Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/srlab/programs/samtools-1.20/samtools' Reference genome folder provided is ../../data/genome/ (absolute path is '/mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/data/genome/)' FastQ format assumed (by default) Processing sequences up to read no. 10000 from the input file Attention: early reports suggested that high values of -p to have diminishing returns. Please test different values using a small subset of data for your hardware setting. Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/output/04.2-bismark-align'): ../../data/CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz ../../data/CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Output will be written into the directory: /mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/output/04.2-bismark-align/CF05-CM05-Zygote_score_L-1-0.6/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,-1,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/output/04.2-bismark-align Now reading in and storing sequence information of the genome specified in: /mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/data/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are ../../data/CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz and ../../data/CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from ../../data/CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz Writing a C -> T converted version of the input file CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz to CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz to CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz (10001 sequences in total) Processing reads up to sequence no. 10000 from ../../data/CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz Writing a C -> T converted version of the input file CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz to CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz to CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz (10001 sequences in total) Input files are CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/data/genome/ with the specified options: -q --score-min L,-1,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz_G_to_A.fastq, with the options: -q --score-min L,-1,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25509:1047_1:N:0:AGTTCAGG+TCTGTTGG/1 99 NC_035783.1_CT_converted 31850541 0 80M1D6M = 31850541 87 TNTTTTTTTTTTAGTATATATATTTATTTTTGAGTAAAGTTAAGTATAGGAAAAAAAGGAAATAGTTGTATTTTATTGAAATTTAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F,FFFFFFF::F,FF:FFFFFF:FFFFFFFFFFFFFF:F:FFFFFFFFFFFFF AS:i:-21 XS:i:-21 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:1A0A44G32^T6 YS:i:-26 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25509:1047_2:N:0:AGTTCAGG+TCTGTTGG/2 147 NC_035783.1_CT_converted 31850541 0 80M1D6M = 31850541 -87 TTTTTTTTTTTTAGTATATATATTTATTTTTGAGTAAAGTTAAGTATAGGAAAAAAAGGAAATAGTTGTATTTTATTGAAATTTAT FFFFFFFFF:FFFFFFF,FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-26 XS:i:-26 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:1A0A44G32^T6 YS:i:-21 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq, with the options: -q --score-min L,-1,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25509:1047_1:N:0:AGTTCAGG+TCTGTTGG/1 77 * 0 0 * * 0 0 TNTTTTTTTTTCAATACATATATTTATTTTTAAATAAAATTAAATATAAAAAAAAAAAAAAATAATTATATTTTATTAAAATTTAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F,FFFFFFF::F,FF:FFFFFF:FFFFFFFFFFFFFF:F:FFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25509:1047_2:N:0:AGTTCAGG+TCTGTTGG/2 141 * 0 0 * * 0 0 GTAAATTTTAATAAAATATAATTATTTTTTTTTTTTTTTATATTTAATTTTATTTAAAAATAAATATATGTATTGAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF,FFFFFFF:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq, with the options: -q --score-min L,-1,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25509:1047_1:N:0:AGTTCAGG+TCTGTTGG/1 77 * 0 0 * * 0 0 TNTTTTTTTTTCAATACATATATTTATTTTTAAATAAAATTAAATATAAAAAAAAAAAAAAATAATTATATTTTATTAAAATTTAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F,FFFFFFF::F,FF:FFFFFF:FFFFFFFFFFFFFF:F:FFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25509:1047_2:N:0:AGTTCAGG+TCTGTTGG/2 141 * 0 0 * * 0 0 GTAAATTTTAATAAAATATAATTATTTTTTTTTTTTTTTATATTTAATTTTATTTAAAAATAAATATATGTATTGAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF,FFFFFFF:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz_G_to_A.fastq, with the options: -q --score-min L,-1,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25509:1047_1:N:0:AGTTCAGG+TCTGTTGG/1 83 NC_035780.1_GA_converted 36883175 2 6M1D80M = 36883175 -87 ATAAATTTCAATAAAATACAACTATTTCCTTTTTTTCCTATACTTAACTTTACTCAAAAATAAATATATATACTAAAAAAAAAANA FFFFFFFFFFFFF:F:FFFFFFFFFFFFFF:FFFFFF:FF,F::FFFFFFF,F:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-15 XS:i:-21 XN:i:0 XM:i:2 XO:i:1 XG:i:1 NM:i:3 MD:Z:6^A77T0T1 YS:i:-20 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25509:1047_2:N:0:AGTTCAGG+TCTGTTGG/2 163 NC_035780.1_GA_converted 36883175 2 6M1D80M = 36883175 87 ATAAATTTCAATAAAATACAACTATTTCCTTTTTTTCCTATACTTAACTTTACTCAAAAATAAATATATATACTAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF,FFFFFFF:FFFFFFFFF AS:i:-20 XS:i:-20 XN:i:0 XM:i:2 XO:i:1 XG:i:1 NM:i:3 MD:Z:6^A77T0T1 YS:i:-15 YT:Z:CP >>> Writing bisulfite mapping results to CF05-CM05-Zygote_L-1-0.6_pe.bam <<< Reading in the sequence files ../../data/CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz and ../../data/CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz 10000 reads; of these: 10000 (100.00%) were paired; of these: 8661 (86.61%) aligned concordantly 0 times 622 (6.22%) aligned concordantly exactly 1 time 717 (7.17%) aligned concordantly >1 times 13.39% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8737 (87.37%) aligned concordantly 0 times 590 (5.90%) aligned concordantly exactly 1 time 673 (6.73%) aligned concordantly >1 times 12.63% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8810 (88.10%) aligned concordantly 0 times 515 (5.15%) aligned concordantly exactly 1 time 675 (6.75%) aligned concordantly >1 times 11.90% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 8663 (86.63%) aligned concordantly 0 times 619 (6.19%) aligned concordantly exactly 1 time 718 (7.18%) aligned concordantly >1 times 13.37% overall alignment rate Processed 10000 sequences in total Successfully deleted the temporary files CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq, CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq, CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 86115 Total methylated C's in CpG context: 2651 Total methylated C's in CHG context: 620 Total methylated C's in CHH context: 2411 Total methylated C's in Unknown context: 115 Total unmethylated C's in CpG context: 9335 Total unmethylated C's in CHG context: 17363 Total unmethylated C's in CHH context: 53735 Total unmethylated C's in Unknown context: 605 C methylated in CpG context: 22.1% C methylated in CHG context: 3.4% C methylated in CHH context: 4.3% C methylated in Unknown context (CN or CHN): 16.0% Bismark completed in 0d 0h 0m 14s ==================== Bismark run complete ====================