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-262-TP1_R1_001.fastp-trim.fq.gz ../../data/03-Peve-bismark/POR-262-TP1_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-262-TP1_R1_001.fastp-trim.fq.gz and ../../data/03-Peve-bismark/POR-262-TP1_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-262-TP1_R1_001.fastp-trim.fq.gz Writing a C -> T converted version of the input file POR-262-TP1_R1_001.fastp-trim.fq.gz to POR-262-TP1_R1_001.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file POR-262-TP1_R1_001.fastp-trim.fq.gz (10001 sequences in total) Processing reads up to sequence no. 10000 from ../../data/03-Peve-bismark/POR-262-TP1_R2_001.fastp-trim.fq.gz Writing a G -> A converted version of the input file POR-262-TP1_R2_001.fastp-trim.fq.gz to POR-262-TP1_R2_001.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file POR-262-TP1_R2_001.fastp-trim.fq.gz (10001 sequences in total) Input files are POR-262-TP1_R1_001.fastp-trim.fq.gz_C_to_T.fastq and POR-262-TP1_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-262-TP1_R1_001.fastp-trim.fq.gz_C_to_T.fastq and POR-262-TP1_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: LH00526:197:22KFKVLT4:3:1101:50395:1056_1:N:0:TAGGAGCT+GTTAAGGC/1 99 Porites_evermani_scaffold_1525_CT_converted 109563 2 135M = 109836 409 TTTTTAGAATTTTTGATTATGATAATTTGTAGTATTTTGAAATGATTTTGTTTTTAGTGGAAAGTTTTTGATTTATTTAATAATATGAGTTTTATTTTTAATGGGTGGTGGTGTTGTTGGAGGTTTGTGATGTTA I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIII9IIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9III AS:i:-36 XS:i:-54 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:8G19T1T22G29G5G45 YS:i:-80 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50395:1056_2:N:0:TAGGAGCT+GTTAAGGC/2 147 Porites_evermani_scaffold_1525_CT_converted 109836 2 65M1D70M = 109563 -409 TTTTATTGTTGGAAAAAGGTGTAAGAATAGGTATTTTTATTTAAAAATGGTTTGATTATATGTTATTAAGATATTATATGTTATAATTATAGTAATTGATTATTTTTAAAATTGTTTTAAAATGTGTGTGAGGGA IIII9II9I9IIIIII9IIIIII9II-IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II9III9IIIIIIIIIIIIIIIIIIIIIIII-I9IIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIII9IIIII AS:i:-80 XS:i:-56 XN:i:0 XM:i:12 XO:i:1 XG:i:1 NM:i:13 MD:Z:3A6A0A6T0G1A36A0T5^T17G21A5T20A3 YS:i:-36 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from POR-262-TP1_R1_001.fastp-trim.fq.gz_C_to_T.fastq and POR-262-TP1_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: LH00526:197:22KFKVLT4:3:1101:50395:1056_1:N:0:TAGGAGCT+GTTAAGGC/1 83 Porites_evermani_scaffold_3161_GA_converted 18199 3 135M = 17926 -408 TAACATCACAAACCTCCAACAACACCACCACCCATTAAAAATAAAACTCATATTATTAAATAAATCAAAAACTTTCCACTAAAAACAAAATCATTTCAAAATACTACAAATTATCATAATCAAAAATTCTAAAAA III9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIIIII9IIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:45C5C67C6C8 YS:i:-74 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50395:1056_2:N:0:TAGGAGCT+GTTAAGGC/2 163 Porites_evermani_scaffold_3161_GA_converted 17926 3 68M1D67M = 18199 408 TCCCTCACACACATTTTAAAACAATTTTAAAAATAATCAATTACTATAATTATAACATATAATATCTTAATAACATATAATCAAACCATTTTTAAATAAAAATACCTATTCTTACACCTTTTTCCAACAATAAAA IIIII9IIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIII9I-IIIIIIIIIIIIIIIIIIIIIIII9III9II-IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II9IIIIII9IIIIII9I9II9IIII AS:i:-74 XN:i:0 XM:i:11 XO:i:1 XG:i:1 NM:i:12 MD:Z:24A5T21C11A3^A7A2T37A0A5T7C2T0 YS:i:-24 YT:Z:CP >>> Writing bisulfite mapping results to POR-262-TP1_pe.bam <<< Reading in the sequence files ../../data/03-Peve-bismark/POR-262-TP1_R1_001.fastp-trim.fq.gz and ../../data/03-Peve-bismark/POR-262-TP1_R2_001.fastp-trim.fq.gz 10000 reads; of these: 10000 reads; of these:10000 ( 10000100.00 (%) were paired; of these:100.00 % ) were paired; of these:5770 ( 57.705811% () aligned concordantly 0 times58.11 % ) aligned concordantly 0 times2386 ( 23.862336% () aligned concordantly exactly 1 time23.36 % ) aligned concordantly exactly 1 time1844 ( 18.441853% () aligned concordantly >1 times18.53 %42.30) aligned concordantly >1 times% overall alignment rate41.89 % overall alignment rate Processed 10000 sequences in total Successfully deleted the temporary files POR-262-TP1_R1_001.fastp-trim.fq.gz_C_to_T.fastq and POR-262-TP1_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: 291313 Total methylated C's in CpG context: 3974 Total methylated C's in CHG context: 245 Total methylated C's in CHH context: 948 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 41079 Total unmethylated C's in CHG context: 50624 Total unmethylated C's in CHH context: 194443 Total unmethylated C's in Unknown context: 404 C methylated in CpG context: 8.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in Unknown context (CN or CHN): 0.5% Bismark completed in 0d 0h 0m 16s ==================== Bismark run complete ====================