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/ (absolute path is '/mmfs1/gscratch/srlab/sr320/github/timeseries_molecular/E-Peve/data/)' 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 10 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/mmfs1/gscratch/srlab/sr320/github/timeseries_molecular/E-Peve/output/04-Peve-bismark-array'): ../../data/03-Peve-bismark/POR-216-TP3_R1_001.fastp-trim.fq.gz ../../data/03-Peve-bismark/POR-216-TP3_R2_001.fastp-trim.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Output will be written into the directory: /mmfs1/gscratch/srlab/sr320/github/timeseries_molecular/E-Peve/output/04-Peve-bismark-array/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 10 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /mmfs1/gscratch/srlab/sr320/github/timeseries_molecular/E-Peve/output/04-Peve-bismark-array Now reading in and storing sequence information of the genome specified in: /mmfs1/gscratch/srlab/sr320/github/timeseries_molecular/E-Peve/data/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are ../../data/03-Peve-bismark/POR-216-TP3_R1_001.fastp-trim.fq.gz and ../../data/03-Peve-bismark/POR-216-TP3_R2_001.fastp-trim.fq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from ../../data/03-Peve-bismark/POR-216-TP3_R1_001.fastp-trim.fq.gz Writing a C -> T converted version of the input file POR-216-TP3_R1_001.fastp-trim.fq.gz to POR-216-TP3_R1_001.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file POR-216-TP3_R1_001.fastp-trim.fq.gz (10001 sequences in total) Processing reads up to sequence no. 10000 from ../../data/03-Peve-bismark/POR-216-TP3_R2_001.fastp-trim.fq.gz Writing a G -> A converted version of the input file POR-216-TP3_R2_001.fastp-trim.fq.gz to POR-216-TP3_R2_001.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file POR-216-TP3_R2_001.fastp-trim.fq.gz (10001 sequences in total) Input files are POR-216-TP3_R1_001.fastp-trim.fq.gz_C_to_T.fastq and POR-216-TP3_R2_001.fastp-trim.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/srlab/sr320/github/timeseries_molecular/E-Peve/data/ with the specified options: -q --score-min L,0,-0.6 -p 10 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from POR-216-TP3_R1_001.fastp-trim.fq.gz_C_to_T.fastq and POR-216-TP3_R2_001.fastp-trim.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 10 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:49116:1056_1:N:0:GAACGGTT+ATTCCTCC/1 99 Porites_evermani_scaffold_2446_CT_converted 67224 8 135M = 67292 205 AAAAATTGTGATTTTTGTAATTTTTTTAAAAATTGTAAAAAATTGGAGAAATTTTAGTTTTTGTTAAAATTAATTAAGTTAAGTGTTATAGGAGGTAGAAGGGTGTTTAGTAAAAATTTGGATTTTTGTAATTTG IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III-IIIII9IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9-II AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:48G4G64G8A6T0 YS:i:-53 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49116:1056_2:N:0:GAACGGTT+ATTCCTCC/2 147 Porites_evermani_scaffold_2446_CT_converted 67292 8 93M2D42M = 67224 -205 ATTAATTAAGTTAAGTGTTATAGGAGGTAGAAGGGTGTTTAGTAAAAATTTGGATTTTTGTAATTTGTGGGGTTTGTTAAAAAAATTGTGAAAAATAAGGAATAATTGTAATGATTTGTGATGGGTATTTTGTTT IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIII9IIIIIIIIII9IIII9IIII9IIIII9-IIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-53 XN:i:0 XM:i:7 XO:i:1 XG:i:2 NM:i:9 MD:Z:50G8A6T26^TT0G23A2G1A12 YS:i:-30 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from POR-216-TP3_R1_001.fastp-trim.fq.gz_C_to_T.fastq and POR-216-TP3_R2_001.fastp-trim.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 10 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:49116:1056_1:N:0:GAACGGTT+ATTCCTCC/1 83 Porites_evermani_scaffold_2160_GA_converted 15973 8 135M = 15905 -203 CAAATTACAAAAATCCAAATTTTTACTAAACACCCTTCTACCTCCTATAACACTTAACTTAATTAATTTTAACAAAAACTAAAATTTCTCCAATTTTTTACAATTTTTAAAAAAATTACAAAAATCACAATTTTT II-9IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9IIIII-III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII AS:i:-36 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:0A14A0C59T2C1C53 YS:i:-48 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49116:1056_2:N:0:GAACGGTT+ATTCCTCC/2 163 Porites_evermani_scaffold_2160_GA_converted 15905 8 135M = 15973 203 AAACAAAATACCCATCACAAATCATTACAATTATTCCTTATTTTTCACAATTTTTTTAACAAACCCCACAAATTACAAAAATCCAAATTTTTACTAAACACCCTTCTACCTCCTATAACACTTAACTTAATTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIII-9IIIII9IIII9IIII9IIIIIIIIII9IIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII AS:i:-48 XN:i:0 XM:i:8 XO:i:0 XG:i:0 NM:i:8 MD:Z:3A8T1C1T0T50A14A0C50 YS:i:-36 YT:Z:CP >>> Writing bisulfite mapping results to POR-216-TP3_pe.bam <<< Reading in the sequence files ../../data/03-Peve-bismark/POR-216-TP3_R1_001.fastp-trim.fq.gz and ../../data/03-Peve-bismark/POR-216-TP3_R2_001.fastp-trim.fq.gz 10000 reads; of these: 10000 (100.00%) were paired; of these: 5479 (54.79%) aligned concordantly 0 times 2531 (25.31%) aligned concordantly exactly 1 time 1990 (19.90%) aligned concordantly >1 times 45.21% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 5504 (55.04%) aligned concordantly 0 times 2550 (25.50%) aligned concordantly exactly 1 time 1946 (19.46%) aligned concordantly >1 times 44.96% overall alignment rate Processed 10000 sequences in total Successfully deleted the temporary files POR-216-TP3_R1_001.fastp-trim.fq.gz_C_to_T.fastq and POR-216-TP3_R2_001.fastp-trim.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: 312943 Total methylated C's in CpG context: 3871 Total methylated C's in CHG context: 337 Total methylated C's in CHH context: 1288 Total methylated C's in Unknown context: 5 Total unmethylated C's in CpG context: 47026 Total unmethylated C's in CHG context: 55079 Total unmethylated C's in CHH context: 205342 Total unmethylated C's in Unknown context: 368 C methylated in CpG context: 7.6% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.3% Bismark completed in 0d 0h 0m 17s ==================== Bismark run complete ====================