 0 times 14833 (14.83%) aligned concordantly exactly 1 time 19704 (19.70%) aligned concordantly >1 times 34.54% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65262 (65.26%) aligned concordantly 0 times 14686 (14.69%) aligned concordantly exactly 1 time 20052 (20.05%) aligned concordantly >1 times 34.74% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-229_S36_L004_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-229_S36_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-229_S36_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1242008 Total methylated C's in CpG context: 48297 Total methylated C's in CHG context: 6642 Total methylated C's in CHH context: 50565 Total methylated C's in Unknown context: 714 Total unmethylated C's in CpG context: 127128 Total unmethylated C's in CHG context: 255980 Total unmethylated C's in CHH context: 753396 Total unmethylated C's in Unknown context: 2903 C methylated in CpG context: 27.5% C methylated in CHG context: 2.5% C methylated in CHH context: 6.3% C methylated in unknown context (CN or CHN): 19.7% Bismark completed in 4d 8h 8m 54s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-230_S37_L004_R1_001_val_1.fq.gz to EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-230_S37_L004_R1_001_val_1.fq.gz to EPI-230_S37_L004_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-230_S37_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-230_S37_L004_R2_001_val_2.fq.gz to EPI-230_S37_L004_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-230_S37_L004_R2_001_val_2.fq.gz to EPI-230_S37_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-230_S37_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-230_S37_L004_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-230_S37_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-230_S37_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-230_S37_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1161:2210_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 ATTTTGTATATGGTATANATTTAGTTTGATTNNTNANATNGGTGAATGATGTNGTATATNNNTTGTTTGATTGGTAAAATGGGTGAATGATGTTATATATG BBBBBFFFFFFFFFFFF#B<>> Writing bisulfite mapping results to EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 94814 (94.81%) aligned concordantly 0 times 1511 (1.51%) aligned concordantly exactly 1 time 3675 (3.67%) aligned concordantly >1 times 5.19% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 94809 (94.81%) aligned concordantly 0 times 1462 (1.46%) aligned concordantly exactly 1 time 3729 (3.73%) aligned concordantly >1 times 5.19% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 66801 (66.80%) aligned concordantly 0 times 14177 (14.18%) aligned concordantly exactly 1 time 19022 (19.02%) aligned concordantly >1 times 33.20% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 67186 (67.19%) aligned concordantly 0 times 14009 (14.01%) aligned concordantly exactly 1 time 18805 (18.80%) aligned concordantly >1 times 32.81% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-230_S37_L004_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-230_S37_L004_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-230_S37_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1138403 Total methylated C's in CpG context: 44328 Total methylated C's in CHG context: 5844 Total methylated C's in CHH context: 44270 Total methylated C's in Unknown context: 609 Total unmethylated C's in CpG context: 115184 Total unmethylated C's in CHG context: 230009 Total unmethylated C's in CHH context: 698768 Total unmethylated C's in Unknown context: 2555 C methylated in CpG context: 27.8% C methylated in CHG context: 2.5% C methylated in CHH context: 6.0% C methylated in unknown context (CN or CHN): 19.2% Bismark completed in 4d 10h 14m 58s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-41_S38_L005_R1_001_val_1.fq.gz to EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-41_S38_L005_R1_001_val_1.fq.gz to EPI-41_S38_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-41_S38_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-41_S38_L005_R2_001_val_2.fq.gz to EPI-41_S38_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-41_S38_L005_R2_001_val_2.fq.gz to EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-41_S38_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1186:2238_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 GTAGTNTTGGTTGGAATATATATTGTATTGTTATTTGTATTTGGTATATAAGNGGTATNGTNGTTGGTGTTTGGTGTGTAAGTAGTATTGTTGTTGGAGTT BBBBB#>> Writing bisulfite mapping results to EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 93477 (93.48%) aligned concordantly 0 times 1717 (1.72%) aligned concordantly exactly 1 time 4806 (4.81%) aligned concordantly >1 times 6.52% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 93316 (93.32%) aligned concordantly 0 times 1833 (1.83%) aligned concordantly exactly 1 time 4851 (4.85%) aligned concordantly >1 times 6.68% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 65010 (65.01%) aligned concordantly 0 times 15264 (15.26%) aligned concordantly exactly 1 time 19726 (19.73%) aligned concordantly >1 times 34.99% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 64786 (64.79%) aligned concordantly 0 times 15033 (15.03%) aligned concordantly exactly 1 time 20181 (20.18%) aligned concordantly >1 times 35.21% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-41_S38_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-41_S38_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1224292 Total methylated C's in CpG context: 52008 Total methylated C's in CHG context: 6689 Total methylated C's in CHH context: 49368 Total methylated C's in Unknown context: 845 Total unmethylated C's in CpG context: 115136 Total unmethylated C's in CHG context: 246587 Total unmethylated C's in CHH context: 754504 Total unmethylated C's in Unknown context: 2783 C methylated in CpG context: 31.1% C methylated in CHG context: 2.6% C methylated in CHH context: 6.1% C methylated in unknown context (CN or CHN): 23.3% Bismark completed in 4d 12h 25m 34s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-42_S39_L005_R1_001_val_1.fq.gz to EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-42_S39_L005_R1_001_val_1.fq.gz to EPI-42_S39_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-42_S39_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-42_S39_L005_R2_001_val_2.fq.gz to EPI-42_S39_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-42_S39_L005_R2_001_val_2.fq.gz to EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-42_S39_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1597:2224_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 AGGTANTATGATGTGATGATGGGGTATGATGTGAAGATGGG BBBBB#BBFFFFFFFFFFFFFFFFBFFBFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:5:1107:1597:2224_2:N:0:CGATGT/2 141 * 0 0 * * 0 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNCCT ####################################<#<>> Writing bisulfite mapping results to EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 93240 (93.24%) aligned concordantly 0 times 1615 (1.61%) aligned concordantly exactly 1 time 5145 (5.14%) aligned concordantly >1 times 6.76% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 93253 (93.25%) aligned concordantly 0 times 1677 (1.68%) aligned concordantly exactly 1 time 5070 (5.07%) aligned concordantly >1 times 6.75% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 61499 (61.50%) aligned concordantly 0 times 16436 (16.44%) aligned concordantly exactly 1 time 22065 (22.07%) aligned concordantly >1 times 38.50% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 61232 (61.23%) aligned concordantly 0 times 16526 (16.53%) aligned concordantly exactly 1 time 22242 (22.24%) aligned concordantly >1 times 38.77% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-42_S39_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-42_S39_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1314425 Total methylated C's in CpG context: 58632 Total methylated C's in CHG context: 7688 Total methylated C's in CHH context: 57277 Total methylated C's in Unknown context: 705 Total unmethylated C's in CpG context: 120145 Total unmethylated C's in CHG context: 264343 Total unmethylated C's in CHH context: 806340 Total unmethylated C's in Unknown context: 3015 C methylated in CpG context: 32.8% C methylated in CHG context: 2.8% C methylated in CHH context: 6.6% C methylated in unknown context (CN or CHN): 19.0% Bismark completed in 4d 14h 37m 10s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-43_S40_L005_R1_001_val_1.fq.gz to EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-43_S40_L005_R1_001_val_1.fq.gz to EPI-43_S40_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-43_S40_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-43_S40_L005_R2_001_val_2.fq.gz to EPI-43_S40_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-43_S40_L005_R2_001_val_2.fq.gz to EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-43_S40_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1481:2240_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 TTTTAATATTAATATATTAAAATATAAAATTTTTATAATTATAATATATATAAATATTATAATATTAATATATTAATATAAAAATTTTATATAATTATAAT BBBBBFF>> Writing bisulfite mapping results to EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 94256 (94.26%) aligned concordantly 0 times 1637 (1.64%) aligned concordantly exactly 1 time 4107 (4.11%) aligned concordantly >1 times 5.74% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 94224 (94.22%) aligned concordantly 0 times 1645 (1.65%) aligned concordantly exactly 1 time 4131 (4.13%) aligned concordantly >1 times 5.78% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 61790 (61.79%) aligned concordantly 0 times 16604 (16.60%) aligned concordantly exactly 1 time 21606 (21.61%) aligned concordantly >1 times 38.21% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 61707 (61.71%) aligned concordantly 0 times 16933 (16.93%) aligned concordantly exactly 1 time 21360 (21.36%) aligned concordantly >1 times 38.29% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-43_S40_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-43_S40_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1338618 Total methylated C's in CpG context: 56405 Total methylated C's in CHG context: 6815 Total methylated C's in CHH context: 48427 Total methylated C's in Unknown context: 650 Total unmethylated C's in CpG context: 126578 Total unmethylated C's in CHG context: 269457 Total unmethylated C's in CHH context: 830936 Total unmethylated C's in Unknown context: 2904 C methylated in CpG context: 30.8% C methylated in CHG context: 2.5% C methylated in CHH context: 5.5% C methylated in unknown context (CN or CHN): 18.3% Bismark completed in 4d 16h 54m 23s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-44_S41_L005_R1_001_val_1.fq.gz to EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-44_S41_L005_R1_001_val_1.fq.gz to EPI-44_S41_L005_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-44_S41_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file EPI-44_S41_L005_R2_001_val_2.fq.gz to EPI-44_S41_L005_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file EPI-44_S41_L005_R2_001_val_2.fq.gz to EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file EPI-44_S41_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R1_001_val_1.fq.gz_G_to_A.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1348:2233_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 AATTTNGGTGTATAGTTTAAGTTAGGAAAGTTTTTTTTATTAAATTGTTTTGTTATGTTTAAATAGATATTTTTTTGGTAGTAT BBBBB#/B>> Writing bisulfite mapping results to EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 92595 (92.59%) aligned concordantly 0 times 1883 (1.88%) aligned concordantly exactly 1 time 5522 (5.52%) aligned concordantly >1 times 7.41% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 92671 (92.67%) aligned concordantly 0 times 1860 (1.86%) aligned concordantly exactly 1 time 5469 (5.47%) aligned concordantly >1 times 7.33% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 61344 (61.34%) aligned concordantly 0 times 16726 (16.73%) aligned concordantly exactly 1 time 21930 (21.93%) aligned concordantly >1 times 38.66% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 61669 (61.67%) aligned concordantly 0 times 16672 (16.67%) aligned concordantly exactly 1 time 21659 (21.66%) aligned concordantly >1 times 38.33% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq, EPI-44_S41_L005_R1_001_val_1.fq.gz_G_to_A.fastq, EPI-44_S41_L005_R2_001_val_2.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1290068 Total methylated C's in CpG context: 59321 Total methylated C's in CHG context: 7220 Total methylated C's in CHH context: 48280 Total methylated C's in Unknown context: 751 Total unmethylated C's in CpG context: 117391 Total unmethylated C's in CHG context: 257855 Total unmethylated C's in CHH context: 800001 Total unmethylated C's in Unknown context: 2747 C methylated in CpG context: 33.6% C methylated in CHG context: 2.7% C methylated in CHH context: 5.7% C methylated in unknown context (CN or CHN): 21.5% Bismark completed in 4d 19h 8m 23s ==================== Bismark run complete ====================