/var/spool/slurm/d/job2706898/slurm_script: line 32: fg: no job control Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 16C_26psu_1_S13_R1_001_val_1.fq.gz 16C_26psu_1_S13_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_26psu_1_S13_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 16C_26psu_1_S13_R1_001_val_1.fq.gz to 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_26psu_1_S13_R1_001_val_1.fq.gz to 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_26psu_1_S13_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATTTATTTATAAAAAAAATAAAAAAAAAATAAAAAAAAATTAATATTATATATTTTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATTTATTTATAAAAAAAATAAAAAAAAAATAAAAAAAAATTAATATTATATATTTTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 0 NC_027306.1_GA_converted 27312195 42 61M * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:61 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/16C_26psu_1_S13_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 16C_26psu_1_S13_R1_001_val_1.fq.gz 100000 reads; of these:100000 reads; of these: 100000 (100000 (100.00%100.00) were unpaired; of these:% ) were unpaired; of these: 78792 (7887678.79 (%78.88) aligned 0 times% ) aligned 0 times 9406 (94049.41 (%9.40) aligned exactly 1 time% ) aligned exactly 1 time 11802 (1172011.80 (%11.72) aligned >1 times% ) aligned >1 times21.21 %21.12 overall alignment rate% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 78436 (78.44%) aligned 0 times 9648 (9.65%) aligned exactly 1 time 11916 (11.92%) aligned >1 times 21.56% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 78397 (78.40%) aligned 0 times 9597 (9.60%) aligned exactly 1 time 12006 (12.01%) aligned >1 times 21.60% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 41443 Mapping efficiency: 41.4% Sequences with no alignments under any condition: 39661 Sequences did not map uniquely: 18896 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 10122 ((converted) top strand) CT/GA: 10203 ((converted) bottom strand) GA/CT: 10507 (complementary to (converted) top strand) GA/GA: 10611 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 811452 Total methylated C's in CpG context: 61638 Total methylated C's in CHG context: 1250 Total methylated C's in CHH context: 6314 Total methylated C's in Unknown context: 81 Total unmethylated C's in CpG context: 18623 Total unmethylated C's in CHG context: 198495 Total unmethylated C's in CHH context: 525132 Total unmethylated C's in Unknown context: 459 C methylated in CpG context: 76.8% C methylated in CHG context: 0.6% C methylated in CHH context: 1.2% C methylated in Unknown context (CN or CHN): 15.0% Bismark completed in 0d 0h 0m 49s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_26psu_1_S13_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 16C_26psu_1_S13_R2_001_val_2.fq.gz to 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_26psu_1_S13_R2_001_val_2.fq.gz to 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_26psu_1_S13_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAGGAAGTGTATGATATTAGTTTTTTTTTGTTTTTTTTTTGTTTTTTTTGTAAATGGATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 16 NC_027306.1_GA_converted 27312195 42 61M * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:61 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAAAAAATATATAATATTAATTTTTTTTTATTTTTTTTTTATTTTTTTTATAAATAAATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAAAAAATATATAATATTAATTTTTTTTTATTTTTTTTTTATTTTTTTTATAAATAAATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/16C_26psu_1_S13_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 16C_26psu_1_S13_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 77397 (77.40%) aligned 0 times 10041 (10.04%) aligned exactly 1 time 12562 (12.56%) aligned >1 times 22.60% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 80549 (80.55%) aligned 0 times 8508 (8.51%) aligned exactly 1 time 10943 (10.94%) aligned >1 times 19.45% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 77349 (77.35%) aligned 0 times 9997 (10.00%) aligned exactly 1 time 12654 (12.65%) aligned >1 times 22.65% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 80638 (80.64%) aligned 0 times 8475 (8.47%) aligned exactly 1 time 10887 (10.89%) aligned >1 times 19.36% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 40333 Mapping efficiency: 40.3% Sequences with no alignments under any condition: 41022 Sequences did not map uniquely: 18645 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 9206 ((converted) top strand) CT/GA: 9226 ((converted) bottom strand) GA/CT: 10909 (complementary to (converted) top strand) GA/GA: 10992 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 789438 Total methylated C's in CpG context: 59962 Total methylated C's in CHG context: 1185 Total methylated C's in CHH context: 6298 Total methylated C's in Unknown context: 77 Total unmethylated C's in CpG context: 18238 Total unmethylated C's in CHG context: 192608 Total unmethylated C's in CHH context: 511147 Total unmethylated C's in Unknown context: 444 C methylated in CpG context: 76.7% C methylated in CHG context: 0.6% C methylated in CHH context: 1.2% C methylated in Unknown context (CN or CHN): 14.8% Bismark completed in 0d 0h 1m 25s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 8C_32psu_3_S7_R1_001_val_1.fq.gz 8C_32psu_3_S7_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_32psu_3_S7_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 8C_32psu_3_S7_R1_001_val_1.fq.gz to 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_32psu_3_S7_R1_001_val_1.fq.gz to 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_32psu_3_S7_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 4 * 0 0 * * 0 0 TTTAAAAATAATTTTATTAAAAAATTATATTTTATAATAATTTAAATATTATGTTTAAAAAAATATGTGTTATGATATAAATTAAATGTTATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 4 * 0 0 * * 0 0 TTTAAAAATAATTTTATTAAAAAATTATATTTTATAATAATTTAAATATTATGTTTAAAAAAATATGTGTTATGATATAAATTAAATGTTATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 16 NC_027320.1_CT_converted 57131408 1 97M * 0 0 TTAATATGATGTTTAGTTTGTATTGTAATGTGTATTTTTTTGGGTGTAGTGTTTAGATTATTGTAAAGTGTGATTTTTTAGTAAGGTTATTTTTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 0 NC_027309.1_GA_converted 6145322 1 97M * 0 0 TTTAAAAATAACCTTACTAAAAAATCACACTTTACAATAATCTAAACACTACACCCAAAAAAATACACATTACAATACAAACTAAACATCATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/8C_32psu_3_S7_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 8C_32psu_3_S7_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76667 (76.67%) aligned 0 times 9784 (9.78%) aligned exactly 1 time 13549 (13.55%) aligned >1 times 23.33% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76793 (76.79%) aligned 0 times 9673 (9.67%) aligned exactly 1 time100000 reads; of these: 13534 (10000013.53 (%) aligned >1 times 23.21%100.00 overall alignment rate% ) were unpaired; of these: 76592 (76.59%) aligned 0 times 9923 (9.92%) aligned exactly 1 time 13485 (13.48%) aligned >1 times 23.41% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76812 (76.81%) aligned 0 times 9696 (9.70%) aligned exactly 1 time 13492 (13.49%) aligned >1 times 23.19% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 42014 Mapping efficiency: 42.0% Sequences with no alignments under any condition: 36014 Sequences did not map uniquely: 21972 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 10534 ((converted) top strand) CT/GA: 10547 ((converted) bottom strand) GA/CT: 10530 (complementary to (converted) top strand) GA/GA: 10403 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 765495 Total methylated C's in CpG context: 59723 Total methylated C's in CHG context: 1155 Total methylated C's in CHH context: 6663 Total methylated C's in Unknown context: 66 Total unmethylated C's in CpG context: 17981 Total unmethylated C's in CHG context: 190257 Total unmethylated C's in CHH context: 489716 Total unmethylated C's in Unknown context: 417 C methylated in CpG context: 76.9% C methylated in CHG context: 0.6% C methylated in CHH context: 1.3% C methylated in Unknown context (CN or CHN): 13.7% Bismark completed in 0d 0h 0m 47s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_32psu_3_S7_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 8C_32psu_3_S7_R2_001_val_2.fq.gz to 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_32psu_3_S7_R2_001_val_2.fq.gz to 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_32psu_3_S7_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 0 NC_027311.1_CT_converted 87079143 1 97M * 0 0 TTAATATGATGTTTAGTTTGTATTGTAATGTGTATTTTTTTGGGTGTAGTGTTTAGATTATTGTAAAGTGTGATTTTTTAGTAAGGTTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 16 NC_027312.1_GA_converted 56312130 1 97M * 0 0 TTTAAAAATAACCTTACTAAAAAATCACACTTTACAATAATCTAAACACTACACCCAAAAAAATACACATTACAATACAAACTAAACATCATATTAA F:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFFFFFFFFFFFFFF:FF,F:FFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 4 * 0 0 * * 0 0 TTAATATAACATTTAATTTATATCATAACACATATTTTTTTAAACATAATATTTAAATTATTATAAAATATAATTTTTTAATAAAATTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 4 * 0 0 * * 0 0 TTAATATAACATTTAATTTATATCATAACACATATTTTTTTAAACATAATATTTAAATTATTATAAAATATAATTTTTTAATAAAATTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/8C_32psu_3_S7_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 8C_32psu_3_S7_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75648 (75.65%) aligned 0 times 10150 (10.15%) aligned exactly 1 time100000 reads; of these: 14202 (10000014.20 (%) aligned >1 times 24.35% overall alignment rate100.00 %) were unpaired; of these: 78343 (78.34%) aligned 0 times 8918 (8.92%) aligned exactly 1 time 12739 (12.74%) aligned >1 times 21.66% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 78415 (78.42%) aligned 0 times 8942 (8.94%) aligned exactly 1 time 12643 (12.64%) aligned >1 times 21.59% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75626 (75.63%) aligned 0 times 10262 (10.26%) aligned exactly 1 time 14112 (14.11%) aligned >1 times 24.37% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 41154 Mapping efficiency: 41.2% Sequences with no alignments under any condition: 37127 Sequences did not map uniquely: 21719 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 9627 ((converted) top strand) CT/GA: 9528 ((converted) bottom strand) GA/CT: 11001 (complementary to (converted) top strand) GA/GA: 10998 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 749327 Total methylated C's in CpG context: 58491 Total methylated C's in CHG context: 1052 Total methylated C's in CHH context: 6168 Total methylated C's in Unknown context: 62 Total unmethylated C's in CpG context: 17438 Total unmethylated C's in CHG context: 185398 Total unmethylated C's in CHH context: 480780 Total unmethylated C's in Unknown context: 410 C methylated in CpG context: 77.0% C methylated in CHG context: 0.6% C methylated in CHH context: 1.3% C methylated in Unknown context (CN or CHN): 13.1% Bismark completed in 0d 0h 1m 25s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 8C_26psu_2_S10_R1_001_val_1.fq.gz 8C_26psu_2_S10_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_26psu_2_S10_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 8C_26psu_2_S10_R1_001_val_1.fq.gz to 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_26psu_2_S10_R1_001_val_1.fq.gz to 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_26psu_2_S10_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 0 NC_027317.1_CT_converted 34397130 0 39M * 0 0 TTATTGTGTGAAAGAAGGTGTGTTTTTAGTTTTTTATAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:11T27 YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 16 NC_027317.1_GA_converted 38626155 0 39M * 0 0 CTATAAAAAACTAAAAACACACCTTCTTTCACACAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:27A11 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATTATATAAAAAAAAATATATTTTTAATTTTTTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATTATATAAAAAAAAATATATTTTTAATTTTTTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/8C_26psu_2_S10_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 8C_26psu_2_S10_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100000100.00 reads; of these:% ) were unpaired; of these: 100000 (76736 (76.74%) aligned 0 times100.00 % ) were unpaired; of these:10543 ( 10.5476765% () aligned exactly 1 time76.77 % ) aligned 0 times12721 ( 12.7210512% () aligned >1 times10.51 %23.26) aligned exactly 1 time% overall alignment rate 12723 (12.72%) aligned >1 times 23.23% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76945 (76.94%) aligned 0 times 10239 (10.24%) aligned exactly 1 time 12816 (12.82%) aligned >1 times 23.05% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76649 (76.65%) aligned 0 times 10611 (10.61%) aligned exactly 1 time 12740 (12.74%) aligned >1 times 23.35% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 45236 Mapping efficiency: 45.2% Sequences with no alignments under any condition: 34460 Sequences did not map uniquely: 20304 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 11105 ((converted) top strand) CT/GA: 11396 ((converted) bottom strand) GA/CT: 11423 (complementary to (converted) top strand) GA/GA: 11312 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 863224 Total methylated C's in CpG context: 64658 Total methylated C's in CHG context: 1378 Total methylated C's in CHH context: 6186 Total methylated C's in Unknown context: 68 Total unmethylated C's in CpG context: 18949 Total unmethylated C's in CHG context: 210976 Total unmethylated C's in CHH context: 561077 Total unmethylated C's in Unknown context: 476 C methylated in CpG context: 77.3% C methylated in CHG context: 0.6% C methylated in CHH context: 1.1% C methylated in Unknown context (CN or CHN): 12.5% Bismark completed in 0d 0h 0m 48s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_26psu_2_S10_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 8C_26psu_2_S10_R2_001_val_2.fq.gz to 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_26psu_2_S10_R2_001_val_2.fq.gz to 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_26psu_2_S10_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATAAAAAATTAAAAATATATTTTTTTTTATATAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATAAAAAATTAAAAATATATTTTTTTTTATATAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 16 NC_027317.1_CT_converted 34396730 0 39M * 0 0 TTATTGTGTGAAAGAAGGTGTGTTTTTAGTTTTTTATAG FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:11T27 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 0 NC_027317.1_GA_converted 38626317 0 39M * 0 0 CTATAAAAAACTAAAAACACACCTTCTTTCACACAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:27A11 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/8C_26psu_2_S10_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 8C_26psu_2_S10_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 78906 (78.91%) aligned 0 times 9334 (9.33%) aligned exactly 1 time 11760 (11.76%) aligned >1 times 21.09% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75408 (75.41%) aligned 0 times100000 reads; of these: 11060 (10000011.06 (%) aligned exactly 1 time 13532 (100.0013.53%%) were unpaired; of these:) aligned >1 times 24.5978867% ( overall alignment rate78.87 %) aligned 0 times 9387 (9.39%) aligned exactly 1 time 11746 (11.75%) aligned >1 times 21.13% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75696 (75.70%) aligned 0 times 10710 (10.71%) aligned exactly 1 time 13594 (13.59%) aligned >1 times 24.30% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 43798 Mapping efficiency: 43.8% Sequences with no alignments under any condition: 36158 Sequences did not map uniquely: 20044 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 10066 ((converted) top strand) CT/GA: 9972 ((converted) bottom strand) GA/CT: 11784 (complementary to (converted) top strand) GA/GA: 11976 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 835153 Total methylated C's in CpG context: 62787 Total methylated C's in CHG context: 1333 Total methylated C's in CHH context: 6876 Total methylated C's in Unknown context: 52 Total unmethylated C's in CpG context: 18117 Total unmethylated C's in CHG context: 203816 Total unmethylated C's in CHH context: 542224 Total unmethylated C's in Unknown context: 424 C methylated in CpG context: 77.6% C methylated in CHG context: 0.6% C methylated in CHH context: 1.3% C methylated in Unknown context (CN or CHN): 10.9% Bismark completed in 0d 0h 1m 24s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz CTRL_8C_26psu_1_S17_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz to CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz to CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz (100001 sequences in total) Input files are CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 GATAATGTTTATTTATTGTAGAGATAGAGATTGTAGAGGTTAGTATAAAGGTTGTGAATTAGGTAGAGAGAGAGAGAGTAAGGGAGAGTGAGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 GATAATGTTTATTTATTGTAGAGATAGAGATTGTAGAGGTTAGTATAAAGGTTGTGAATTAGGTAGAGAGAGAGAGAGTAAGGGAGAGTGAGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 AATAATATTTATTTATTATAAAAATAAAAATCATAAAAATTAATATAAAAATCATAAATTAAATAAAAAAAAAAAAAATAAAAAAAAATAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 AATAATATTTATTTATTATAAAAATAAAAATCATAAAAATTAATATAAAAATCATAAATTAAATAAAAAAAAAAAAAATAAAAAAAAATAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 78283 (78.28%) aligned 0 times 10284 (10.28%) aligned exactly 1 time 11433 (11.43%) aligned >1 times 21.72% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 78043100000 ( reads; of these:78.04 % ) aligned 0 times100000 ( 10516 (10.52%100.00) aligned exactly 1 time% ) were unpaired; of these: 11441 (7688611.44 (%76.89) aligned >1 times% ) aligned 0 times21.96 % overall alignment rate11007 (11.01%) aligned exactly 1 time 12107 (12.11%) aligned >1 times 23.11% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76738 (76.74%) aligned 0 times 11199 (11.20%) aligned exactly 1 time 12063 (12.06%) aligned >1 times 23.26% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 46582 Mapping efficiency: 46.6% Sequences with no alignments under any condition: 34815 Sequences did not map uniquely: 18603 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 11323 ((converted) top strand) CT/GA: 11046 ((converted) bottom strand) GA/CT: 12029 (complementary to (converted) top strand) GA/GA: 12184 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 908066 Total methylated C's in CpG context: 63199 Total methylated C's in CHG context: 1313 Total methylated C's in CHH context: 6370 Total methylated C's in Unknown context: 70 Total unmethylated C's in CpG context: 18368 Total unmethylated C's in CHG context: 210308 Total unmethylated C's in CHH context: 608508 Total unmethylated C's in Unknown context: 547 C methylated in CpG context: 77.5% C methylated in CHG context: 0.6% C methylated in CHH context: 1.0% C methylated in Unknown context (CN or CHN): 11.3% Bismark completed in 0d 0h 0m 47s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz to CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz to CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz (100001 sequences in total) Input files are CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 TTTTTTTATTTTTTTTTATTTTTTTTTTTTTTATTTAATTTATGATTTTTATATTAATTTTTATGATTTTTATTTTTATAATAAATAAATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 TTTTTTTATTTTTTTTTATTTTTTTTTTTTTTATTTAATTTATGATTTTTATATTAATTTTTATGATTTTTATTTTTATAATAAATAAATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 CTCTCTCACTCTCCCTTACTCTCTCTCTCTCTACCTAATTCACAACCTTTATACTAACCTCTACAATCTCTATCTCTACAATAAATAAACATTATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 CTCTCTCACTCTCCCTTACTCTCTCTCTCTCTACCTAATTCACAACCTTTATACTAACCTCTACAATCTCTATCTCTACAATAAATAAACATTATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/CTRL_8C_26psu_1_S17_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 79393 (79.39%) aligned 0 times 9569 (9.57%) aligned exactly 1 time 11038 (11.04%) aligned >1 times 20.61% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 79381 (79.38%) aligned 0 times 9704 (9.70%) aligned exactly 1 time 10915 (10.91%) aligned >1 times 20.62% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76374 (76.37%) aligned 0 times 11226 (11.23%) aligned exactly 1 time 12400 (12.40%) aligned >1 times 23.63% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76598 (76.60%) aligned 0 times 10994 (10.99%) aligned exactly 1 time 12408 (12.41%) aligned >1 times 23.40% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 44737 Mapping efficiency: 44.7% Sequences with no alignments under any condition: 36795 Sequences did not map uniquely: 18468 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 10318 ((converted) top strand) CT/GA: 10397 ((converted) bottom strand) GA/CT: 12109 (complementary to (converted) top strand) GA/GA: 11913 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 870157 Total methylated C's in CpG context: 60251 Total methylated C's in CHG context: 1300 Total methylated C's in CHH context: 6664 Total methylated C's in Unknown context: 73 Total unmethylated C's in CpG context: 17898 Total unmethylated C's in CHG context: 200778 Total unmethylated C's in CHH context: 583266 Total unmethylated C's in Unknown context: 479 C methylated in CpG context: 77.1% C methylated in CHG context: 0.6% C methylated in CHH context: 1.1% C methylated in Unknown context (CN or CHN): 13.2% Bismark completed in 0d 0h 1m 24s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 16C_32psu_4_S4_R1_001_val_1.fq.gz 16C_32psu_4_S4_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_32psu_4_S4_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 16C_32psu_4_S4_R1_001_val_1.fq.gz to 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_32psu_4_S4_R1_001_val_1.fq.gz to 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_32psu_4_S4_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 GATTATTGAGATTTTTTTTTTAATTTTATTTTGAAAGAGGTGTTTTTATTGGAGTAATGGTTTAAGGTATTGTATTGTAGTGGTTGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 GATTATTGAGATTTTTTTTTTAATTTTATTTTGAAAGAGGTGTTTTTATTGGAGTAATGGTTTAAGGTATTGTATTGTAGTGGTTGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 AATTATCAAAATTTTTTTTTTAATTTTATTTTAAAAAAAATATTTTTATTAAAATAATAATTTAAAATATTATATTATAATAATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 AATTATCAAAATTTTTTTTTTAATTTTATTTTAAAAAAAATATTTTTATTAAAATAATAATTTAAAATATTATATTATAATAATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/16C_32psu_4_S4_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 16C_32psu_4_S4_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 81386 (81.39%) aligned 0 times 9315 (9.31%) aligned exactly 1 time 9299 (9.30%) aligned >1 times 18.61% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 81197 (81.20%) aligned 0 times 9417 (9.42%) aligned exactly 1 time 9386 (9.39%) aligned >1 times 18.80% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 78802 (78.80%) aligned 0 times 10809 (10.81%) aligned exactly 1 time 10389 (10.39%) aligned >1 times 21.20% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 78701 (78.70%) aligned 0 times 10791 (10.79%) aligned exactly 1 time 10508 (10.51%) aligned >1 times 21.30% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 44140 Mapping efficiency: 44.1% Sequences with no alignments under any condition: 40710 Sequences did not map uniquely: 15150 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 10139 ((converted) top strand) CT/GA: 10325 ((converted) bottom strand) GA/CT: 11847 (complementary to (converted) top strand) GA/GA: 11829 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 932490 Total methylated C's in CpG context: 64346 Total methylated C's in CHG context: 1468 Total methylated C's in CHH context: 6473 Total methylated C's in Unknown context: 99 Total unmethylated C's in CpG context: 19570 Total unmethylated C's in CHG context: 220445 Total unmethylated C's in CHH context: 620188 Total unmethylated C's in Unknown context: 596 C methylated in CpG context: 76.7% C methylated in CHG context: 0.7% C methylated in CHH context: 1.0% C methylated in Unknown context (CN or CHN): 14.2% Bismark completed in 0d 0h 0m 44s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_32psu_4_S4_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 16C_32psu_4_S4_R2_001_val_2.fq.gz to 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_32psu_4_S4_R2_001_val_2.fq.gz to 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_32psu_4_S4_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 TTTAATTATTATAATATAATATTTTAAATTATTATTTTAATAAAAATATTTTTTTTAAAATAAAATTAAAAAAAAAATTTTGATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 TTTAATTATTATAATATAATATTTTAAATTATTATTTTAATAAAAATATTTTTTTTAAAATAAAATTAAAAAAAAAATTTTGATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 CTCAACCACTACAATACAATACCTTAAACCATTACTCCAATAAAAACACCTCTTTCAAAATAAAATTAAAAAAAAAATCTCAATAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 CTCAACCACTACAATACAATACCTTAAACCATTACTCCAATAAAAACACCTCTTTCAAAATAAAATTAAAAAAAAAATCTCAATAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.2/16C_32psu_4_S4_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 16C_32psu_4_S4_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 81707 (81.71%) aligned 0 times 9129 (9.13%) aligned exactly 1 time 9164 (9.16%) aligned >1 times 18.29% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 81690 (81.69%) aligned 0 times 9104 (9.10%) aligned exactly 1 time 9206 (9.21%) aligned >1 times 18.31% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 79481 (79.48%) aligned 0 times 10316 (10.32%) aligned exactly 1 time 10203 (10.20%) aligned >1 times 20.52% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 79419 (79.42%) aligned 0 times 10382 (10.38%) aligned exactly 1 time 10199 (10.20%) aligned >1 times 20.58% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 42509 Mapping efficiency: 42.5% Sequences with no alignments under any condition: 42588 Sequences did not map uniquely: 14903 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 9933 ((converted) top strand) CT/GA: 9902 ((converted) bottom strand) GA/CT: 11295 (complementary to (converted) top strand) GA/GA: 11379 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 894213 Total methylated C's in CpG context: 61569 Total methylated C's in CHG context: 1408 Total methylated C's in CHH context: 5934 Total methylated C's in Unknown context: 89 Total unmethylated C's in CpG context: 18728 Total unmethylated C's in CHG context: 211243 Total unmethylated C's in CHH context: 595331 Total unmethylated C's in Unknown context: 572 C methylated in CpG context: 76.7% C methylated in CHG context: 0.7% C methylated in CHH context: 1.0% C methylated in Unknown context (CN or CHN): 13.5% Bismark completed in 0d 0h 1m 22s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 16C_26psu_1_S13_R1_001_val_1.fq.gz 16C_26psu_1_S13_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_26psu_1_S13_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 16C_26psu_1_S13_R1_001_val_1.fq.gz to 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_26psu_1_S13_R1_001_val_1.fq.gz to 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_26psu_1_S13_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATTTATTTATAAAAAAAATAAAAAAAAAATAAAAAAAAATTAATATTATATATTTTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATTTATTTATAAAAAAAATAAAAAAAAAATAAAAAAAAATTAATATTATATATTTTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 0 NC_027306.1_GA_converted 27312195 42 61M * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:61 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/16C_26psu_1_S13_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 16C_26psu_1_S13_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75793 (75.79%) aligned 0 times 9143 (9.14%) aligned exactly 1 time 15064 (15.06%) aligned >1 times 24.21% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75967 (75.97%) aligned 0 times 9118 (9.12%) aligned exactly 1 time 14915 (14.91%) aligned >1 times 24.03% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75458 (75.46%) aligned 0 times 9377 (9.38%) aligned exactly 1 time 15165 (15.16%) aligned >1 times 24.54% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75331 (75.33%) aligned 0 times 9350 (9.35%) aligned exactly 1 time 15319 (15.32%) aligned >1 times 24.67% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 44824 Mapping efficiency: 44.8% Sequences with no alignments under any condition: 34965 Sequences did not map uniquely: 20211 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 10929 ((converted) top strand) CT/GA: 11072 ((converted) bottom strand) GA/CT: 11342 (complementary to (converted) top strand) GA/GA: 11481 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 881877 Total methylated C's in CpG context: 66371 Total methylated C's in CHG context: 1582 Total methylated C's in CHH context: 8718 Total methylated C's in Unknown context: 247 Total unmethylated C's in CpG context: 20478 Total unmethylated C's in CHG context: 215667 Total unmethylated C's in CHH context: 569061 Total unmethylated C's in Unknown context: 939 C methylated in CpG context: 76.4% C methylated in CHG context: 0.7% C methylated in CHH context: 1.5% C methylated in Unknown context (CN or CHN): 20.8% Bismark completed in 0d 0h 0m 48s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_26psu_1_S13_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 16C_26psu_1_S13_R2_001_val_2.fq.gz to 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_26psu_1_S13_R2_001_val_2.fq.gz to 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_26psu_1_S13_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAGGAAGTGTATGATATTAGTTTTTTTTTGTTTTTTTTTTGTTTTTTTTGTAAATGGATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 16 NC_027306.1_GA_converted 27312195 42 61M * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:61 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAAAAAATATATAATATTAATTTTTTTTTATTTTTTTTTTATTTTTTTTATAAATAAATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAAAAAATATATAATATTAATTTTTTTTTATTTTTTTTTTATTTTTTTTATAAATAAATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/16C_26psu_1_S13_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 16C_26psu_1_S13_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 74317 (74.32%) aligned 0 times 9719 (9.72%) aligned exactly 1 time 15964 (15.96%) aligned >1 times 25.68% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 74257 (74.26%) aligned 0 times 9691 (9.69%) aligned exactly 1 time 16052 (16.05%) aligned >1 times 25.74% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 77713 (77.71%) aligned 0 times 8386 (8.39%) aligned exactly 1 time 13901 (13.90%) aligned >1 times 22.29% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 77690 (77.69%) aligned 0 times 8350 (8.35%) aligned exactly 1 time 13960 (13.96%) aligned >1 times 22.31% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 43770 Mapping efficiency: 43.8% Sequences with no alignments under any condition: 36268 Sequences did not map uniquely: 19962 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 10057 ((converted) top strand) CT/GA: 10139 ((converted) bottom strand) GA/CT: 11733 (complementary to (converted) top strand) GA/GA: 11841 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 862501 Total methylated C's in CpG context: 64796 Total methylated C's in CHG context: 1458 Total methylated C's in CHH context: 8096 Total methylated C's in Unknown context: 219 Total unmethylated C's in CpG context: 20019 Total unmethylated C's in CHG context: 209898 Total unmethylated C's in CHH context: 558234 Total unmethylated C's in Unknown context: 948 C methylated in CpG context: 76.4% C methylated in CHG context: 0.7% C methylated in CHH context: 1.4% C methylated in Unknown context (CN or CHN): 18.8% Bismark completed in 0d 0h 1m 29s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 8C_32psu_3_S7_R1_001_val_1.fq.gz 8C_32psu_3_S7_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_32psu_3_S7_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 8C_32psu_3_S7_R1_001_val_1.fq.gz to 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_32psu_3_S7_R1_001_val_1.fq.gz to 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_32psu_3_S7_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 4 * 0 0 * * 0 0 TTTAAAAATAATTTTATTAAAAAATTATATTTTATAATAATTTAAATATTATGTTTAAAAAAATATGTGTTATGATATAAATTAAATGTTATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 4 * 0 0 * * 0 0 TTTAAAAATAATTTTATTAAAAAATTATATTTTATAATAATTTAAATATTATGTTTAAAAAAATATGTGTTATGATATAAATTAAATGTTATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 16 NC_027320.1_CT_converted 57131408 1 97M * 0 0 TTAATATGATGTTTAGTTTGTATTGTAATGTGTATTTTTTTGGGTGTAGTGTTTAGATTATTGTAAAGTGTGATTTTTTAGTAAGGTTATTTTTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 0 NC_027309.1_GA_converted 6145322 1 97M * 0 0 TTTAAAAATAACCTTACTAAAAAATCACACTTTACAATAATCTAAACACTACACCCAAAAAAATACACATTACAATACAAACTAAACATCATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/8C_32psu_3_S7_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 8C_32psu_3_S7_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73420 (73.42%) aligned 0 times 9481 (9.48%) aligned exactly 1 time 17099 (17.10%) aligned >1 times 26.58% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73403 (73.40%) aligned 0 times 9465 (9.46%) aligned exactly 1 time 17132 (17.13%) aligned >1 times 26.60% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73638 (73.64%) aligned 0 times 9311 (9.31%) aligned exactly 1 time 17051 (17.05%) aligned >1 times 26.36% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73641 (73.64%) aligned 0 times 9316 (9.32%) aligned exactly 1 time 17043 (17.04%) aligned >1 times 26.36% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 45202 Mapping efficiency: 45.2% Sequences with no alignments under any condition: 31441 Sequences did not map uniquely: 23357 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 11371 ((converted) top strand) CT/GA: 11344 ((converted) bottom strand) GA/CT: 11308 (complementary to (converted) top strand) GA/GA: 11179 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 827688 Total methylated C's in CpG context: 64114 Total methylated C's in CHG context: 1392 Total methylated C's in CHH context: 8627 Total methylated C's in Unknown context: 197 Total unmethylated C's in CpG context: 19733 Total unmethylated C's in CHG context: 205663 Total unmethylated C's in CHH context: 528159 Total unmethylated C's in Unknown context: 890 C methylated in CpG context: 76.5% C methylated in CHG context: 0.7% C methylated in CHH context: 1.6% C methylated in Unknown context (CN or CHN): 18.1% Bismark completed in 0d 0h 0m 47s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_32psu_3_S7_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 8C_32psu_3_S7_R2_001_val_2.fq.gz to 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_32psu_3_S7_R2_001_val_2.fq.gz to 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_32psu_3_S7_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 0 NC_027311.1_CT_converted 87079143 1 97M * 0 0 TTAATATGATGTTTAGTTTGTATTGTAATGTGTATTTTTTTGGGTGTAGTGTTTAGATTATTGTAAAGTGTGATTTTTTAGTAAGGTTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 16 NC_027312.1_GA_converted 56312130 1 97M * 0 0 TTTAAAAATAACCTTACTAAAAAATCACACTTTACAATAATCTAAACACTACACCCAAAAAAATACACATTACAATACAAACTAAACATCATATTAA F:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFFFFFFFFFFFFFF:FF,F:FFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 4 * 0 0 * * 0 0 TTAATATAACATTTAATTTATATCATAACACATATTTTTTTAAACATAATATTTAAATTATTATAAAATATAATTTTTTAATAAAATTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 4 * 0 0 * * 0 0 TTAATATAACATTTAATTTATATCATAACACATATTTTTTTAAACATAATATTTAAATTATTATAAAATATAATTTTTTAATAAAATTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/8C_32psu_3_S7_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 8C_32psu_3_S7_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75249 (75.25%) aligned 0 times 8640 (8.64%) aligned exactly 1 time 16111 (16.11%) aligned >1 times 24.75% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 72460 (72.46%) aligned 0 times 9737 (9.74%) aligned exactly 1 time 17803 (17.80%) aligned >1 times 27.54% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 72446 (72.45%) aligned 0 times 9804 (9.80%) aligned exactly 1 time 17750 (17.75%) aligned >1 times 27.55% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75274 (75.27%) aligned 0 times 8680 (8.68%) aligned exactly 1 time 16046 (16.05%) aligned >1 times 24.73% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 44367 Mapping efficiency: 44.4% Sequences with no alignments under any condition: 32568 Sequences did not map uniquely: 23065 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 10402 ((converted) top strand) CT/GA: 10333 ((converted) bottom strand) GA/CT: 11816 (complementary to (converted) top strand) GA/GA: 11816 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 812651 Total methylated C's in CpG context: 63079 Total methylated C's in CHG context: 1289 Total methylated C's in CHH context: 8427 Total methylated C's in Unknown context: 191 Total unmethylated C's in CpG context: 19142 Total unmethylated C's in CHG context: 201035 Total unmethylated C's in CHH context: 519679 Total unmethylated C's in Unknown context: 885 C methylated in CpG context: 76.7% C methylated in CHG context: 0.6% C methylated in CHH context: 1.6% C methylated in Unknown context (CN or CHN): 17.8% Bismark completed in 0d 0h 1m 25s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 8C_26psu_2_S10_R1_001_val_1.fq.gz 8C_26psu_2_S10_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_26psu_2_S10_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 8C_26psu_2_S10_R1_001_val_1.fq.gz to 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_26psu_2_S10_R1_001_val_1.fq.gz to 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_26psu_2_S10_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 0 NC_027317.1_CT_converted 34397130 0 39M * 0 0 TTATTGTGTGAAAGAAGGTGTGTTTTTAGTTTTTTATAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:11T27 YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 16 NC_027317.1_GA_converted 38626155 0 39M * 0 0 CTATAAAAAACTAAAAACACACCTTCTTTCACACAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:27A11 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATTATATAAAAAAAAATATATTTTTAATTTTTTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATTATATAAAAAAAAATATATTTTTAATTTTTTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/8C_26psu_2_S10_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 8C_26psu_2_S10_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73543 (73.54%) aligned 0 times 10252 (10.25%) aligned exactly 1 time 16205 (16.20%) aligned >1 times 26.46% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73590 (73.59%) aligned 0 times 10171 (10.17%) aligned exactly 1 time 16239 (16.24%) aligned >1 times 26.41% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73799 (73.80%) aligned 0 times 9918 (9.92%) aligned exactly 1 time 16283 (16.28%) aligned >1 times 26.20% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73612 (73.61%) aligned 0 times 10155 (10.15%) aligned exactly 1 time 16233 (16.23%) aligned >1 times 26.39% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 48493 Mapping efficiency: 48.5% Sequences with no alignments under any condition: 29948 Sequences did not map uniquely: 21559 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 11929 ((converted) top strand) CT/GA: 12190 ((converted) bottom strand) GA/CT: 12239 (complementary to (converted) top strand) GA/GA: 12135 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 928999 Total methylated C's in CpG context: 68873 Total methylated C's in CHG context: 1648 Total methylated C's in CHH context: 8481 Total methylated C's in Unknown context: 195 Total unmethylated C's in CpG context: 20634 Total unmethylated C's in CHG context: 227291 Total unmethylated C's in CHH context: 602072 Total unmethylated C's in Unknown context: 926 C methylated in CpG context: 76.9% C methylated in CHG context: 0.7% C methylated in CHH context: 1.4% C methylated in Unknown context (CN or CHN): 17.4% Bismark completed in 0d 0h 0m 49s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_26psu_2_S10_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 8C_26psu_2_S10_R2_001_val_2.fq.gz to 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_26psu_2_S10_R2_001_val_2.fq.gz to 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_26psu_2_S10_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATAAAAAATTAAAAATATATTTTTTTTTATATAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATAAAAAATTAAAAATATATTTTTTTTTATATAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 16 NC_027317.1_CT_converted 34396730 0 39M * 0 0 TTATTGTGTGAAAGAAGGTGTGTTTTTAGTTTTTTATAG FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:11T27 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 0 NC_027317.1_GA_converted 38626317 0 39M * 0 0 CTATAAAAAACTAAAAACACACCTTCTTTCACACAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:27A11 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/8C_26psu_2_S10_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 8C_26psu_2_S10_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75888 (75.89%) aligned 0 times 9081 (9.08%) aligned exactly 1 time 15031 (15.03%) aligned >1 times100000 reads; of these:24.11 % overall alignment rate100000 (100.00%) were unpaired; of these: 75864 (75.86%) aligned 0 times 9169 (9.17%) aligned exactly 1 time 14967 (14.97%) aligned >1 times 24.14% overall alignment rate 100000100000 reads; of these: reads; of these: 100000100000 ( (100.00100.00%%) were unpaired; of these:) were unpaired; of these: 7243772184 ( (72.4472.18%%) aligned 0 times) aligned 0 times 1043410722 ( (10.4310.72%%) aligned exactly 1 time) aligned exactly 1 time 1712917094 ( (17.1317.09%%) aligned >1 times) aligned >1 times 27.5627.82%% overall alignment rate overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 47128 Mapping efficiency: 47.1% Sequences with no alignments under any condition: 31541 Sequences did not map uniquely: 21331 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 10880 ((converted) top strand) CT/GA: 10799 ((converted) bottom strand) GA/CT: 12600 (complementary to (converted) top strand) GA/GA: 12849 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 903820 Total methylated C's in CpG context: 67228 Total methylated C's in CHG context: 1593 Total methylated C's in CHH context: 9180 Total methylated C's in Unknown context: 185 Total unmethylated C's in CpG context: 19858 Total unmethylated C's in CHG context: 220305 Total unmethylated C's in CHH context: 585656 Total unmethylated C's in Unknown context: 875 C methylated in CpG context: 77.2% C methylated in CHG context: 0.7% C methylated in CHH context: 1.5% C methylated in Unknown context (CN or CHN): 17.5% Bismark completed in 0d 0h 1m 35s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz CTRL_8C_26psu_1_S17_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz to CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz to CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz (100001 sequences in total) Input files are CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 GATAATGTTTATTTATTGTAGAGATAGAGATTGTAGAGGTTAGTATAAAGGTTGTGAATTAGGTAGAGAGAGAGAGAGTAAGGGAGAGTGAGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 GATAATGTTTATTTATTGTAGAGATAGAGATTGTAGAGGTTAGTATAAAGGTTGTGAATTAGGTAGAGAGAGAGAGAGTAAGGGAGAGTGAGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 AATAATATTTATTTATTATAAAAATAAAAATCATAAAAATTAATATAAAAATCATAAATTAAATAAAAAAAAAAAAAATAAAAAAAAATAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 AATAATATTTATTTATTATAAAAATAAAAATCATAAAAATTAATATAAAAATCATAAATTAAATAAAAAAAAAAAAAATAAAAAAAAATAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73856 (73.86%) aligned 0 times 10680 (10.68%) aligned exactly 1 time 15464 (15.46%) aligned >1 times 26.14% overall alignment rate 100000100000 reads; of these: reads; of these: 100000100000 ( (100.00%) were unpaired; of these:100.00 % ) were unpaired; of these:73695 ( 73.6975102% () aligned 0 times75.10 % ) aligned 0 times10883 ( 10.8810163% () aligned exactly 1 time10.16 % ) aligned exactly 1 time15422 ( 15.4214735% () aligned >1 times14.73 %26.30) aligned >1 times% overall alignment rate24.90 % overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75280 (75.28%) aligned 0 times 10021 (10.02%) aligned exactly 1 time 14699 (14.70%) aligned >1 times 24.72% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 49920 Mapping efficiency: 49.9% Sequences with no alignments under any condition: 30255 Sequences did not map uniquely: 19825 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12184 ((converted) top strand) CT/GA: 11855 ((converted) bottom strand) GA/CT: 12843 (complementary to (converted) top strand) GA/GA: 13038 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 976683 Total methylated C's in CpG context: 67473 Total methylated C's in CHG context: 1568 Total methylated C's in CHH context: 7868 Total methylated C's in Unknown context: 199 Total unmethylated C's in CpG context: 20155 Total unmethylated C's in CHG context: 226608 Total unmethylated C's in CHH context: 653011 Total unmethylated C's in Unknown context: 1008 C methylated in CpG context: 77.0% C methylated in CHG context: 0.7% C methylated in CHH context: 1.2% C methylated in Unknown context (CN or CHN): 16.5% Bismark completed in 0d 0h 0m 49s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz to CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz to CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz (100001 sequences in total) Input files are CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 TTTTTTTATTTTTTTTTATTTTTTTTTTTTTTATTTAATTTATGATTTTTATATTAATTTTTATGATTTTTATTTTTATAATAAATAAATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 TTTTTTTATTTTTTTTTATTTTTTTTTTTTTTATTTAATTTATGATTTTTATATTAATTTTTATGATTTTTATTTTTATAATAAATAAATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 CTCTCTCACTCTCCCTTACTCTCTCTCTCTCTACCTAATTCACAACCTTTATACTAACCTCTACAATCTCTATCTCTACAATAAATAAACATTATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 CTCTCTCACTCTCCCTTACTCTCTCTCTCTCTACCTAATTCACAACCTTTATACTAACCTCTACAATCTCTATCTCTACAATAAATAAACATTATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/CTRL_8C_26psu_1_S17_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76418 (76.42%) aligned 0 times100000 reads; of these: 9510 (1000009.51 (%) aligned exactly 1 time 14072 (100.0014.07%%) were unpaired; of these:) aligned >1 times 23.5876422% ( overall alignment rate76.42 %) aligned 0 times 9462 (9.46%) aligned exactly 1 time 14116 (14.12%) aligned >1 times 23.58% overall alignment rate 100000 reads; of these:100000 reads; of these: 100000 (100000 (100.00%100.00) were unpaired; of these:% ) were unpaired; of these: 73485 (7328873.48 (%73.29) aligned 0 times% ) aligned 0 times 10735 (1087810.73 (%10.88) aligned exactly 1 time% ) aligned exactly 1 time 15780 (1583415.78 (%15.83) aligned >1 times% ) aligned >1 times26.52 %26.71 overall alignment rate% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 48213 Mapping efficiency: 48.2% Sequences with no alignments under any condition: 32054 Sequences did not map uniquely: 19733 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 11172 ((converted) top strand) CT/GA: 11258 ((converted) bottom strand) GA/CT: 13003 (complementary to (converted) top strand) GA/GA: 12780 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 943100 Total methylated C's in CpG context: 64531 Total methylated C's in CHG context: 1567 Total methylated C's in CHH context: 8348 Total methylated C's in Unknown context: 216 Total unmethylated C's in CpG context: 19672 Total unmethylated C's in CHG context: 217465 Total unmethylated C's in CHH context: 631517 Total unmethylated C's in Unknown context: 959 C methylated in CpG context: 76.6% C methylated in CHG context: 0.7% C methylated in CHH context: 1.3% C methylated in Unknown context (CN or CHN): 18.4% Bismark completed in 0d 0h 1m 25s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 16C_32psu_4_S4_R1_001_val_1.fq.gz 16C_32psu_4_S4_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_32psu_4_S4_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 16C_32psu_4_S4_R1_001_val_1.fq.gz to 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_32psu_4_S4_R1_001_val_1.fq.gz to 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_32psu_4_S4_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 GATTATTGAGATTTTTTTTTTAATTTTATTTTGAAAGAGGTGTTTTTATTGGAGTAATGGTTTAAGGTATTGTATTGTAGTGGTTGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 GATTATTGAGATTTTTTTTTTAATTTTATTTTGAAAGAGGTGTTTTTATTGGAGTAATGGTTTAAGGTATTGTATTGTAGTGGTTGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 AATTATCAAAATTTTTTTTTTAATTTTATTTTAAAAAAAATATTTTTATTAAAATAATAATTTAAAATATTATATTATAATAATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 AATTATCAAAATTTTTTTTTTAATTTTATTTTAAAAAAAATATTTTTATTAAAATAATAATTTAAAATATTATATTATAATAATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/16C_32psu_4_S4_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 16C_32psu_4_S4_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 78452 (78.45%) aligned 0 times 9366 (9.37%) aligned exactly 1 time 12182 (12.18%) aligned >1 times 21.55% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 78663 (78.66%) aligned 0 times 9238 (9.24%) aligned exactly 1 time 12099 (12.10%) aligned >1 times 21.34% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75865 (75.86%) aligned 0 times 10611 (10.61%) aligned exactly 1 time 13524 (13.52%) aligned >1 times 24.14% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75836 (75.84%) aligned 0 times 10574 (10.57%) aligned exactly 1 time 13590 (13.59%) aligned >1 times 24.16% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 47868 Mapping efficiency: 47.9% Sequences with no alignments under any condition: 35839 Sequences did not map uniquely: 16293 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 11072 ((converted) top strand) CT/GA: 11221 ((converted) bottom strand) GA/CT: 12759 (complementary to (converted) top strand) GA/GA: 12816 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1012253 Total methylated C's in CpG context: 69294 Total methylated C's in CHG context: 1733 Total methylated C's in CHH context: 8416 Total methylated C's in Unknown context: 256 Total unmethylated C's in CpG context: 21668 Total unmethylated C's in CHG context: 239504 Total unmethylated C's in CHH context: 671638 Total unmethylated C's in Unknown context: 1127 C methylated in CpG context: 76.2% C methylated in CHG context: 0.7% C methylated in CHH context: 1.2% C methylated in Unknown context (CN or CHN): 18.5% Bismark completed in 0d 0h 0m 49s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_32psu_4_S4_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 16C_32psu_4_S4_R2_001_val_2.fq.gz to 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_32psu_4_S4_R2_001_val_2.fq.gz to 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_32psu_4_S4_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 TTTAATTATTATAATATAATATTTTAAATTATTATTTTAATAAAAATATTTTTTTTAAAATAAAATTAAAAAAAAAATTTTGATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 TTTAATTATTATAATATAATATTTTAAATTATTATTTTAATAAAAATATTTTTTTTAAAATAAAATTAAAAAAAAAATTTTGATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 CTCAACCACTACAATACAATACCTTAAACCATTACTCCAATAAAAACACCTCTTTCAAAATAAAATTAAAAAAAAAATCTCAATAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 CTCAACCACTACAATACAATACCTTAAACCATTACTCCAATAAAAACACCTCTTTCAAAATAAAATTAAAAAAAAAATCTCAATAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.3/16C_32psu_4_S4_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 16C_32psu_4_S4_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 78835 (78.83%) aligned 0 times 9230 (9.23%) aligned exactly 1 time 11935 (11.94%) aligned >1 times 21.16% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 78876 (78.88%) aligned 0 times 9153 (9.15%) aligned exactly 1 time 11971 (11.97%) aligned >1 times 21.12% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76603 (76.60%) aligned 0 times 10087 (10.09%) aligned exactly 1 time 13310 (13.31%) aligned >1 times 23.40% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76457 (76.46%) aligned 0 times 10297 (10.30%) aligned exactly 1 time 13246 (13.25%) aligned >1 times 23.54% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 46428 Mapping efficiency: 46.4% Sequences with no alignments under any condition: 37473 Sequences did not map uniquely: 16099 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 10964 ((converted) top strand) CT/GA: 10894 ((converted) bottom strand) GA/CT: 12228 (complementary to (converted) top strand) GA/GA: 12342 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 979597 Total methylated C's in CpG context: 66722 Total methylated C's in CHG context: 1703 Total methylated C's in CHH context: 8037 Total methylated C's in Unknown context: 262 Total unmethylated C's in CpG context: 20800 Total unmethylated C's in CHG context: 231180 Total unmethylated C's in CHH context: 651155 Total unmethylated C's in Unknown context: 1108 C methylated in CpG context: 76.2% C methylated in CHG context: 0.7% C methylated in CHH context: 1.2% C methylated in Unknown context (CN or CHN): 19.1% Bismark completed in 0d 0h 1m 28s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 16C_26psu_1_S13_R1_001_val_1.fq.gz 16C_26psu_1_S13_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_26psu_1_S13_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 16C_26psu_1_S13_R1_001_val_1.fq.gz to 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_26psu_1_S13_R1_001_val_1.fq.gz to 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_26psu_1_S13_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATTTATTTATAAAAAAAATAAAAAAAAAATAAAAAAAAATTAATATTATATATTTTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATTTATTTATAAAAAAAATAAAAAAAAAATAAAAAAAAATTAATATTATATATTTTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 0 NC_027306.1_GA_converted 27312195 42 61M * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:61 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/16C_26psu_1_S13_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 16C_26psu_1_S13_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73569 (73.57%) aligned 0 times 8904 (8.90%) aligned exactly 1 time 17527 (17.53%) aligned >1 times 26.43% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 72887 (72.89%) aligned 0 times 9206 (9.21%) aligned exactly 1 time 17907 (17.91%) aligned >1 times 27.11% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73413 (73.41%) aligned 0 times 8942 (8.94%) aligned exactly 1 time 17645 (17.64%) aligned >1 times 26.59% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73048 (73.05%) aligned 0 times 9154 (9.15%) aligned exactly 1 time 17798 (17.80%) aligned >1 times 26.95% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 47616 Mapping efficiency: 47.6% Sequences with no alignments under any condition: 31283 Sequences did not map uniquely: 21101 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 11615 ((converted) top strand) CT/GA: 11802 ((converted) bottom strand) GA/CT: 12067 (complementary to (converted) top strand) GA/GA: 12132 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 940863 Total methylated C's in CpG context: 70436 Total methylated C's in CHG context: 1910 Total methylated C's in CHH context: 11437 Total methylated C's in Unknown context: 456 Total unmethylated C's in CpG context: 22085 Total unmethylated C's in CHG context: 229422 Total unmethylated C's in CHH context: 605573 Total unmethylated C's in Unknown context: 1742 C methylated in CpG context: 76.1% C methylated in CHG context: 0.8% C methylated in CHH context: 1.9% C methylated in Unknown context (CN or CHN): 20.7% Bismark completed in 0d 0h 0m 46s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_26psu_1_S13_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 16C_26psu_1_S13_R2_001_val_2.fq.gz to 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_26psu_1_S13_R2_001_val_2.fq.gz to 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_26psu_1_S13_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAGGAAGTGTATGATATTAGTTTTTTTTTGTTTTTTTTTTGTTTTTTTTGTAAATGGATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 16 NC_027306.1_GA_converted 27312195 42 61M * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:61 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAAAAAATATATAATATTAATTTTTTTTTATTTTTTTTTTATTTTTTTTATAAATAAATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAAAAAATATATAATATTAATTTTTTTTTATTTTTTTTTTATTTTTTTTATAAATAAATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/16C_26psu_1_S13_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 16C_26psu_1_S13_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71888 (71.89%) aligned 0 times 9480 (9.48%) aligned exactly 1 time 18632 (18.63%) aligned >1 times 28.11% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71806 (71.81%) aligned 0 times 9469 (9.47%) aligned exactly 1 time 18725 (18.73%) aligned >1 times 28.19% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75350 (75.35%) aligned 0 times 8263 (8.26%) aligned exactly 1 time 16387 (16.39%) aligned >1 times 24.65% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 75247 (75.25%) aligned 0 times 8368 (8.37%) aligned exactly 1 time 16385 (16.39%) aligned >1 times 24.75% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 46701 Mapping efficiency: 46.7% Sequences with no alignments under any condition: 32471 Sequences did not map uniquely: 20828 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 10793 ((converted) top strand) CT/GA: 10856 ((converted) bottom strand) GA/CT: 12468 (complementary to (converted) top strand) GA/GA: 12584 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 924527 Total methylated C's in CpG context: 68912 Total methylated C's in CHG context: 1773 Total methylated C's in CHH context: 11330 Total methylated C's in Unknown context: 423 Total unmethylated C's in CpG context: 21670 Total unmethylated C's in CHG context: 224217 Total unmethylated C's in CHH context: 596625 Total unmethylated C's in Unknown context: 1732 C methylated in CpG context: 76.1% C methylated in CHG context: 0.8% C methylated in CHH context: 1.9% C methylated in Unknown context (CN or CHN): 19.6% Bismark completed in 0d 0h 1m 29s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 8C_32psu_3_S7_R1_001_val_1.fq.gz 8C_32psu_3_S7_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_32psu_3_S7_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 8C_32psu_3_S7_R1_001_val_1.fq.gz to 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_32psu_3_S7_R1_001_val_1.fq.gz to 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_32psu_3_S7_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 4 * 0 0 * * 0 0 TTTAAAAATAATTTTATTAAAAAATTATATTTTATAATAATTTAAATATTATGTTTAAAAAAATATGTGTTATGATATAAATTAAATGTTATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 4 * 0 0 * * 0 0 TTTAAAAATAATTTTATTAAAAAATTATATTTTATAATAATTTAAATATTATGTTTAAAAAAATATGTGTTATGATATAAATTAAATGTTATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 16 NC_027320.1_CT_converted 57131408 1 97M * 0 0 TTAATATGATGTTTAGTTTGTATTGTAATGTGTATTTTTTTGGGTGTAGTGTTTAGATTATTGTAAAGTGTGATTTTTTAGTAAGGTTATTTTTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 0 NC_027309.1_GA_converted 6145322 1 97M * 0 0 TTTAAAAATAACCTTACTAAAAAATCACACTTTACAATAATCTAAACACTACACCCAAAAAAATACACATTACAATACAAACTAAACATCATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/8C_32psu_3_S7_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 8C_32psu_3_S7_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 70978 (70.98%) aligned 0 times 9370 (9.37%) aligned exactly 1 time 19652 (19.65%) aligned >1 times 29.02% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71051 (71.05%) aligned 0 times 9222 (9.22%) aligned exactly 1 time 19727 (19.73%) aligned >1 times 28.95% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71161 (71.16%) aligned 0 times 9130 (9.13%) aligned exactly 1 time 19709 (19.71%) aligned >1 times 28.84% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71231 (71.23%) aligned 0 times 9081 (9.08%) aligned exactly 1 time 19688 (19.69%) aligned >1 times 28.77% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 47943 Mapping efficiency: 47.9% Sequences with no alignments under any condition: 27859 Sequences did not map uniquely: 24198 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12041 ((converted) top strand) CT/GA: 12065 ((converted) bottom strand) GA/CT: 11979 (complementary to (converted) top strand) GA/GA: 11858 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 883108 Total methylated C's in CpG context: 67891 Total methylated C's in CHG context: 1748 Total methylated C's in CHH context: 12161 Total methylated C's in Unknown context: 412 Total unmethylated C's in CpG context: 21330 Total unmethylated C's in CHG context: 218424 Total unmethylated C's in CHH context: 561554 Total unmethylated C's in Unknown context: 1573 C methylated in CpG context: 76.1% C methylated in CHG context: 0.8% C methylated in CHH context: 2.1% C methylated in Unknown context (CN or CHN): 20.8% Bismark completed in 0d 0h 0m 48s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_32psu_3_S7_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 8C_32psu_3_S7_R2_001_val_2.fq.gz to 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_32psu_3_S7_R2_001_val_2.fq.gz to 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_32psu_3_S7_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 0 NC_027311.1_CT_converted 87079143 1 97M * 0 0 TTAATATGATGTTTAGTTTGTATTGTAATGTGTATTTTTTTGGGTGTAGTGTTTAGATTATTGTAAAGTGTGATTTTTTAGTAAGGTTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 16 NC_027312.1_GA_converted 56312130 1 97M * 0 0 TTTAAAAATAACCTTACTAAAAAATCACACTTTACAATAATCTAAACACTACACCCAAAAAAATACACATTACAATACAAACTAAACATCATATTAA F:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFFFFFFFFFFFFFF:FF,F:FFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 4 * 0 0 * * 0 0 TTAATATAACATTTAATTTATATCATAACACATATTTTTTTAAACATAATATTTAAATTATTATAAAATATAATTTTTTAATAAAATTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 4 * 0 0 * * 0 0 TTAATATAACATTTAATTTATATCATAACACATATTTTTTTAAACATAATATTTAAATTATTATAAAATATAATTTTTTAATAAAATTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/8C_32psu_3_S7_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 8C_32psu_3_S7_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 72817 (72.82%) aligned 0 times 8560 (8.56%) aligned exactly 1 time 18623 (18.62%) aligned >1 times 27.18% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 72987 (72.99%) aligned 0 times 8510 (8.51%) aligned exactly 1 time 18503 (18.50%) aligned >1 times 27.01% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69927 (69.93%) aligned 0 times 9713 (9.71%) aligned exactly 1 time 20360 (20.36%) aligned >1 times 30.07% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 70031 (70.03%) aligned 0 times 9536 (9.54%) aligned exactly 1 time 20433 (20.43%) aligned >1 times 29.97% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 47065 Mapping efficiency: 47.1% Sequences with no alignments under any condition: 29007 Sequences did not map uniquely: 23928 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 11035 ((converted) top strand) CT/GA: 11010 ((converted) bottom strand) GA/CT: 12489 (complementary to (converted) top strand) GA/GA: 12531 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 867300 Total methylated C's in CpG context: 66654 Total methylated C's in CHG context: 1627 Total methylated C's in CHH context: 11534 Total methylated C's in Unknown context: 387 Total unmethylated C's in CpG context: 20775 Total unmethylated C's in CHG context: 213345 Total unmethylated C's in CHH context: 553365 Total unmethylated C's in Unknown context: 1508 C methylated in CpG context: 76.2% C methylated in CHG context: 0.8% C methylated in CHH context: 2.0% C methylated in Unknown context (CN or CHN): 20.4% Bismark completed in 0d 0h 1m 28s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 8C_26psu_2_S10_R1_001_val_1.fq.gz 8C_26psu_2_S10_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_26psu_2_S10_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 8C_26psu_2_S10_R1_001_val_1.fq.gz to 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_26psu_2_S10_R1_001_val_1.fq.gz to 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_26psu_2_S10_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 0 NC_027317.1_CT_converted 34397130 0 39M * 0 0 TTATTGTGTGAAAGAAGGTGTGTTTTTAGTTTTTTATAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:11T27 YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 16 NC_027317.1_GA_converted 38626155 0 39M * 0 0 CTATAAAAAACTAAAAACACACCTTCTTTCACACAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:27A11 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATTATATAAAAAAAAATATATTTTTAATTTTTTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATTATATAAAAAAAAATATATTTTTAATTTTTTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/8C_26psu_2_S10_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 8C_26psu_2_S10_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71170 (71.17%) aligned 0 times 10017 (10.02%) aligned exactly 1 time 18813 (18.81%) aligned >1 times 28.83% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71351 (71.35%) aligned 0 times 9730 (9.73%) aligned exactly 1 time 18919 (18.92%) aligned >1 times 28.65% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71322 (71.32%) aligned 0 times 9889 (9.89%) aligned exactly 1 time 18789 (18.79%) aligned >1 times 28.68% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71278 (71.28%) aligned 0 times 9881 (9.88%) aligned exactly 1 time 18841 (18.84%) aligned >1 times 28.72% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 51214 Mapping efficiency: 51.2% Sequences with no alignments under any condition: 26474 Sequences did not map uniquely: 22312 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12619 ((converted) top strand) CT/GA: 12892 ((converted) bottom strand) GA/CT: 12932 (complementary to (converted) top strand) GA/GA: 12771 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 984262 Total methylated C's in CpG context: 72327 Total methylated C's in CHG context: 1942 Total methylated C's in CHH context: 11194 Total methylated C's in Unknown context: 383 Total unmethylated C's in CpG context: 22155 Total unmethylated C's in CHG context: 240635 Total unmethylated C's in CHH context: 636009 Total unmethylated C's in Unknown context: 1654 C methylated in CpG context: 76.6% C methylated in CHG context: 0.8% C methylated in CHH context: 1.7% C methylated in Unknown context (CN or CHN): 18.8% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_26psu_2_S10_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 8C_26psu_2_S10_R2_001_val_2.fq.gz to 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_26psu_2_S10_R2_001_val_2.fq.gz to 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_26psu_2_S10_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATAAAAAATTAAAAATATATTTTTTTTTATATAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATAAAAAATTAAAAATATATTTTTTTTTATATAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 16 NC_027317.1_CT_converted 34396730 0 39M * 0 0 TTATTGTGTGAAAGAAGGTGTGTTTTTAGTTTTTTATAG FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:11T27 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 0 NC_027317.1_GA_converted 38626317 0 39M * 0 0 CTATAAAAAACTAAAAACACACCTTCTTTCACACAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:27A11 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/8C_26psu_2_S10_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 8C_26psu_2_S10_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73568 (73.57%) aligned 0 times 8944 (8.94%) aligned exactly 1 time 17488 (17.49%) aligned >1 times 26.43% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73638 (73.64%) aligned 0 times 8960 (8.96%) aligned exactly 1 time 17402 (17.40%) aligned >1 times 26.36% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 70019 (70.02%) aligned 0 times 10159 (10.16%) aligned exactly 1 time 19822 (19.82%) aligned >1 times 29.98% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69767 (69.77%) aligned 0 times 10489 (10.49%) aligned exactly 1 time 19744 (19.74%) aligned >1 times 30.23% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 49933 Mapping efficiency: 49.9% Sequences with no alignments under any condition: 27942 Sequences did not map uniquely: 22125 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 11561 ((converted) top strand) CT/GA: 11471 ((converted) bottom strand) GA/CT: 13344 (complementary to (converted) top strand) GA/GA: 13557 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 961758 Total methylated C's in CpG context: 70804 Total methylated C's in CHG context: 1904 Total methylated C's in CHH context: 11556 Total methylated C's in Unknown context: 367 Total unmethylated C's in CpG context: 21521 Total unmethylated C's in CHG context: 234072 Total unmethylated C's in CHH context: 621901 Total unmethylated C's in Unknown context: 1617 C methylated in CpG context: 76.7% C methylated in CHG context: 0.8% C methylated in CHH context: 1.8% C methylated in Unknown context (CN or CHN): 18.5% Bismark completed in 0d 0h 1m 34s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz CTRL_8C_26psu_1_S17_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz to CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz to CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz (100001 sequences in total) Input files are CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 GATAATGTTTATTTATTGTAGAGATAGAGATTGTAGAGGTTAGTATAAAGGTTGTGAATTAGGTAGAGAGAGAGAGAGTAAGGGAGAGTGAGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 GATAATGTTTATTTATTGTAGAGATAGAGATTGTAGAGGTTAGTATAAAGGTTGTGAATTAGGTAGAGAGAGAGAGAGTAAGGGAGAGTGAGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 AATAATATTTATTTATTATAAAAATAAAAATCATAAAAATTAATATAAAAATCATAAATTAAATAAAAAAAAAAAAAATAAAAAAAAATAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 AATAATATTTATTTATTATAAAAATAAAAATCATAAAAATTAATATAAAAATCATAAATTAAATAAAAAAAAAAAAAATAAAAAAAAATAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 72999 (73.00%) aligned 0 times 9832 (9.83%) aligned exactly 1 time 17169 (17.17%) aligned >1 times 27.00% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 72831 (72.83%) aligned 0 times 9998 (10.00%) aligned exactly 1 time 17171 (17.17%) aligned >1 times 27.17% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71590 (71.59%) aligned 0 times 10385 (10.38%) aligned exactly 1 time 18025 (18.02%) aligned >1 times 28.41% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71357 (71.36%) aligned 0 times 10715 (10.71%) aligned exactly 1 time 17928 (17.93%) aligned >1 times 28.64% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 52626 Mapping efficiency: 52.6% Sequences with no alignments under any condition: 26755 Sequences did not map uniquely: 20619 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12906 ((converted) top strand) CT/GA: 12530 ((converted) bottom strand) GA/CT: 13476 (complementary to (converted) top strand) GA/GA: 13714 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1032265 Total methylated C's in CpG context: 70805 Total methylated C's in CHG context: 1830 Total methylated C's in CHH context: 9927 Total methylated C's in Unknown context: 372 Total unmethylated C's in CpG context: 21686 Total unmethylated C's in CHG context: 239514 Total unmethylated C's in CHH context: 688503 Total unmethylated C's in Unknown context: 1703 C methylated in CpG context: 76.6% C methylated in CHG context: 0.8% C methylated in CHH context: 1.4% C methylated in Unknown context (CN or CHN): 17.9% Bismark completed in 0d 0h 0m 52s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz to CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz to CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz (100001 sequences in total) Input files are CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 TTTTTTTATTTTTTTTTATTTTTTTTTTTTTTATTTAATTTATGATTTTTATATTAATTTTTATGATTTTTATTTTTATAATAAATAAATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 TTTTTTTATTTTTTTTTATTTTTTTTTTTTTTATTTAATTTATGATTTTTATATTAATTTTTATGATTTTTATTTTTATAATAAATAAATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 CTCTCTCACTCTCCCTTACTCTCTCTCTCTCTACCTAATTCACAACCTTTATACTAACCTCTACAATCTCTATCTCTACAATAAATAAACATTATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 CTCTCTCACTCTCCCTTACTCTCTCTCTCTCTACCTAATTCACAACCTTTATACTAACCTCTACAATCTCTATCTCTACAATAAATAAACATTATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/CTRL_8C_26psu_1_S17_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 74128 (74.13%) aligned 0 times 9354 (9.35%) aligned exactly 1 time 16518 (16.52%) aligned >1 times 25.87% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 74138 (74.14%) aligned 0 times 9277 (9.28%) aligned exactly 1 time 16585 (16.59%) aligned >1 times 25.86% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71005 (71.00%) aligned 0 times 10576 (10.58%) aligned exactly 1 time 18419 (18.42%) aligned >1 times 29.00% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71127 (71.13%) aligned 0 times 10477 (10.48%) aligned exactly 1 time 18396 (18.40%) aligned >1 times 28.87% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 50947 Mapping efficiency: 50.9% Sequences with no alignments under any condition: 28515 Sequences did not map uniquely: 20538 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 11828 ((converted) top strand) CT/GA: 11950 ((converted) bottom strand) GA/CT: 13711 (complementary to (converted) top strand) GA/GA: 13458 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1000634 Total methylated C's in CpG context: 67936 Total methylated C's in CHG context: 1795 Total methylated C's in CHH context: 10271 Total methylated C's in Unknown context: 439 Total unmethylated C's in CpG context: 21067 Total unmethylated C's in CHG context: 230361 Total unmethylated C's in CHH context: 669204 Total unmethylated C's in Unknown context: 1655 C methylated in CpG context: 76.3% C methylated in CHG context: 0.8% C methylated in CHH context: 1.5% C methylated in Unknown context (CN or CHN): 21.0% Bismark completed in 0d 0h 1m 29s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 16C_32psu_4_S4_R1_001_val_1.fq.gz 16C_32psu_4_S4_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_32psu_4_S4_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 16C_32psu_4_S4_R1_001_val_1.fq.gz to 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_32psu_4_S4_R1_001_val_1.fq.gz to 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_32psu_4_S4_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 GATTATTGAGATTTTTTTTTTAATTTTATTTTGAAAGAGGTGTTTTTATTGGAGTAATGGTTTAAGGTATTGTATTGTAGTGGTTGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 GATTATTGAGATTTTTTTTTTAATTTTATTTTGAAAGAGGTGTTTTTATTGGAGTAATGGTTTAAGGTATTGTATTGTAGTGGTTGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 AATTATCAAAATTTTTTTTTTAATTTTATTTTAAAAAAAATATTTTTATTAAAATAATAATTTAAAATATTATATTATAATAATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 AATTATCAAAATTTTTTTTTTAATTTTATTTTAAAAAAAATATTTTTATTAAAATAATAATTTAAAATATTATATTATAATAATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/16C_32psu_4_S4_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 16C_32psu_4_S4_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76276 (76.28%) aligned 0 times 9162 (9.16%) aligned exactly 1 time 14562 (14.56%) aligned >1 times 23.72% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76504 (76.50%) aligned 0 times 9035 (9.04%) aligned exactly 1 time 14461 (14.46%) aligned >1 times 23.50% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73502 (73.50%) aligned 0 times 10428 (10.43%) aligned exactly 1 time 16070 (16.07%) aligned >1 times 26.50% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73485 (73.48%) aligned 0 times 10466 (10.47%) aligned exactly 1 time 16049 (16.05%) aligned >1 times 26.52% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 50838 Mapping efficiency: 50.8% Sequences with no alignments under any condition: 32147 Sequences did not map uniquely: 17015 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 11812 ((converted) top strand) CT/GA: 11875 ((converted) bottom strand) GA/CT: 13566 (complementary to (converted) top strand) GA/GA: 13585 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1076198 Total methylated C's in CpG context: 73229 Total methylated C's in CHG context: 2037 Total methylated C's in CHH context: 11403 Total methylated C's in Unknown context: 510 Total unmethylated C's in CpG context: 23263 Total unmethylated C's in CHG context: 254186 Total unmethylated C's in CHH context: 712080 Total unmethylated C's in Unknown context: 1955 C methylated in CpG context: 75.9% C methylated in CHG context: 0.8% C methylated in CHH context: 1.6% C methylated in Unknown context (CN or CHN): 20.7% Bismark completed in 0d 0h 0m 48s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_32psu_4_S4_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 16C_32psu_4_S4_R2_001_val_2.fq.gz to 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_32psu_4_S4_R2_001_val_2.fq.gz to 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_32psu_4_S4_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 TTTAATTATTATAATATAATATTTTAAATTATTATTTTAATAAAAATATTTTTTTTAAAATAAAATTAAAAAAAAAATTTTGATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 TTTAATTATTATAATATAATATTTTAAATTATTATTTTAATAAAAATATTTTTTTTAAAATAAAATTAAAAAAAAAATTTTGATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 CTCAACCACTACAATACAATACCTTAAACCATTACTCCAATAAAAACACCTCTTTCAAAATAAAATTAAAAAAAAAATCTCAATAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.4 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 CTCAACCACTACAATACAATACCTTAAACCATTACTCCAATAAAAACACCTCTTTCAAAATAAAATTAAAAAAAAAATCTCAATAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.4/16C_32psu_4_S4_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 16C_32psu_4_S4_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76532 (76.53%) aligned 0 times 9210 (9.21%) aligned exactly 1 time 14258 (14.26%) aligned >1 times 23.47% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 76512 (76.51%) aligned 0 times 9319 (9.32%) aligned exactly 1 time 14169 (14.17%) aligned >1 times 23.49% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 74133 (74.13%) aligned 0 times 10121 (10.12%) aligned exactly 1 time 15746 (15.75%) aligned >1 times 25.87% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 74336 (74.34%) aligned 0 times 9901 (9.90%) aligned exactly 1 time 15763 (15.76%) aligned >1 times 25.66% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 49658 Mapping efficiency: 49.7% Sequences with no alignments under any condition: 33456 Sequences did not map uniquely: 16886 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 11814 ((converted) top strand) CT/GA: 11769 ((converted) bottom strand) GA/CT: 12985 (complementary to (converted) top strand) GA/GA: 13090 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1051615 Total methylated C's in CpG context: 70829 Total methylated C's in CHG context: 2002 Total methylated C's in CHH context: 10929 Total methylated C's in Unknown context: 504 Total unmethylated C's in CpG context: 22644 Total unmethylated C's in CHG context: 247516 Total unmethylated C's in CHH context: 697695 Total unmethylated C's in Unknown context: 1983 C methylated in CpG context: 75.8% C methylated in CHG context: 0.8% C methylated in CHH context: 1.5% C methylated in Unknown context (CN or CHN): 20.3% Bismark completed in 0d 0h 1m 26s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 16C_26psu_1_S13_R1_001_val_1.fq.gz 16C_26psu_1_S13_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_26psu_1_S13_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 16C_26psu_1_S13_R1_001_val_1.fq.gz to 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_26psu_1_S13_R1_001_val_1.fq.gz to 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_26psu_1_S13_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATTTATTTATAAAAAAAATAAAAAAAAAATAAAAAAAAATTAATATTATATATTTTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATTTATTTATAAAAAAAATAAAAAAAAAATAAAAAAAAATTAATATTATATATTTTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 0 NC_027306.1_GA_converted 27312195 42 61M * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:61 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/16C_26psu_1_S13_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 16C_26psu_1_S13_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71110 (71.11%) aligned 0 times 8932 (8.93%) aligned exactly 1 time 19958 (19.96%) aligned >1 times 28.89% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71287 (71.29%) aligned 0 times 8871 (8.87%) aligned exactly 1 time 19842 (19.84%) aligned >1 times 28.71% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 70697 (70.70%) aligned 0 times 9094 (9.09%) aligned exactly 1 time 20209 (20.21%) aligned >1 times 29.30% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 70493 (70.49%) aligned 0 times 9118 (9.12%) aligned exactly 1 time 20389 (20.39%) aligned >1 times 29.51% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 50312 Mapping efficiency: 50.3% Sequences with no alignments under any condition: 27892 Sequences did not map uniquely: 21796 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12261 ((converted) top strand) CT/GA: 12474 ((converted) bottom strand) GA/CT: 12728 (complementary to (converted) top strand) GA/GA: 12849 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 996813 Total methylated C's in CpG context: 74405 Total methylated C's in CHG context: 2306 Total methylated C's in CHH context: 14351 Total methylated C's in Unknown context: 754 Total unmethylated C's in CpG context: 23924 Total unmethylated C's in CHG context: 242439 Total unmethylated C's in CHH context: 639388 Total unmethylated C's in Unknown context: 2791 C methylated in CpG context: 75.7% C methylated in CHG context: 0.9% C methylated in CHH context: 2.2% C methylated in Unknown context (CN or CHN): 21.3% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_26psu_1_S13_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 16C_26psu_1_S13_R2_001_val_2.fq.gz to 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_26psu_1_S13_R2_001_val_2.fq.gz to 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_26psu_1_S13_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAGGAAGTGTATGATATTAGTTTTTTTTTGTTTTTTTTTTGTTTTTTTTGTAAATGGATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 16 NC_027306.1_GA_converted 27312195 42 61M * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:61 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAAAAAATATATAATATTAATTTTTTTTTATTTTTTTTTTATTTTTTTTATAAATAAATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAAAAAATATATAATATTAATTTTTTTTTATTTTTTTTTTATTTTTTTTATAAATAAATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/16C_26psu_1_S13_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 16C_26psu_1_S13_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 72924 (72.92%) aligned 0 times 8277 (8.28%) aligned exactly 1 time 18799 (18.80%) aligned >1 times 27.08% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69382 (69.38%) aligned 0 times 9473 (9.47%) aligned exactly 1 time 21145 (21.14%) aligned >1 times 30.62% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69527 (69.53%) aligned 0 times 9338 (9.34%) aligned exactly 1 time 21135 (21.14%) aligned >1 times 30.47% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 73126 (73.13%) aligned 0 times 8205 (8.21%) aligned exactly 1 time 18669 (18.67%) aligned >1 times 26.87% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 49466 Mapping efficiency: 49.5% Sequences with no alignments under any condition: 28942 Sequences did not map uniquely: 21592 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 11492 ((converted) top strand) CT/GA: 11527 ((converted) bottom strand) GA/CT: 13171 (complementary to (converted) top strand) GA/GA: 13276 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 983426 Total methylated C's in CpG context: 72761 Total methylated C's in CHG context: 2146 Total methylated C's in CHH context: 14523 Total methylated C's in Unknown context: 770 Total unmethylated C's in CpG context: 23553 Total unmethylated C's in CHG context: 237326 Total unmethylated C's in CHH context: 633117 Total unmethylated C's in Unknown context: 2792 C methylated in CpG context: 75.5% C methylated in CHG context: 0.9% C methylated in CHH context: 2.2% C methylated in Unknown context (CN or CHN): 21.6% Bismark completed in 0d 0h 1m 29s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 8C_32psu_3_S7_R1_001_val_1.fq.gz 8C_32psu_3_S7_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_32psu_3_S7_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 8C_32psu_3_S7_R1_001_val_1.fq.gz to 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_32psu_3_S7_R1_001_val_1.fq.gz to 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_32psu_3_S7_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 4 * 0 0 * * 0 0 TTTAAAAATAATTTTATTAAAAAATTATATTTTATAATAATTTAAATATTATGTTTAAAAAAATATGTGTTATGATATAAATTAAATGTTATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 4 * 0 0 * * 0 0 TTTAAAAATAATTTTATTAAAAAATTATATTTTATAATAATTTAAATATTATGTTTAAAAAAATATGTGTTATGATATAAATTAAATGTTATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 16 NC_027320.1_CT_converted 57131408 1 97M * 0 0 TTAATATGATGTTTAGTTTGTATTGTAATGTGTATTTTTTTGGGTGTAGTGTTTAGATTATTGTAAAGTGTGATTTTTTAGTAAGGTTATTTTTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 0 NC_027309.1_GA_converted 6145322 1 97M * 0 0 TTTAAAAATAACCTTACTAAAAAATCACACTTTACAATAATCTAAACACTACACCCAAAAAAATACACATTACAATACAAACTAAACATCATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/8C_32psu_3_S7_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 8C_32psu_3_S7_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68694 (68.69%) aligned 0 times 9059 (9.06%) aligned exactly 1 time 22247 (22.25%) aligned >1 times 31.31% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68715 (68.72%) aligned 0 times 9162 (9.16%) aligned exactly 1 time 22123 (22.12%) aligned >1 times 31.29% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68876 (68.88%) aligned 0 times 9080 (9.08%) aligned exactly 1 time 22044 (22.04%) aligned >1 times 31.12% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68775 (68.78%) aligned 0 times 9145 (9.14%) aligned exactly 1 time 22080 (22.08%) aligned >1 times 31.23% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 50405 Mapping efficiency: 50.4% Sequences with no alignments under any condition: 24716 Sequences did not map uniquely: 24879 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12622 ((converted) top strand) CT/GA: 12673 ((converted) bottom strand) GA/CT: 12619 (complementary to (converted) top strand) GA/GA: 12491 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 931861 Total methylated C's in CpG context: 71165 Total methylated C's in CHG context: 2048 Total methylated C's in CHH context: 14735 Total methylated C's in Unknown context: 681 Total unmethylated C's in CpG context: 23127 Total unmethylated C's in CHG context: 229775 Total unmethylated C's in CHH context: 591011 Total unmethylated C's in Unknown context: 2509 C methylated in CpG context: 75.5% C methylated in CHG context: 0.9% C methylated in CHH context: 2.4% C methylated in Unknown context (CN or CHN): 21.3% Bismark completed in 0d 0h 0m 48s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_32psu_3_S7_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 8C_32psu_3_S7_R2_001_val_2.fq.gz to 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_32psu_3_S7_R2_001_val_2.fq.gz to 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_32psu_3_S7_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 0 NC_027311.1_CT_converted 87079143 1 97M * 0 0 TTAATATGATGTTTAGTTTGTATTGTAATGTGTATTTTTTTGGGTGTAGTGTTTAGATTATTGTAAAGTGTGATTTTTTAGTAAGGTTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 16 NC_027312.1_GA_converted 56312130 1 97M * 0 0 TTTAAAAATAACCTTACTAAAAAATCACACTTTACAATAATCTAAACACTACACCCAAAAAAATACACATTACAATACAAACTAAACATCATATTAA F:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFFFFFFFFFFFFFF:FF,F:FFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 4 * 0 0 * * 0 0 TTAATATAACATTTAATTTATATCATAACACATATTTTTTTAAACATAATATTTAAATTATTATAAAATATAATTTTTTAATAAAATTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 4 * 0 0 * * 0 0 TTAATATAACATTTAATTTATATCATAACACATATTTTTTTAAACATAATATTTAAATTATTATAAAATATAATTTTTTAATAAAATTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/8C_32psu_3_S7_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 8C_32psu_3_S7_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 67592 (67.59%) aligned 0 times 9528 (9.53%) aligned exactly 1 time 22880 (22.88%) aligned >1 times 32.41% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 67702 (67.70%) aligned 0 times 9334 (9.33%) aligned exactly 1 time 22964 (22.96%) aligned >1 times 32.30% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 70535 (70.53%) aligned 0 times 8528 (8.53%) aligned exactly 1 time 20937 (20.94%) aligned >1 times 29.46% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 70634 (70.63%) aligned 0 times 8539 (8.54%) aligned exactly 1 time 20827 (20.83%) aligned >1 times 29.37% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 49525 Mapping efficiency: 49.5% Sequences with no alignments under any condition: 25855 Sequences did not map uniquely: 24620 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 11657 ((converted) top strand) CT/GA: 11574 ((converted) bottom strand) GA/CT: 13106 (complementary to (converted) top strand) GA/GA: 13188 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 917997 Total methylated C's in CpG context: 69848 Total methylated C's in CHG context: 1918 Total methylated C's in CHH context: 14674 Total methylated C's in Unknown context: 681 Total unmethylated C's in CpG context: 22344 Total unmethylated C's in CHG context: 224613 Total unmethylated C's in CHH context: 584600 Total unmethylated C's in Unknown context: 2416 C methylated in CpG context: 75.8% C methylated in CHG context: 0.8% C methylated in CHH context: 2.4% C methylated in Unknown context (CN or CHN): 22.0% Bismark completed in 0d 0h 1m 28s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 8C_26psu_2_S10_R1_001_val_1.fq.gz 8C_26psu_2_S10_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_26psu_2_S10_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 8C_26psu_2_S10_R1_001_val_1.fq.gz to 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_26psu_2_S10_R1_001_val_1.fq.gz to 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_26psu_2_S10_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 0 NC_027317.1_CT_converted 34397130 1 39M * 0 0 TTATTGTGTGAAAGAAGGTGTGTTTTTAGTTTTTTATAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:11T27 YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 16 NC_027317.1_GA_converted 38626155 1 39M * 0 0 CTATAAAAAACTAAAAACACACCTTCTTTCACACAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:27A11 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATTATATAAAAAAAAATATATTTTTAATTTTTTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATTATATAAAAAAAAATATATTTTTAATTTTTTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/8C_26psu_2_S10_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 8C_26psu_2_S10_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68882 (68.88%) aligned 0 times 9874 (9.87%) aligned exactly 1 time 21244 (21.24%) aligned >1 times 31.12% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69038 (69.04%) aligned 0 times 9820 (9.82%) aligned exactly 1 time 21142 (21.14%) aligned >1 times 30.96% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69118 (69.12%) aligned 0 times 9677 (9.68%) aligned exactly 1 time 21205 (21.20%) aligned >1 times 30.88% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69047 (69.05%) aligned 0 times 9586 (9.59%) aligned exactly 1 time 21367 (21.37%) aligned >1 times 30.95% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 53663 Mapping efficiency: 53.7% Sequences with no alignments under any condition: 23425 Sequences did not map uniquely: 22912 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 13263 ((converted) top strand) CT/GA: 13514 ((converted) bottom strand) GA/CT: 13553 (complementary to (converted) top strand) GA/GA: 13333 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1034830 Total methylated C's in CpG context: 75638 Total methylated C's in CHG context: 2303 Total methylated C's in CHH context: 14137 Total methylated C's in Unknown context: 684 Total unmethylated C's in CpG context: 23725 Total unmethylated C's in CHG context: 252393 Total unmethylated C's in CHH context: 666634 Total unmethylated C's in Unknown context: 2627 C methylated in CpG context: 76.1% C methylated in CHG context: 0.9% C methylated in CHH context: 2.1% C methylated in Unknown context (CN or CHN): 20.7% Bismark completed in 0d 0h 0m 47s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_26psu_2_S10_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 8C_26psu_2_S10_R2_001_val_2.fq.gz to 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_26psu_2_S10_R2_001_val_2.fq.gz to 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_26psu_2_S10_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATAAAAAATTAAAAATATATTTTTTTTTATATAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATAAAAAATTAAAAATATATTTTTTTTTATATAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 16 NC_027317.1_CT_converted 34396730 1 39M * 0 0 TTATTGTGTGAAAGAAGGTGTGTTTTTAGTTTTTTATAG FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:11T27 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 0 NC_027317.1_GA_converted 38626317 1 39M * 0 0 CTATAAAAAACTAAAAACACACCTTCTTTCACACAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:27A11 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/8C_26psu_2_S10_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 8C_26psu_2_S10_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100000100.00 reads; of these:% ) were unpaired; of these: 100000 (71450 (71.45%) aligned 0 times 100.00 %8853) were unpaired; of these: ( 8.85 %71343) aligned exactly 1 time ( 71.34 %19697) aligned 0 times ( 19.70 %8974) aligned >1 times ( 8.9728.55%%) aligned exactly 1 time overall alignment rate 19683 (19.68%) aligned >1 times 28.66% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 67663 (67.66%) aligned 0 times 10001 (10.00%) aligned exactly 1 time 22336 (22.34%) aligned >1 times 32.34% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 67464 (67.46%) aligned 0 times 10253 (10.25%) aligned exactly 1 time 22283 (22.28%) aligned >1 times 32.54% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 52459 Mapping efficiency: 52.5% Sequences with no alignments under any condition: 24778 Sequences did not map uniquely: 22763 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12192 ((converted) top strand) CT/GA: 12055 ((converted) bottom strand) GA/CT: 14010 (complementary to (converted) top strand) GA/GA: 14202 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1015357 Total methylated C's in CpG context: 74013 Total methylated C's in CHG context: 2261 Total methylated C's in CHH context: 14814 Total methylated C's in Unknown context: 658 Total unmethylated C's in CpG context: 23008 Total unmethylated C's in CHG context: 245717 Total unmethylated C's in CHH context: 655544 Total unmethylated C's in Unknown context: 2556 C methylated in CpG context: 76.3% C methylated in CHG context: 0.9% C methylated in CHH context: 2.2% C methylated in Unknown context (CN or CHN): 20.5% Bismark completed in 0d 0h 1m 26s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz CTRL_8C_26psu_1_S17_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz to CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz to CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz (100001 sequences in total) Input files are CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 GATAATGTTTATTTATTGTAGAGATAGAGATTGTAGAGGTTAGTATAAAGGTTGTGAATTAGGTAGAGAGAGAGAGAGTAAGGGAGAGTGAGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 GATAATGTTTATTTATTGTAGAGATAGAGATTGTAGAGGTTAGTATAAAGGTTGTGAATTAGGTAGAGAGAGAGAGAGTAAGGGAGAGTGAGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 AATAATATTTATTTATTATAAAAATAAAAATCATAAAAATTAATATAAAAATCATAAATTAAATAAAAAAAAAAAAAATAAAAAAAAATAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 AATAATATTTATTTATTATAAAAATAAAAATCATAAAAATTAATATAAAAATCATAAATTAAATAAAAAAAAAAAAAATAAAAAAAAATAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 70753 (70.75%) aligned 0 times 9665 (9.66%) aligned exactly 1 time 19582 (19.58%) aligned >1 times 29.25% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 70607 (70.61%) aligned 0 times 9890 (9.89%) aligned exactly 1 time 19503 (19.50%) aligned >1 times 29.39% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69233 (69.23%) aligned 0 times 10328 (10.33%) aligned exactly 1 time 20439 (20.44%) aligned >1 times 30.77% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69026 (69.03%) aligned 0 times 10530 (10.53%) aligned exactly 1 time 20444 (20.44%) aligned >1 times 30.97% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 55056 Mapping efficiency: 55.1% Sequences with no alignments under any condition: 23710 Sequences did not map uniquely: 21234 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 13535 ((converted) top strand) CT/GA: 13098 ((converted) bottom strand) GA/CT: 14081 (complementary to (converted) top strand) GA/GA: 14342 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1082195 Total methylated C's in CpG context: 73587 Total methylated C's in CHG context: 2118 Total methylated C's in CHH context: 12403 Total methylated C's in Unknown context: 606 Total unmethylated C's in CpG context: 23043 Total unmethylated C's in CHG context: 251193 Total unmethylated C's in CHH context: 719851 Total unmethylated C's in Unknown context: 2698 C methylated in CpG context: 76.2% C methylated in CHG context: 0.8% C methylated in CHH context: 1.7% C methylated in Unknown context (CN or CHN): 18.3% Bismark completed in 0d 0h 0m 47s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz to CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz to CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz (100001 sequences in total) Input files are CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 TTTTTTTATTTTTTTTTATTTTTTTTTTTTTTATTTAATTTATGATTTTTATATTAATTTTTATGATTTTTATTTTTATAATAAATAAATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 TTTTTTTATTTTTTTTTATTTTTTTTTTTTTTATTTAATTTATGATTTTTATATTAATTTTTATGATTTTTATTTTTATAATAAATAAATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 CTCTCTCACTCTCCCTTACTCTCTCTCTCTCTACCTAATTCACAACCTTTATACTAACCTCTACAATCTCTATCTCTACAATAAATAAACATTATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 CTCTCTCACTCTCCCTTACTCTCTCTCTCTCTACCTAATTCACAACCTTTATACTAACCTCTACAATCTCTATCTCTACAATAAATAAACATTATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/CTRL_8C_26psu_1_S17_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71862 (71.86%) aligned 0 times 9289 (9.29%) aligned exactly 1 time 18849 (18.85%) aligned >1 times 28.14% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71887 (71.89%) aligned 0 times 9350 (9.35%) aligned exactly 1 time 18763 (18.76%) aligned >1 times 28.11% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68878 (68.88%) aligned 0 times 10305 (10.30%) aligned exactly 1 time 20817 (20.82%) aligned >1 times 31.12% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68751 (68.75%) aligned 0 times 10455 (10.46%) aligned exactly 1 time 20794 (20.79%) aligned >1 times 31.25% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 53593 Mapping efficiency: 53.6% Sequences with no alignments under any condition: 25303 Sequences did not map uniquely: 21104 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12482 ((converted) top strand) CT/GA: 12628 ((converted) bottom strand) GA/CT: 14382 (complementary to (converted) top strand) GA/GA: 14101 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1057139 Total methylated C's in CpG context: 70836 Total methylated C's in CHG context: 2158 Total methylated C's in CHH context: 13722 Total methylated C's in Unknown context: 693 Total unmethylated C's in CpG context: 22598 Total unmethylated C's in CHG context: 242443 Total unmethylated C's in CHH context: 705382 Total unmethylated C's in Unknown context: 2662 C methylated in CpG context: 75.8% C methylated in CHG context: 0.9% C methylated in CHH context: 1.9% C methylated in Unknown context (CN or CHN): 20.7% Bismark completed in 0d 0h 1m 26s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 16C_32psu_4_S4_R1_001_val_1.fq.gz 16C_32psu_4_S4_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_32psu_4_S4_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 16C_32psu_4_S4_R1_001_val_1.fq.gz to 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_32psu_4_S4_R1_001_val_1.fq.gz to 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_32psu_4_S4_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 GATTATTGAGATTTTTTTTTTAATTTTATTTTGAAAGAGGTGTTTTTATTGGAGTAATGGTTTAAGGTATTGTATTGTAGTGGTTGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 GATTATTGAGATTTTTTTTTTAATTTTATTTTGAAAGAGGTGTTTTTATTGGAGTAATGGTTTAAGGTATTGTATTGTAGTGGTTGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 AATTATCAAAATTTTTTTTTTAATTTTATTTTAAAAAAAATATTTTTATTAAAATAATAATTTAAAATATTATATTATAATAATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 AATTATCAAAATTTTTTTTTTAATTTTATTTTAAAAAAAATATTTTTATTAAAATAATAATTTAAAATATTATATTATAATAATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/16C_32psu_4_S4_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 16C_32psu_4_S4_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 74100 (74.10%) aligned 0 times 9146 (9.15%) aligned exactly 1 time 16754 (16.75%) aligned >1 times 25.90% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71220 (71.22%) aligned 0 times 10273 (10.27%) aligned exactly 1 time 18507 (18.51%) aligned >1 times 28.78% overall alignment rate 100000 reads; of these: 100000100000 reads; of these: ( 100000 (100.00%) were unpaired; of these: 100.00 %71189) were unpaired; of these: ( 71.19 %74330) aligned 0 times ( 74.33 %10307) aligned 0 times ( 10.31 %8997) aligned exactly 1 time ( 9.00 %18504) aligned exactly 1 time ( 18.50 %16673) aligned >1 times ( 16.6728.81%%) aligned >1 times overall alignment rate 25.67% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 53643 Mapping efficiency: 53.6% Sequences with no alignments under any condition: 28673 Sequences did not map uniquely: 17684 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12494 ((converted) top strand) CT/GA: 12567 ((converted) bottom strand) GA/CT: 14275 (complementary to (converted) top strand) GA/GA: 14307 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1137104 Total methylated C's in CpG context: 76873 Total methylated C's in CHG context: 2406 Total methylated C's in CHH context: 14475 Total methylated C's in Unknown context: 824 Total unmethylated C's in CpG context: 24966 Total unmethylated C's in CHG context: 268165 Total unmethylated C's in CHH context: 750219 Total unmethylated C's in Unknown context: 3151 C methylated in CpG context: 75.5% C methylated in CHG context: 0.9% C methylated in CHH context: 1.9% C methylated in Unknown context (CN or CHN): 20.7% Bismark completed in 0d 0h 0m 49s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_32psu_4_S4_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 16C_32psu_4_S4_R2_001_val_2.fq.gz to 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_32psu_4_S4_R2_001_val_2.fq.gz to 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_32psu_4_S4_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 TTTAATTATTATAATATAATATTTTAAATTATTATTTTAATAAAAATATTTTTTTTAAAATAAAATTAAAAAAAAAATTTTGATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 TTTAATTATTATAATATAATATTTTAAATTATTATTTTAATAAAAATATTTTTTTTAAAATAAAATTAAAAAAAAAATTTTGATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 CTCAACCACTACAATACAATACCTTAAACCATTACTCCAATAAAAACACCTCTTTCAAAATAAAATTAAAAAAAAAATCTCAATAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.5 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 CTCAACCACTACAATACAATACCTTAAACCATTACTCCAATAAAAACACCTCTTTCAAAATAAAATTAAAAAAAAAATCTCAATAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.5/16C_32psu_4_S4_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 16C_32psu_4_S4_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 74290 (74.29%) aligned 0 times 9237 (9.24%) aligned exactly 1 time 16473 (16.47%) aligned >1 times 25.71% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 74268 (74.27%) aligned 0 times 9296 (9.30%) aligned exactly 1 time 16436 (16.44%) aligned >1 times 25.73% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 71927 (71.93%) aligned 0 times 9973 (9.97%) aligned exactly 1 time 18100 (18.10%) aligned >1 times 28.07% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 72152 (72.15%) aligned 0 times 9832 (9.83%) aligned exactly 1 time 18016 (18.02%) aligned >1 times 27.85% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 52522 Mapping efficiency: 52.5% Sequences with no alignments under any condition: 29928 Sequences did not map uniquely: 17550 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12594 ((converted) top strand) CT/GA: 12512 ((converted) bottom strand) GA/CT: 13658 (complementary to (converted) top strand) GA/GA: 13758 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1113857 Total methylated C's in CpG context: 74566 Total methylated C's in CHG context: 2348 Total methylated C's in CHH context: 13546 Total methylated C's in Unknown context: 796 Total unmethylated C's in CpG context: 24304 Total unmethylated C's in CHG context: 261579 Total unmethylated C's in CHH context: 737514 Total unmethylated C's in Unknown context: 3137 C methylated in CpG context: 75.4% C methylated in CHG context: 0.9% C methylated in CHH context: 1.8% C methylated in Unknown context (CN or CHN): 20.2% Bismark completed in 0d 0h 1m 32s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 16C_26psu_1_S13_R1_001_val_1.fq.gz 16C_26psu_1_S13_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_26psu_1_S13_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 16C_26psu_1_S13_R1_001_val_1.fq.gz to 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_26psu_1_S13_R1_001_val_1.fq.gz to 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_26psu_1_S13_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATTTATTTATAAAAAAAATAAAAAAAAAATAAAAAAAAATTAATATTATATATTTTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATTTATTTATAAAAAAAATAAAAAAAAAATAAAAAAAAATTAATATTATATATTTTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 4 * 0 0 * * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_1:N:0:NGTCAA 0 NC_027306.1_GA_converted 27312195 42 61M * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:61 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/16C_26psu_1_S13_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 16C_26psu_1_S13_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68874 (68.87%) aligned 0 times 8990 (8.99%) aligned exactly 1 time 22136 (22.14%) aligned >1 times 31.13% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68926 (68.93%) aligned 0 times 8987 (8.99%) aligned exactly 1 time 22087 (22.09%) aligned >1 times 31.07% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68097 (68.10%) aligned 0 times 9207 (9.21%) aligned exactly 1 time 22696 (22.70%) aligned >1 times 31.90% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68240 (68.24%) aligned 0 times 9153 (9.15%) aligned exactly 1 time 22607 (22.61%) aligned >1 times 31.76% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_26psu_1_S13_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 52913 Mapping efficiency: 52.9% Sequences with no alignments under any condition: 24656 Sequences did not map uniquely: 22431 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12924 ((converted) top strand) CT/GA: 13071 ((converted) bottom strand) GA/CT: 13380 (complementary to (converted) top strand) GA/GA: 13538 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1050770 Total methylated C's in CpG context: 77759 Total methylated C's in CHG context: 2673 Total methylated C's in CHH context: 18321 Total methylated C's in Unknown context: 1122 Total unmethylated C's in CpG context: 25759 Total unmethylated C's in CHG context: 254376 Total unmethylated C's in CHH context: 671882 Total unmethylated C's in Unknown context: 4161 C methylated in CpG context: 75.1% C methylated in CHG context: 1.0% C methylated in CHH context: 2.7% C methylated in Unknown context (CN or CHN): 21.2% Bismark completed in 0d 0h 0m 47s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_26psu_1_S13_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 16C_26psu_1_S13_R2_001_val_2.fq.gz to 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_26psu_1_S13_R2_001_val_2.fq.gz to 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_26psu_1_S13_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAGGAAGTGTATGATATTAGTTTTTTTTTGTTTTTTTTTTGTTTTTTTTGTAAATGGATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 16 NC_027306.1_GA_converted 27312195 42 61M * 0 0 AATCCATTTACAAAAAAAACAAAAAAAAAACAAAAAAAAACTAATATCATACACTTCCTTT FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:61 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAAAAAATATATAATATTAATTTTTTTTTATTTTTTTTTTATTTTTTTTATAAATAAATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1262:1016_2:N:0:NGTCAA 4 * 0 0 * * 0 0 AAAAAAAATATATAATATTAATTTTTTTTTATTTTTTTTTTATTTTTTTTATAAATAAATT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/16C_26psu_1_S13_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 16C_26psu_1_S13_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 67068 (67.07%) aligned 0 times 9418 (9.42%) aligned exactly 1 time 23514 (23.51%) aligned >1 times 32.93% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 67031 (67.03%) aligned 0 times 9510 (9.51%) aligned exactly 1 time 23459 (23.46%) aligned >1 times 32.97% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 70649 (70.65%) aligned 0 times 8353 (8.35%) aligned exactly 1 time 20998 (21.00%) aligned >1 times 29.35% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 70769 (70.77%) aligned 0 times 8314 (8.31%) aligned exactly 1 time 20917 (20.92%) aligned >1 times 29.23% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_26psu_1_S13_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_26psu_1_S13_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 52081 Mapping efficiency: 52.1% Sequences with no alignments under any condition: 25661 Sequences did not map uniquely: 22258 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12090 ((converted) top strand) CT/GA: 12132 ((converted) bottom strand) GA/CT: 13879 (complementary to (converted) top strand) GA/GA: 13980 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1039579 Total methylated C's in CpG context: 76228 Total methylated C's in CHG context: 2512 Total methylated C's in CHH context: 18276 Total methylated C's in Unknown context: 1151 Total unmethylated C's in CpG context: 25308 Total unmethylated C's in CHG context: 249054 Total unmethylated C's in CHH context: 668201 Total unmethylated C's in Unknown context: 4232 C methylated in CpG context: 75.1% C methylated in CHG context: 1.0% C methylated in CHH context: 2.7% C methylated in Unknown context (CN or CHN): 21.4% Bismark completed in 0d 0h 1m 26s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 8C_32psu_3_S7_R1_001_val_1.fq.gz 8C_32psu_3_S7_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_32psu_3_S7_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 8C_32psu_3_S7_R1_001_val_1.fq.gz to 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_32psu_3_S7_R1_001_val_1.fq.gz to 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_32psu_3_S7_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 4 * 0 0 * * 0 0 TTTAAAAATAATTTTATTAAAAAATTATATTTTATAATAATTTAAATATTATGTTTAAAAAAATATGTGTTATGATATAAATTAAATGTTATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 4 * 0 0 * * 0 0 TTTAAAAATAATTTTATTAAAAAATTATATTTTATAATAATTTAAATATTATGTTTAAAAAAATATGTGTTATGATATAAATTAAATGTTATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 16 NC_027320.1_CT_converted 57131408 1 97M * 0 0 TTAATATGATGTTTAGTTTGTATTGTAATGTGTATTTTTTTGGGTGTAGTGTTTAGATTATTGTAAAGTGTGATTTTTTAGTAAGGTTATTTTTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_1:N:0:NAGATC 0 NC_027309.1_GA_converted 6145322 1 97M * 0 0 TTTAAAAATAACCTTACTAAAAAATCACACTTTACAATAATCTAAACACTACACCCAAAAAAATACACATTACAATACAAACTAAACATCATATTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/8C_32psu_3_S7_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 8C_32psu_3_S7_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 66386 (66.39%) aligned 0 times 9239 (9.24%) aligned exactly 1 time 24375 (24.38%) aligned >1 times 33.61% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 66325 (66.33%) aligned 0 times 9153 (9.15%) aligned exactly 1 time 24522 (24.52%) aligned >1 times 33.67% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 66320 (66.32%) aligned 0 times 9228 (9.23%) aligned exactly 1 time 24452 (24.45%) aligned >1 times 33.68% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 66356 (66.36%) aligned 0 times 9155 (9.15%) aligned exactly 1 time 24489 (24.49%) aligned >1 times 33.64% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_32psu_3_S7_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 52686 Mapping efficiency: 52.7% Sequences with no alignments under any condition: 21859 Sequences did not map uniquely: 25455 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 13175 ((converted) top strand) CT/GA: 13216 ((converted) bottom strand) GA/CT: 13258 (complementary to (converted) top strand) GA/GA: 13037 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 977266 Total methylated C's in CpG context: 74108 Total methylated C's in CHG context: 2392 Total methylated C's in CHH context: 18432 Total methylated C's in Unknown context: 984 Total unmethylated C's in CpG context: 24640 Total unmethylated C's in CHG context: 239877 Total unmethylated C's in CHH context: 617817 Total unmethylated C's in Unknown context: 3745 C methylated in CpG context: 75.0% C methylated in CHG context: 1.0% C methylated in CHH context: 2.9% C methylated in Unknown context (CN or CHN): 20.8% Bismark completed in 0d 0h 0m 47s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_32psu_3_S7_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 8C_32psu_3_S7_R2_001_val_2.fq.gz to 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_32psu_3_S7_R2_001_val_2.fq.gz to 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_32psu_3_S7_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 0 NC_027311.1_CT_converted 87079143 1 97M * 0 0 TTAATATGATGTTTAGTTTGTATTGTAATGTGTATTTTTTTGGGTGTAGTGTTTAGATTATTGTAAAGTGTGATTTTTTAGTAAGGTTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 16 NC_027312.1_GA_converted 56312130 1 97M * 0 0 TTTAAAAATAACCTTACTAAAAAATCACACTTTACAATAATCTAAACACTACACCCAAAAAAATACACATTACAATACAAACTAAACATCATATTAA F:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFFFFFFFFFFFFFF:FF,F:FFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 4 * 0 0 * * 0 0 TTAATATAACATTTAATTTATATCATAACACATATTTTTTTAAACATAATATTTAAATTATTATAAAATATAATTTTTTAATAAAATTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1931:1016_2:N:0:NAGATC 4 * 0 0 * * 0 0 TTAATATAACATTTAATTTATATCATAACACATATTTTTTTAAACATAATATTTAAATTATTATAAAATATAATTTTTTAATAAAATTATTTTTAAA FFFFFFFF:F,FF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/8C_32psu_3_S7_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 8C_32psu_3_S7_R2_001_val_2.fq.gz 100000100000 reads; of these: reads; of these: 100000100000 ( (100.00100.00%%) were unpaired; of these:) were unpaired; of these: 6528268211 ( (65.2868.21%%) aligned 0 times) aligned 0 times 93918594 ( (9.398.59%%) aligned exactly 1 time) aligned exactly 1 time 2532723195 ( (25.3323.20%%) aligned >1 times) aligned >1 times 34.7231.79%% overall alignment rate overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 65242 (65.24%) aligned 0 times 9471 (9.47%) aligned exactly 1 time 25287 (25.29%) aligned >1 times 34.76% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68229 (68.23%) aligned 0 times 8670 (8.67%) aligned exactly 1 time 23101 (23.10%) aligned >1 times 31.77% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_32psu_3_S7_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_32psu_3_S7_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 51885 Mapping efficiency: 51.9% Sequences with no alignments under any condition: 22939 Sequences did not map uniquely: 25176 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12239 ((converted) top strand) CT/GA: 12102 ((converted) bottom strand) GA/CT: 13752 (complementary to (converted) top strand) GA/GA: 13792 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 966716 Total methylated C's in CpG context: 72722 Total methylated C's in CHG context: 2317 Total methylated C's in CHH context: 19196 Total methylated C's in Unknown context: 1037 Total unmethylated C's in CpG context: 23914 Total unmethylated C's in CHG context: 234794 Total unmethylated C's in CHH context: 613773 Total unmethylated C's in Unknown context: 3663 C methylated in CpG context: 75.3% C methylated in CHG context: 1.0% C methylated in CHH context: 3.0% C methylated in Unknown context (CN or CHN): 22.1% Bismark completed in 0d 0h 1m 26s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 8C_26psu_2_S10_R1_001_val_1.fq.gz 8C_26psu_2_S10_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_26psu_2_S10_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 8C_26psu_2_S10_R1_001_val_1.fq.gz to 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_26psu_2_S10_R1_001_val_1.fq.gz to 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_26psu_2_S10_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 0 NC_027317.1_CT_converted 34397130 1 39M * 0 0 TTATTGTGTGAAAGAAGGTGTGTTTTTAGTTTTTTATAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:11T27 YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 16 NC_027317.1_GA_converted 38626155 1 39M * 0 0 CTATAAAAAACTAAAAACACACCTTCTTTCACACAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:27A11 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATTATATAAAAAAAAATATATTTTTAATTTTTTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_1:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATTATATAAAAAAAAATATATTTTTAATTTTTTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/8C_26psu_2_S10_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 8C_26psu_2_S10_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 66641 (66.64%) aligned 0 times 9859 (9.86%) aligned exactly 1 time 23500 (23.50%) aligned >1 times 33.36% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 66718 (66.72%) aligned 0 times 9642 (9.64%) aligned exactly 1 time 23640 (23.64%) aligned >1 times 10000033.28 reads; of these:% overall alignment rate 100000 (100.00%) were unpaired; of these: 66831 (66.83%) aligned 0 times 9692 (9.69%) aligned exactly 1 time 23477 (23.48%) aligned >1 times 33.17% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 66796 (66.80%) aligned 0 times 9837 (9.84%) aligned exactly 1 time 23367 (23.37%) aligned >1 times 33.20% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_26psu_2_S10_R1_001_val_1.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 55881 Mapping efficiency: 55.9% Sequences with no alignments under any condition: 20702 Sequences did not map uniquely: 23417 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 13850 ((converted) top strand) CT/GA: 14049 ((converted) bottom strand) GA/CT: 14089 (complementary to (converted) top strand) GA/GA: 13893 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1079670 Total methylated C's in CpG context: 78390 Total methylated C's in CHG context: 2617 Total methylated C's in CHH context: 16833 Total methylated C's in Unknown context: 1012 Total unmethylated C's in CpG context: 25189 Total unmethylated C's in CHG context: 262738 Total unmethylated C's in CHH context: 693903 Total unmethylated C's in Unknown context: 3755 C methylated in CpG context: 75.7% C methylated in CHG context: 1.0% C methylated in CHH context: 2.4% C methylated in Unknown context (CN or CHN): 21.2% Bismark completed in 0d 0h 0m 47s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 8C_26psu_2_S10_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 8C_26psu_2_S10_R2_001_val_2.fq.gz to 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 8C_26psu_2_S10_R2_001_val_2.fq.gz to 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 8C_26psu_2_S10_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATAAAAAATTAAAAATATATTTTTTTTTATATAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 4 * 0 0 * * 0 0 TTATAAAAAATTAAAAATATATTTTTTTTTATATAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 16 NC_027317.1_CT_converted 34396730 1 39M * 0 0 TTATTGTGTGAAAGAAGGTGTGTTTTTAGTTTTTTATAG FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:11T27 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1588:1016_2:N:0:NAGCTT 0 NC_027317.1_GA_converted 38626317 1 39M * 0 0 CTATAAAAAACTAAAAACACACCTTCTTTCACACAATAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:27A11 YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/8C_26psu_2_S10_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 8C_26psu_2_S10_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69122 (69.12%) aligned 0 times 9053 (9.05%) aligned exactly 1 time 21825 (21.82%) aligned >1 times 30.88% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69232 (69.23%) aligned 0 times 8935 (8.94%) aligned exactly 1 time 21833 (21.83%) aligned >1 times 30.77% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 65284 (65.28%) aligned 0 times 10020 (10.02%) aligned exactly 1 time 24696 (24.70%) aligned >1 times 34.72% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 65190 (65.19%) aligned 0 times 10225 (10.22%) aligned exactly 1 time 24585 (24.59%) aligned >1 times 34.81% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 8C_26psu_2_S10_R2_001_val_2.fq.gz_C_to_T.fastq and 8C_26psu_2_S10_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 54815 Mapping efficiency: 54.8% Sequences with no alignments under any condition: 21963 Sequences did not map uniquely: 23222 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12782 ((converted) top strand) CT/GA: 12586 ((converted) bottom strand) GA/CT: 14667 (complementary to (converted) top strand) GA/GA: 14780 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1065379 Total methylated C's in CpG context: 76825 Total methylated C's in CHG context: 2579 Total methylated C's in CHH context: 18673 Total methylated C's in Unknown context: 972 Total unmethylated C's in CpG context: 24575 Total unmethylated C's in CHG context: 256344 Total unmethylated C's in CHH context: 686383 Total unmethylated C's in Unknown context: 3815 C methylated in CpG context: 75.8% C methylated in CHG context: 1.0% C methylated in CHH context: 2.6% C methylated in Unknown context (CN or CHN): 20.3% Bismark completed in 0d 0h 1m 25s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz CTRL_8C_26psu_1_S17_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz to CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz to CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz (100001 sequences in total) Input files are CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 GATAATGTTTATTTATTGTAGAGATAGAGATTGTAGAGGTTAGTATAAAGGTTGTGAATTAGGTAGAGAGAGAGAGAGTAAGGGAGAGTGAGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 GATAATGTTTATTTATTGTAGAGATAGAGATTGTAGAGGTTAGTATAAAGGTTGTGAATTAGGTAGAGAGAGAGAGAGTAAGGGAGAGTGAGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 AATAATATTTATTTATTATAAAAATAAAAATCATAAAAATTAATATAAAAATCATAAATTAAATAAAAAAAAAAAAAATAAAAAAAAATAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_1:N:0:NTAGAG 4 * 0 0 * * 0 0 AATAATATTTATTTATTATAAAAATAAAAATCATAAAAATTAATATAAAAATCATAAATTAAATAAAAAAAAAAAAAATAAAAAAAAATAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 66921 (66.92%) aligned 0 times 10352 (10.35%) aligned exactly 1 time 22727 (22.73%) aligned >1 times 33.08% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 66723 (66.72%) aligned 0 times 10475 (10.47%) aligned exactly 1 time 22802 (22.80%) aligned >1 times 33.28% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68580 (68.58%) aligned 0 times 9700 (9.70%) aligned exactly 1 time 21720 (21.72%) aligned >1 times 31.42% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68448 (68.45%) aligned 0 times 9829 (9.83%) aligned exactly 1 time 21723 (21.72%) aligned >1 times 31.55% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 57317 Mapping efficiency: 57.3% Sequences with no alignments under any condition: 20992 Sequences did not map uniquely: 21691 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 14085 ((converted) top strand) CT/GA: 13658 ((converted) bottom strand) GA/CT: 14671 (complementary to (converted) top strand) GA/GA: 14903 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1129158 Total methylated C's in CpG context: 76294 Total methylated C's in CHG context: 2433 Total methylated C's in CHH context: 15142 Total methylated C's in Unknown context: 875 Total unmethylated C's in CpG context: 24451 Total unmethylated C's in CHG context: 261309 Total unmethylated C's in CHH context: 749529 Total unmethylated C's in Unknown context: 3895 C methylated in CpG context: 75.7% C methylated in CHG context: 0.9% C methylated in CHH context: 2.0% C methylated in Unknown context (CN or CHN): 18.3% Bismark completed in 0d 0h 0m 49s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz to CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz to CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz (100001 sequences in total) Input files are CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 TTTTTTTATTTTTTTTTATTTTTTTTTTTTTTATTTAATTTATGATTTTTATATTAATTTTTATGATTTTTATTTTTATAATAAATAAATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 TTTTTTTATTTTTTTTTATTTTTTTTTTTTTTATTTAATTTATGATTTTTATATTAATTTTTATGATTTTTATTTTTATAATAAATAAATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 CTCTCTCACTCTCCCTTACTCTCTCTCTCTCTACCTAATTCACAACCTTTATACTAACCTCTACAATCTCTATCTCTACAATAAATAAACATTATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:1298:1016_2:N:0:NTAGAG 4 * 0 0 * * 0 0 CTCTCTCACTCTCCCTTACTCTCTCTCTCTCTACCTAATTCACAACCTTTATACTAACCTCTACAATCTCTATCTCTACAATAAATAAACATTATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:F:FFFF:FFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/CTRL_8C_26psu_1_S17_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69681 (69.68%) aligned 0 times 9378 (9.38%) aligned exactly 1 time 20941 (20.94%) aligned >1 times 30.32% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69700 (69.70%) aligned 0 times 9335 (9.34%) aligned exactly 1 time 20965 (20.96%) aligned >1 times 30.30% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 66564 (66.56%) aligned 0 times 10350 (10.35%) aligned exactly 1 time 23086 (23.09%) aligned >1 times 33.44% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 66514 (66.51%) aligned 0 times 10401 (10.40%) aligned exactly 1 time 23085 (23.09%) aligned >1 times 33.49% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_C_to_T.fastq and CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 55904 Mapping efficiency: 55.9% Sequences with no alignments under any condition: 22490 Sequences did not map uniquely: 21606 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 13020 ((converted) top strand) CT/GA: 13212 ((converted) bottom strand) GA/CT: 14978 (complementary to (converted) top strand) GA/GA: 14694 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1105799 Total methylated C's in CpG context: 73524 Total methylated C's in CHG context: 2408 Total methylated C's in CHH context: 16498 Total methylated C's in Unknown context: 973 Total unmethylated C's in CpG context: 24065 Total unmethylated C's in CHG context: 252817 Total unmethylated C's in CHH context: 736487 Total unmethylated C's in Unknown context: 3886 C methylated in CpG context: 75.3% C methylated in CHG context: 0.9% C methylated in CHH context: 2.2% C methylated in Unknown context (CN or CHN): 20.0% Bismark completed in 0d 0h 1m 28s ==================== Bismark run complete ==================== Bowtie 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/strigg/data/Ssalar/GENOMES/chr1-29MT/ (absolute path is '/gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200612'): 16C_32psu_4_S4_R1_001_val_1.fq.gz 16C_32psu_4_S4_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 Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20200612 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ chr NC_027300.1 (159038749 bp) chr NC_027301.1 (72943711 bp) chr NC_027302.1 (92503428 bp) chr NC_027303.1 (82398023 bp) chr NC_027304.1 (80503876 bp) chr NC_027305.1 (87043187 bp) chr NC_027306.1 (58785265 bp) chr NC_027307.1 (26434011 bp) chr NC_027308.1 (141712163 bp) chr NC_027309.1 (116138521 bp) chr NC_027310.1 (93888508 bp) chr NC_027311.1 (91880962 bp) chr NC_027312.1 (107758822 bp) chr NC_027313.1 (93901823 bp) chr NC_027314.1 (103963436 bp) chr NC_027315.1 (87796322 bp) chr NC_027316.1 (57682537 bp) chr NC_027317.1 (70695409 bp) chr NC_027318.1 (82978132 bp) chr NC_027319.1 (86795997 bp) chr NC_027320.1 (58021487 bp) chr NC_027321.1 (63420196 bp) chr NC_027322.1 (49854004 bp) chr NC_027323.1 (48650976 bp) chr NC_027324.1 (51481326 bp) chr NC_027325.1 (47900953 bp) chr NC_027326.1 (43943985 bp) chr NC_027327.1 (39600944 bp) chr NC_027328.1 (42488238 bp) chr NC_001960.1 (16665 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_32psu_4_S4_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file 16C_32psu_4_S4_R1_001_val_1.fq.gz to 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_32psu_4_S4_R1_001_val_1.fq.gz to 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_32psu_4_S4_R1_001_val_1.fq.gz (100001 sequences in total) Input files are 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 GATTATTGAGATTTTTTTTTTAATTTTATTTTGAAAGAGGTGTTTTTATTGGAGTAATGGTTTAAGGTATTGTATTGTAGTGGTTGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 GATTATTGAGATTTTTTTTTTAATTTTATTTTGAAAGAGGTGTTTTTATTGGAGTAATGGTTTAAGGTATTGTATTGTAGTGGTTGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 AATTATCAAAATTTTTTTTTTAATTTTATTTTAAAAAAAATATTTTTATTAAAATAATAATTTAAAATATTATATTATAATAATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_1:N:0:NGACCA 4 * 0 0 * * 0 0 AATTATCAAAATTTTTTTTTTAATTTTATTTTAAAAAAAATATTTTTATTAAAATAATAATTTAAAATATTATATTATAATAATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/16C_32psu_4_S4_R1_001_val_1_bismark_bt2.bam <<< Reading in the sequence file 16C_32psu_4_S4_R1_001_val_1.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68873 (68.87%) aligned 0 times 10381 (10.38%) aligned exactly 1 time 20746 (20.75%) aligned >1 times 31.13% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 68969 (68.97%) aligned 0 times 10232 (10.23%) aligned exactly 1 time 20799 (20.80%) aligned >1 times 31.03% overall alignment rate 100000100000 reads; of these: reads; of these: 100000100000 ( (100.00100.00%%) were unpaired; of these:) were unpaired; of these: 7207971988 ( (72.0871.99%%) aligned 0 times) aligned 0 times 91309232 ( (9.139.23%%) aligned exactly 1 time) aligned exactly 1 time 1879118780 ( (18.7918.78%%) aligned >1 times) aligned >1 times 27.9228.01%% overall alignment rate overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_32psu_4_S4_R1_001_val_1.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R1_001_val_1.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 56387 Mapping efficiency: 56.4% Sequences with no alignments under any condition: 25482 Sequences did not map uniquely: 18131 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 13205 ((converted) top strand) CT/GA: 13190 ((converted) bottom strand) GA/CT: 14985 (complementary to (converted) top strand) GA/GA: 15007 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1195685 Total methylated C's in CpG context: 80233 Total methylated C's in CHG context: 2729 Total methylated C's in CHH context: 17356 Total methylated C's in Unknown context: 1173 Total unmethylated C's in CpG context: 26870 Total unmethylated C's in CHG context: 280835 Total unmethylated C's in CHH context: 787662 Total unmethylated C's in Unknown context: 4690 C methylated in CpG context: 74.9% C methylated in CHG context: 1.0% C methylated in CHH context: 2.2% C methylated in Unknown context (CN or CHN): 20.0% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 100000 from 16C_32psu_4_S4_R2_001_val_2.fq.gz Writing a C -> T converted version of the input file 16C_32psu_4_S4_R2_001_val_2.fq.gz to 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 16C_32psu_4_S4_R2_001_val_2.fq.gz to 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 16C_32psu_4_S4_R2_001_val_2.fq.gz (100001 sequences in total) Input files are 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 TTTAATTATTATAATATAATATTTTAAATTATTATTTTAATAAAAATATTTTTTTTAAAATAAAATTAAAAAAAAAATTTTGATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 TTTAATTATTATAATATAATATTTTAAATTATTATTTTAATAAAAATATTTTTTTTAAAATAAAATTAAAAAAAAAATTTTGATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 CTCAACCACTACAATACAATACCTTAAACCATTACTCCAATAAAAACACCTCTTTCAAAATAAAATTAAAAAAAAAATCTCAATAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq with options -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: A00177:85:HCW7VDRXX:1:2101:2022:1016_2:N:0:NGACCA 4 * 0 0 * * 0 0 CTCAACCACTACAATACAATACCTTAAACCATTACTCCAATAAAAACACCTCTTTCAAAATAAAATTAAAAAAAAAATCTCAATAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UU >>> Writing bisulfite mapping results to /gscratch/scrubbed/strigg/analyses/20200612/AS_0.6/16C_32psu_4_S4_R2_001_val_2_bismark_bt2.bam <<< Reading in the sequence file 16C_32psu_4_S4_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 72030 (72.03%) aligned 0 times 9302 (9.30%) aligned exactly 1 time 18668 (18.67%) aligned >1 times 27.97% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69926 (69.93%) aligned 0 times 9803 (9.80%) aligned exactly 1 time 20271 (20.27%) aligned >1 times 30.07% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 72047 (72.05%) aligned 0 times 9401 (9.40%) aligned exactly 1 time 18552 (18.55%) aligned >1 times 27.95% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 69844 (69.84%) aligned 0 times 9893 (9.89%) aligned exactly 1 time 20263 (20.26%) aligned >1 times 30.16% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 16C_32psu_4_S4_R2_001_val_2.fq.gz_C_to_T.fastq and 16C_32psu_4_S4_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 55224 Mapping efficiency: 55.2% Sequences with no alignments under any condition: 26686 Sequences did not map uniquely: 18090 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 13287 ((converted) top strand) CT/GA: 13199 ((converted) bottom strand) GA/CT: 14351 (complementary to (converted) top strand) GA/GA: 14387 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1172484 Total methylated C's in CpG context: 77898 Total methylated C's in CHG context: 2697 Total methylated C's in CHH context: 16930 Total methylated C's in Unknown context: 1184 Total unmethylated C's in CpG context: 26108 Total unmethylated C's in CHG context: 274269 Total unmethylated C's in CHH context: 774582 Total unmethylated C's in Unknown context: 4639 C methylated in CpG context: 74.9% C methylated in CHG context: 1.0% C methylated in CHH context: 2.1% C methylated in Unknown context (CN or CHN): 20.3% Bismark completed in 0d 0h 1m 28s ==================== Bismark run complete ====================