/var/spool/slurm/d/job1155861/slurm_script: line 22: 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.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 Created output directory /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test/AS-0.2/! Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test/AS-0.2/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz to Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz to Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz to Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz to Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 TNTTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 CNCCAATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AATAAAATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 CNCCAATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AATAAAATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 TNTTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F1_S20_L001_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99922 (99.92%) aligned concordantly 0 times 22 (0.02%) aligned concordantly exactly 1 time 56 (0.06%) aligned concordantly >1 times 0.08% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99919 (99.92%) aligned concordantly 0 times 26 (0.03%) aligned concordantly exactly 1 time 55 (0.06%) aligned concordantly >1 times 0.08% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99943 (99.94%) aligned concordantly 0 times 21 (0.02%) aligned concordantly exactly 1 time 36 (0.04%) aligned concordantly >1 times 0.06% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99945 (99.94%) aligned concordantly 0 times 15 (0.01%) aligned concordantly exactly 1 time 40 (0.04%) aligned concordantly >1 times 0.06% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 83 Mapping efficiency: 0.1% Sequence pairs with no alignments under any condition: 99829 Sequence pairs did not map uniquely: 88 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 22 ((converted) top strand) GA/CT/CT: 20 (complementary to (converted) top strand) GA/CT/GA: 20 (complementary to (converted) bottom strand) CT/GA/GA: 21 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 3775 Total methylated C's in CpG context: 10 Total methylated C's in CHG context: 9 Total methylated C's in CHH context: 20 Total methylated C's in Unknown context: 3 Total unmethylated C's in CpG context: 620 Total unmethylated C's in CHG context: 633 Total unmethylated C's in CHH context: 2483 Total unmethylated C's in Unknown context: 21 C methylated in CpG context: 1.6% C methylated in CHG context: 1.4% C methylated in CHH context: 0.8% C methylated in unknown context (CN or CHN): 12.5% Bismark completed in 0d 0h 0m 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.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/20190806_100K_Calig_test/AS-0.2/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz to Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz to Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz to Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz to Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 TNATTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTGTTTTTTTTAGGAAGTGTTAGGTATAATTTTGTTTGGTATAAAATAAATAAAGGATTAATTTTATTTTATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TCCACAATTCCAAACAACTCACTAAACTACCACCCAACTAAACAAATAATAAAATTAAACACAATACTTTCCATATCAATATTTCTTTCCTCAACATTTTTAATCAAAAAATAACCTTCAAACTCAATAATATAAAATAAATAACTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 CNACTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTATTTTTTTTAAAAAATATTAAATATAATTTTATTTAATATAAAATAAATAAAAAATTAATTTTATTTTATAAATTATTTATTTTATATTATTAAATTTAAAAATTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TTTATAATTTTAAATAATTTATTAAATTATTATTTAATTAAATAAATAATAAAATTAAATATAATATTTTTTATATTAATATTTTTTTTTTTAATATTTTTAATTAAAAAATAATTTTTAAATTTAATAATATAAAATAAATAATTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 CNACTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTATTTTTTTTAAAAAATATTAAATATAATTTTATTTAATATAAAATAAATAAAAAATTAATTTTATTTTATAAATTATTTATTTTATATTATTAAATTTAAAAATTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TTTATAATTTTAAATAATTTATTAAATTATTATTTAATTAAATAAATAATAAAATTAAATATAATATTTTTTATATTAATATTTTTTTTTTTAATATTTTTAATTAAAAAATAATTTTTAAATTTAATAATATAAAATAAATAATTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 TNATTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTGTTTTTTTTAGGAAGTGTTAGGTATAATTTTGTTTGGTATAAAATAAATAAAGGATTAATTTTATTTTATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TCCACAATTCCAAACAACTCACTAAACTACCACCCAACTAAACAAATAATAAAATTAAACACAATACTTTCCATATCAATATTTCTTTCCTCAACATTTTTAATCAAAAAATAACCTTCAAACTCAATAATATAAAATAAATAACTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F1_S20_L002_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99909 (99.91%) aligned concordantly 0 times 18 (0.02%) aligned concordantly exactly 1 time 73 (0.07%) aligned concordantly >1 times 0.09% overall alignment rate 100000 reads; of these: 100000 (100.00100000% reads; of these:) were paired; of these: 10000099896 ( (99.90%) aligned concordantly 0 times 100.00 %29) were paired; of these: ( 0.03 %99861) aligned concordantly exactly 1 time ( 99.86 %75) aligned concordantly 0 times ( 0.07 %35) aligned concordantly >1 times ( 0.040.10%%) aligned concordantly exactly 1 time overall alignment rate 104 (1000000.10 reads; of these:% ) aligned concordantly >1 times 1000000.14 (% overall alignment rate 100.00%) were paired; of these: 99859 (99.86%) aligned concordantly 0 times 40 (0.04%) aligned concordantly exactly 1 time 101 (0.10%) aligned concordantly >1 times 0.14% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 136 Mapping efficiency: 0.1% Sequence pairs with no alignments under any condition: 99711 Sequence pairs did not map uniquely: 153 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 46 ((converted) top strand) GA/CT/CT: 19 (complementary to (converted) top strand) GA/CT/GA: 33 (complementary to (converted) bottom strand) CT/GA/GA: 38 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 6645 Total methylated C's in CpG context: 10 Total methylated C's in CHG context: 4 Total methylated C's in CHH context: 74 Total methylated C's in Unknown context: 1 Total unmethylated C's in CpG context: 997 Total unmethylated C's in CHG context: 1119 Total unmethylated C's in CHH context: 4441 Total unmethylated C's in Unknown context: 21 C methylated in CpG context: 1.0% C methylated in CHG context: 0.4% C methylated in CHH context: 1.6% C methylated in unknown context (CN or CHN): 4.5% Bismark completed in 0d 0h 0m 31s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.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/20190806_100K_Calig_test/AS-0.2/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz to Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz to Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz to Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz to Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANTTGAATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTCTTATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANCTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTTTTATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANCTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTTTTATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANTTGAATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTCTTATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F2_S22_L001_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99915 (99.92%) aligned concordantly 0 times 29 (0.03%) aligned concordantly exactly 1 time 56 (0.06%) aligned concordantly >1 times 0.09% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99923 (99.92%) aligned concordantly 0 times 15 (0.01%) aligned concordantly exactly 1 time 62 (0.06%) aligned concordantly >1 times 0.08% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99926 (99.93%) aligned concordantly 0 times 21 (0.02%) aligned concordantly exactly 1 time 53 (0.05%) aligned concordantly >1 times 0.07% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99933 (99.93%) aligned concordantly 0 times 15 (0.01%) aligned concordantly exactly 1 time 52 (0.05%) aligned concordantly >1 times 0.07% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 93 Mapping efficiency: 0.1% Sequence pairs with no alignments under any condition: 99813 Sequence pairs did not map uniquely: 94 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 20 ((converted) top strand) GA/CT/CT: 19 (complementary to (converted) top strand) GA/CT/GA: 25 (complementary to (converted) bottom strand) CT/GA/GA: 29 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 4463 Total methylated C's in CpG context: 5 Total methylated C's in CHG context: 5 Total methylated C's in CHH context: 24 Total methylated C's in Unknown context: 5 Total unmethylated C's in CpG context: 779 Total unmethylated C's in CHG context: 801 Total unmethylated C's in CHH context: 2849 Total unmethylated C's in Unknown context: 25 C methylated in CpG context: 0.6% C methylated in CHG context: 0.6% C methylated in CHH context: 0.8% C methylated in unknown context (CN or CHN): 16.7% Bismark completed in 0d 0h 0m 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.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/20190806_100K_Calig_test/AS-0.2/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz to Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz to Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz to Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz to Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 77 * 0 0 * * 0 0 ANATAATTTATAAAAATTTAATTTTTATTTTTTTTAATTTTATTTTAATTTTTTTATTTTTTAAAAATAATATATTAAATTTAATAAATATATTTTAGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 141 * 0 0 * * 0 0 CCTAAAATATATTTATTAAATTTAATATATTATTTTTAAAAAATAAAAAAATTAAAATAAAATTAAAAAAAATAAAAATTAAATTTTTATAAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 77 * 0 0 * * 0 0 ANACAATCCACAAAAACCTAATTTCTACCTTCCCTAACTCCACCCTAACCTCTCCACCCTCCAAAAATAACACACTAAATTCAATAAATATATTTTAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 141 * 0 0 * * 0 0 TTTAAAATATATTTATTGAATTTAGTGTGTTATTTTTGGAGGGTGGAGAGGTTAGGGTGGAGTTAGGGAAGGTAGAAATTAGGTTTTTGTGGATTGTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 77 * 0 0 * * 0 0 ANACAATCCACAAAAACCTAATTTCTACCTTCCCTAACTCCACCCTAACCTCTCCACCCTCCAAAAATAACACACTAAATTCAATAAATATATTTTAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 141 * 0 0 * * 0 0 TTTAAAATATATTTATTGAATTTAGTGTGTTATTTTTGGAGGGTGGAGAGGTTAGGGTGGAGTTAGGGAAGGTAGAAATTAGGTTTTTGTGGATTGTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 77 * 0 0 * * 0 0 ANATAATTTATAAAAATTTAATTTTTATTTTTTTTAATTTTATTTTAATTTTTTTATTTTTTAAAAATAATATATTAAATTTAATAAATATATTTTAGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 141 * 0 0 * * 0 0 CCTAAAATATATTTATTAAATTTAATATATTATTTTTAAAAAATAAAAAAATTAAAATAAAATTAAAAAAAATAAAAATTAAATTTTTATAAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F2_S22_L002_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99990 (99.99%) aligned concordantly 0 times 0 (0.00%) aligned concordantly exactly 1 time 10 (0.01%) aligned concordantly >1 times 0.01% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99988 (99.99%) aligned concordantly 0 times 4 (0.00%) aligned concordantly exactly 1 time 8 (0.01%) aligned concordantly >1 times 0.01% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99989 (99.99%) aligned concordantly 0 times 1 (0.00%) aligned concordantly exactly 1 time 10 (0.01%) aligned concordantly >1 times 0.01% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99988 (99.99%) aligned concordantly 0 times 3 (0.00%) aligned concordantly exactly 1 time 9 (0.01%) aligned concordantly >1 times 0.01% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 13 Mapping efficiency: 0.0% Sequence pairs with no alignments under any condition: 99974 Sequence pairs did not map uniquely: 13 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2 ((converted) top strand) GA/CT/CT: 4 (complementary to (converted) top strand) GA/CT/GA: 5 (complementary to (converted) bottom strand) CT/GA/GA: 2 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 573 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 2 Total methylated C's in CHH context: 5 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 75 Total unmethylated C's in CHG context: 109 Total unmethylated C's in CHH context: 382 Total unmethylated C's in Unknown context: 4 C methylated in CpG context: 0.0% C methylated in CHG context: 1.8% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 30s ==================== Bismark run complete ==================== /var/spool/slurm/d/job1155861/slurm_script: line 39: 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.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 Created output directory /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test/AS-0.6/! Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test/AS-0.6/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz to Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz to Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz to Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz to Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 TNTTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 CNCCAATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AATAAAATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 CNCCAATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AATAAAATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 TNTTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F1_S20_L001_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99815 (99.81%) aligned concordantly 0 times 46 (0.05%) aligned concordantly exactly 1 time 139 (0.14%) aligned concordantly >1 times 0.18% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99862 (99.86%) aligned concordantly 0 times 31 (0.03%) aligned concordantly exactly 1 time 107 (0.11%) aligned concordantly >1 times 0.14% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99826 (99.83%) aligned concordantly 0 times 35 (0.04%) aligned concordantly exactly 1 time 139 (0.14%) aligned concordantly >1 times 0.17% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99851 (99.85%) aligned concordantly 0 times 40 (0.04%) aligned concordantly exactly 1 time 109 (0.11%) aligned concordantly >1 times 0.15% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 226 Mapping efficiency: 0.2% Sequence pairs with no alignments under any condition: 99612 Sequence pairs did not map uniquely: 162 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 64 ((converted) top strand) GA/CT/CT: 54 (complementary to (converted) top strand) GA/CT/GA: 51 (complementary to (converted) bottom strand) CT/GA/GA: 57 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 10048 Total methylated C's in CpG context: 35 Total methylated C's in CHG context: 24 Total methylated C's in CHH context: 113 Total methylated C's in Unknown context: 25 Total unmethylated C's in CpG context: 1647 Total unmethylated C's in CHG context: 1621 Total unmethylated C's in CHH context: 6608 Total unmethylated C's in Unknown context: 104 C methylated in CpG context: 2.1% C methylated in CHG context: 1.5% C methylated in CHH context: 1.7% C methylated in unknown context (CN or CHN): 19.4% Bismark completed in 0d 0h 0m 36s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.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/20190806_100K_Calig_test/AS-0.6/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz to Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz to Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz to Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz to Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 TNATTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTGTTTTTTTTAGGAAGTGTTAGGTATAATTTTGTTTGGTATAAAATAAATAAAGGATTAATTTTATTTTATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TCCACAATTCCAAACAACTCACTAAACTACCACCCAACTAAACAAATAATAAAATTAAACACAATACTTTCCATATCAATATTTCTTTCCTCAACATTTTTAATCAAAAAATAACCTTCAAACTCAATAATATAAAATAAATAACTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 CNACTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTATTTTTTTTAAAAAATATTAAATATAATTTTATTTAATATAAAATAAATAAAAAATTAATTTTATTTTATAAATTATTTATTTTATATTATTAAATTTAAAAATTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TTTATAATTTTAAATAATTTATTAAATTATTATTTAATTAAATAAATAATAAAATTAAATATAATATTTTTTATATTAATATTTTTTTTTTTAATATTTTTAATTAAAAAATAATTTTTAAATTTAATAATATAAAATAAATAATTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 CNACTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTATTTTTTTTAAAAAATATTAAATATAATTTTATTTAATATAAAATAAATAAAAAATTAATTTTATTTTATAAATTATTTATTTTATATTATTAAATTTAAAAATTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TTTATAATTTTAAATAATTTATTAAATTATTATTTAATTAAATAAATAATAAAATTAAATATAATATTTTTTATATTAATATTTTTTTTTTTAATATTTTTAATTAAAAAATAATTTTTAAATTTAATAATATAAAATAAATAATTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 TNATTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTGTTTTTTTTAGGAAGTGTTAGGTATAATTTTGTTTGGTATAAAATAAATAAAGGATTAATTTTATTTTATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TCCACAATTCCAAACAACTCACTAAACTACCACCCAACTAAACAAATAATAAAATTAAACACAATACTTTCCATATCAATATTTCTTTCCTCAACATTTTTAATCAAAAAATAACCTTCAAACTCAATAATATAAAATAAATAACTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F1_S20_L002_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99775 (99.78%) aligned concordantly 0 times 52 (0.05%) aligned concordantly exactly 1 time 173 (0.17%) aligned concordantly >1 times 0.23% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99760 (99.76%) aligned concordantly 0 times100000 reads; of these: 61 (1000000.06 (%) aligned concordantly exactly 1 time 100.00 %179) were paired; of these: ( 0.18 %99692) aligned concordantly >1 times ( 99.690.24%%) aligned concordantly 0 times overall alignment rate 74 (0.07%) aligned concordantly exactly 1 time 234 (0.23%) aligned concordantly >1 times 0.31% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99699 (99.70%) aligned concordantly 0 times 62 (0.06%) aligned concordantly exactly 1 time 239 (0.24%) aligned concordantly >1 times 0.30% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 383 Mapping efficiency: 0.4% Sequence pairs with no alignments under any condition: 99350 Sequence pairs did not map uniquely: 267 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 115 ((converted) top strand) GA/CT/CT: 75 (complementary to (converted) top strand) GA/CT/GA: 89 (complementary to (converted) bottom strand) CT/GA/GA: 104 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 17569 Total methylated C's in CpG context: 36 Total methylated C's in CHG context: 45 Total methylated C's in CHH context: 251 Total methylated C's in Unknown context: 23 Total unmethylated C's in CpG context: 2521 Total unmethylated C's in CHG context: 2892 Total unmethylated C's in CHH context: 11824 Total unmethylated C's in Unknown context: 171 C methylated in CpG context: 1.4% C methylated in CHG context: 1.5% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 11.9% Bismark completed in 0d 0h 0m 36s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.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/20190806_100K_Calig_test/AS-0.6/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz to Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz to Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz to Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz to Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANTTGAATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTCTTATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANCTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTTTTATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANCTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTTTTATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANTTGAATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTCTTATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F2_S22_L001_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99848 (99.85%) aligned concordantly 0 times 30 (0.03%) aligned concordantly exactly 1 time 122 (0.12%) aligned concordantly >1 times 0.15% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99844 (99.84%) aligned concordantly 0 times 37 (0.04%) aligned concordantly exactly 1 time 119 (0.12%) aligned concordantly >1 times 0.16% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99856 (99.86%) aligned concordantly 0 times 22 (0.02%) aligned concordantly exactly 1 time 122 (0.12%) aligned concordantly >1 times 0.14% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99842 (99.84%) aligned concordantly 0 times 35 (0.04%) aligned concordantly exactly 1 time 123 (0.12%) aligned concordantly >1 times 0.16% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 209 Mapping efficiency: 0.2% Sequence pairs with no alignments under any condition: 99646 Sequence pairs did not map uniquely: 145 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 37 ((converted) top strand) GA/CT/CT: 59 (complementary to (converted) top strand) GA/CT/GA: 51 (complementary to (converted) bottom strand) CT/GA/GA: 62 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 9989 Total methylated C's in CpG context: 18 Total methylated C's in CHG context: 24 Total methylated C's in CHH context: 116 Total methylated C's in Unknown context: 11 Total unmethylated C's in CpG context: 1662 Total unmethylated C's in CHG context: 1732 Total unmethylated C's in CHH context: 6437 Total unmethylated C's in Unknown context: 101 C methylated in CpG context: 1.1% C methylated in CHG context: 1.4% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 9.8% Bismark completed in 0d 0h 0m 33s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.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/20190806_100K_Calig_test/AS-0.6/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz to Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz to Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz to Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz to Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 77 * 0 0 * * 0 0 ANATAATTTATAAAAATTTAATTTTTATTTTTTTTAATTTTATTTTAATTTTTTTATTTTTTAAAAATAATATATTAAATTTAATAAATATATTTTAGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 141 * 0 0 * * 0 0 CCTAAAATATATTTATTAAATTTAATATATTATTTTTAAAAAATAAAAAAATTAAAATAAAATTAAAAAAAATAAAAATTAAATTTTTATAAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 99 Cr_scaffold0000004_GA_converted 20587397 2 41M1D58M = 20587397 -100 ANACAATCCACAAAAACCTAATTTCTACCTTCCCTAACTCCACCCTAACCTCTCCACCCTCCAAAAATAACACACTAAATTCAATAAATATATTTTAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-45 XS:i:-47 XN:i:0 XM:i:7 XO:i:1 XG:i:1 NM:i:8 MD:Z:1C1A16C1C18^T47A7T1C0 YS:i:-44 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 147 Cr_scaffold0000004_GA_converted 20587397 2 41M1D58M = 20587397 -100 ACACAATCCACAAAAACCTAATTTCTACCTTCCCTAACTCCACCCTAACCTCTCCACCCTCCAAAAATAACACACTAAATTCAATAAATATATTTTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-44 XS:i:-46 XN:i:0 XM:i:6 XO:i:1 XG:i:1 NM:i:7 MD:Z:3A16C1C18^T47A7T1C0 YS:i:-45 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 83 Cr_scaffold0000009_CT_converted 11629674 0 88M1I10M = 11629674 -98 TTTAAAATATATTTATTGAATTTAGTGTGTTATTTTTGGAGGGTGGAGAGGTTAGGGTGGAGTTAGGGAAGGTAGAAATTAGGTTTTTGTGGATTGTNT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-39 XS:i:-39 XN:i:0 XM:i:6 XO:i:1 XG:i:1 NM:i:7 MD:Z:0G1A7T67G15T1G1 YS:i:-38 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 163 Cr_scaffold0000009_CT_converted 11629674 0 88M1I10M = 11629674 -98 TTTAAAATATATTTATTGAATTTAGTGTGTTATTTTTGGAGGGTGGAGAGGTTAGGGTGGAGTTAGGGAAGGTAGAAATTAGGTTTTTGTGGATTGTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-38 XS:i:-38 XN:i:0 XM:i:5 XO:i:1 XG:i:1 NM:i:6 MD:Z:0G1A7T67G15T3 YS:i:-39 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 77 * 0 0 * * 0 0 ANATAATTTATAAAAATTTAATTTTTATTTTTTTTAATTTTATTTTAATTTTTTTATTTTTTAAAAATAATATATTAAATTTAATAAATATATTTTAGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 141 * 0 0 * * 0 0 CCTAAAATATATTTATTAAATTTAATATATTATTTTTAAAAAATAAAAAAATTAAAATAAAATTAAAAAAAATAAAAATTAAATTTTTATAAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F2_S22_L002_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99975 (99.97%) aligned concordantly 0 times 5 (0.01%) aligned concordantly exactly 1 time 20 (0.02%) aligned concordantly >1 times 0.03% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99973 (99.97%) aligned concordantly 0 times 6 (0.01%) aligned concordantly exactly 1 time 21 (0.02%) aligned concordantly >1 times 0.03% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99969 (99.97%) aligned concordantly 0 times 8 (0.01%) aligned concordantly exactly 1 time 23 (0.02%) aligned concordantly >1 times 0.03% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99972 (99.97%) aligned concordantly 0 times 3 (0.00%) aligned concordantly exactly 1 time 25 (0.03%) aligned concordantly >1 times 0.03% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 42 Mapping efficiency: 0.0% Sequence pairs with no alignments under any condition: 99935 Sequence pairs did not map uniquely: 23 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 9 ((converted) top strand) GA/CT/CT: 9 (complementary to (converted) top strand) GA/CT/GA: 13 (complementary to (converted) bottom strand) CT/GA/GA: 11 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1850 Total methylated C's in CpG context: 5 Total methylated C's in CHG context: 7 Total methylated C's in CHH context: 24 Total methylated C's in Unknown context: 5 Total unmethylated C's in CpG context: 291 Total unmethylated C's in CHG context: 302 Total unmethylated C's in CHH context: 1221 Total unmethylated C's in Unknown context: 20 C methylated in CpG context: 1.7% C methylated in CHG context: 2.3% C methylated in CHH context: 1.9% C methylated in unknown context (CN or CHN): 20.0% Bismark completed in 0d 0h 0m 33s ==================== Bismark run complete ==================== /var/spool/slurm/d/job1155861/slurm_script: line 55: 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.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 Created output directory /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test/AS-1/! Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test/AS-1/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz to Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz to Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz to Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz to Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 TNTTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 CNCCAATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AATAAAATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 CNCCAATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AATAAAATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 TNTTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F1_S20_L001_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99780 (99.78%) aligned concordantly 0 times 58 (0.06%) aligned concordantly exactly 1 time 162 (0.16%) aligned concordantly >1 times 0.22% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99729 (99.73%) aligned concordantly 0 times 62 (0.06%) aligned concordantly exactly 1 time 209 (0.21%) aligned concordantly >1 times 0.27% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99742 (99.74%) aligned concordantly 0 times 41 (0.04%) aligned concordantly exactly 1 time 217 (0.22%) aligned concordantly >1 times 0.26% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99805 (99.81%) aligned concordantly 0 times 38 (0.04%) aligned concordantly exactly 1 time 157 (0.16%) aligned concordantly >1 times 0.20% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 361 Mapping efficiency: 0.4% Sequence pairs with no alignments under any condition: 99457 Sequence pairs did not map uniquely: 182 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 108 ((converted) top strand) GA/CT/CT: 87 (complementary to (converted) top strand) GA/CT/GA: 75 (complementary to (converted) bottom strand) CT/GA/GA: 91 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 15834 Total methylated C's in CpG context: 62 Total methylated C's in CHG context: 50 Total methylated C's in CHH context: 360 Total methylated C's in Unknown context: 52 Total unmethylated C's in CpG context: 2570 Total unmethylated C's in CHG context: 2543 Total unmethylated C's in CHH context: 10249 Total unmethylated C's in Unknown context: 279 C methylated in CpG context: 2.4% C methylated in CHG context: 1.9% C methylated in CHH context: 3.4% C methylated in unknown context (CN or CHN): 15.7% Bismark completed in 0d 0h 0m 39s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.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/20190806_100K_Calig_test/AS-1/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz to Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz to Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz to Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz to Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 TNATTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTGTTTTTTTTAGGAAGTGTTAGGTATAATTTTGTTTGGTATAAAATAAATAAAGGATTAATTTTATTTTATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TCCACAATTCCAAACAACTCACTAAACTACCACCCAACTAAACAAATAATAAAATTAAACACAATACTTTCCATATCAATATTTCTTTCCTCAACATTTTTAATCAAAAAATAACCTTCAAACTCAATAATATAAAATAAATAACTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 CNACTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTATTTTTTTTAAAAAATATTAAATATAATTTTATTTAATATAAAATAAATAAAAAATTAATTTTATTTTATAAATTATTTATTTTATATTATTAAATTTAAAAATTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TTTATAATTTTAAATAATTTATTAAATTATTATTTAATTAAATAAATAATAAAATTAAATATAATATTTTTTATATTAATATTTTTTTTTTTAATATTTTTAATTAAAAAATAATTTTTAAATTTAATAATATAAAATAAATAATTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 CNACTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTATTTTTTTTAAAAAATATTAAATATAATTTTATTTAATATAAAATAAATAAAAAATTAATTTTATTTTATAAATTATTTATTTTATATTATTAAATTTAAAAATTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TTTATAATTTTAAATAATTTATTAAATTATTATTTAATTAAATAAATAATAAAATTAAATATAATATTTTTTATATTAATATTTTTTTTTTTAATATTTTTAATTAAAAAATAATTTTTAAATTTAATAATATAAAATAAATAATTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 TNATTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTGTTTTTTTTAGGAAGTGTTAGGTATAATTTTGTTTGGTATAAAATAAATAAAGGATTAATTTTATTTTATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TCCACAATTCCAAACAACTCACTAAACTACCACCCAACTAAACAAATAATAAAATTAAACACAATACTTTCCATATCAATATTTCTTTCCTCAACATTTTTAATCAAAAAATAACCTTCAAACTCAATAATATAAAATAAATAACTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F1_S20_L002_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99652 (99.65%) aligned concordantly 0 times 81 (0.08%) aligned concordantly exactly 1 time 267 (0.27%) aligned concordantly >1 times 0.35% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99664 (99.66%) aligned concordantly 0 times 71 (0.07%) aligned concordantly exactly 1 time 265 (0.27%) aligned concordantly >1 times 0.34% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99558 (99.56%) aligned concordantly 0 times 111 (0.11%) aligned concordantly exactly 1 time 331 (0.33%) aligned concordantly >1 times 0.44% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99578 (99.58%) aligned concordantly 0 times 90 (0.09%) aligned concordantly exactly 1 time 332 (0.33%) aligned concordantly >1 times 0.42% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 570 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99108 Sequence pairs did not map uniquely: 322 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 169 ((converted) top strand) GA/CT/CT: 112 (complementary to (converted) top strand) GA/CT/GA: 134 (complementary to (converted) bottom strand) CT/GA/GA: 155 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 25394 Total methylated C's in CpG context: 86 Total methylated C's in CHG context: 98 Total methylated C's in CHH context: 539 Total methylated C's in Unknown context: 64 Total unmethylated C's in CpG context: 3761 Total unmethylated C's in CHG context: 4081 Total unmethylated C's in CHH context: 16829 Total unmethylated C's in Unknown context: 435 C methylated in CpG context: 2.2% C methylated in CHG context: 2.3% C methylated in CHH context: 3.1% C methylated in unknown context (CN or CHN): 12.8% Bismark completed in 0d 0h 0m 39s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.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/20190806_100K_Calig_test/AS-1/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz to Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz to Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz to Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz to Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANTTGAATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTCTTATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANCTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTTTTATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANCTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTTTTATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANTTGAATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTCTTATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F2_S22_L001_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99791 (99.79%) aligned concordantly 0 times 40 (0.04%) aligned concordantly exactly 1 time 169 (0.17%) aligned concordantly >1 times 0.21% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99783 (99.78%) aligned concordantly 0 times 39 (0.04%) aligned concordantly exactly 1 time 178 (0.18%) aligned concordantly >1 times 0.22% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99769 (99.77%) aligned concordantly 0 times 48 (0.05%) aligned concordantly exactly 1 time 183 (0.18%) aligned concordantly >1 times 0.23% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99789 (99.79%) aligned concordantly 0 times 45 (0.04%) aligned concordantly exactly 1 time 166 (0.17%) aligned concordantly >1 times 0.21% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 304 Mapping efficiency: 0.3% Sequence pairs with no alignments under any condition: 99514 Sequence pairs did not map uniquely: 182 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 69 ((converted) top strand) GA/CT/CT: 89 (complementary to (converted) top strand) GA/CT/GA: 72 (complementary to (converted) bottom strand) CT/GA/GA: 74 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 13810 Total methylated C's in CpG context: 45 Total methylated C's in CHG context: 38 Total methylated C's in CHH context: 279 Total methylated C's in Unknown context: 30 Total unmethylated C's in CpG context: 2238 Total unmethylated C's in CHG context: 2320 Total unmethylated C's in CHH context: 8890 Total unmethylated C's in Unknown context: 238 C methylated in CpG context: 2.0% C methylated in CHG context: 1.6% C methylated in CHH context: 3.0% C methylated in unknown context (CN or CHN): 11.2% Bismark completed in 0d 0h 0m 37s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.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/20190806_100K_Calig_test/AS-1/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz to Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz to Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz to Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz to Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 77 * 0 0 * * 0 0 ANATAATTTATAAAAATTTAATTTTTATTTTTTTTAATTTTATTTTAATTTTTTTATTTTTTAAAAATAATATATTAAATTTAATAAATATATTTTAGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 141 * 0 0 * * 0 0 CCTAAAATATATTTATTAAATTTAATATATTATTTTTAAAAAATAAAAAAATTAAAATAAAATTAAAAAAAATAAAAATTAAATTTTTATAAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 99 Cr_scaffold0000004_GA_converted 20587397 0 41M1D58M = 20587397 -100 ANACAATCCACAAAAACCTAATTTCTACCTTCCCTAACTCCACCCTAACCTCTCCACCCTCCAAAAATAACACACTAAATTCAATAAATATATTTTAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-45 XS:i:-45 XN:i:0 XM:i:7 XO:i:1 XG:i:1 NM:i:8 MD:Z:1C1A16C1C18^T47A7T1C0 YS:i:-44 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 147 Cr_scaffold0000004_GA_converted 20587397 0 41M1D58M = 20587397 -100 ACACAATCCACAAAAACCTAATTTCTACCTTCCCTAACTCCACCCTAACCTCTCCACCCTCCAAAAATAACACACTAAATTCAATAAATATATTTTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-44 XS:i:-44 XN:i:0 XM:i:6 XO:i:1 XG:i:1 NM:i:7 MD:Z:3A16C1C18^T47A7T1C0 YS:i:-45 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 83 Cr_scaffold0000009_CT_converted 11629674 0 88M1I10M = 11629674 -98 TTTAAAATATATTTATTGAATTTAGTGTGTTATTTTTGGAGGGTGGAGAGGTTAGGGTGGAGTTAGGGAAGGTAGAAATTAGGTTTTTGTGGATTGTNT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-39 XS:i:-39 XN:i:0 XM:i:6 XO:i:1 XG:i:1 NM:i:7 MD:Z:0G1A7T67G15T1G1 YS:i:-38 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 163 Cr_scaffold0000009_CT_converted 11629674 0 88M1I10M = 11629674 -98 TTTAAAATATATTTATTGAATTTAGTGTGTTATTTTTGGAGGGTGGAGAGGTTAGGGTGGAGTTAGGGAAGGTAGAAATTAGGTTTTTGTGGATTGTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-38 XS:i:-38 XN:i:0 XM:i:5 XO:i:1 XG:i:1 NM:i:6 MD:Z:0G1A7T67G15T3 YS:i:-39 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 77 * 0 0 * * 0 0 ANATAATTTATAAAAATTTAATTTTTATTTTTTTTAATTTTATTTTAATTTTTTTATTTTTTAAAAATAATATATTAAATTTAATAAATATATTTTAGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 141 * 0 0 * * 0 0 CCTAAAATATATTTATTAAATTTAATATATTATTTTTAAAAAATAAAAAAATTAAAATAAAATTAAAAAAAATAAAAATTAAATTTTTATAAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F2_S22_L002_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99955 (99.95%) aligned concordantly 0 times 14 (0.01%) aligned concordantly exactly 1 time 31 (0.03%) aligned concordantly >1 times 0.04% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99952 (99.95%) aligned concordantly 0 times 9 (0.01%) aligned concordantly exactly 1 time 39 (0.04%) aligned concordantly >1 times 0.05% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99953 (99.95%) aligned concordantly 0 times 11 (0.01%) aligned concordantly exactly 1 time 36 (0.04%) aligned concordantly >1 times 0.05% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99959 (99.96%) aligned concordantly 0 times 11 (0.01%) aligned concordantly exactly 1 time 30 (0.03%) aligned concordantly >1 times 0.04% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 77 Mapping efficiency: 0.1% Sequence pairs with no alignments under any condition: 99894 Sequence pairs did not map uniquely: 29 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 22 ((converted) top strand) GA/CT/CT: 15 (complementary to (converted) top strand) GA/CT/GA: 20 (complementary to (converted) bottom strand) CT/GA/GA: 20 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 3219 Total methylated C's in CpG context: 18 Total methylated C's in CHG context: 24 Total methylated C's in CHH context: 121 Total methylated C's in Unknown context: 8 Total unmethylated C's in CpG context: 484 Total unmethylated C's in CHG context: 503 Total unmethylated C's in CHH context: 2069 Total unmethylated C's in Unknown context: 75 C methylated in CpG context: 3.6% C methylated in CHG context: 4.6% C methylated in CHH context: 5.5% C methylated in unknown context (CN or CHN): 9.6% Bismark completed in 0d 0h 0m 35s ==================== Bismark run complete ==================== /var/spool/slurm/d/job1155861/slurm_script: line 71: 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.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 Created output directory /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test/AS-1_I60/! Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test/AS-1_I60/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz to Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz to Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz to Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz to Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 TNTTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 CNCCAATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AATAAAATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 CNCCAATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AATAAAATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 TNTTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F1_S20_L001_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99786 (99.79%) aligned concordantly 0 times 56 (0.06%) aligned concordantly exactly 1 time 158 (0.16%) aligned concordantly >1 times 0.21% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99750 (99.75%) aligned concordantly 0 times 38 (0.04%) aligned concordantly exactly 1 time 212 (0.21%) aligned concordantly >1 times 0.25% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99734 (99.73%) aligned concordantly 0 times 62 (0.06%) aligned concordantly exactly 1 time 204 (0.20%) aligned concordantly >1 times 0.27% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99813 (99.81%) aligned concordantly 0 times 33 (0.03%) aligned concordantly exactly 1 time 154 (0.15%) aligned concordantly >1 times 0.19% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 352 Mapping efficiency: 0.4% Sequence pairs with no alignments under any condition: 99472 Sequence pairs did not map uniquely: 176 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 108 ((converted) top strand) GA/CT/CT: 85 (complementary to (converted) top strand) GA/CT/GA: 72 (complementary to (converted) bottom strand) CT/GA/GA: 87 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 15668 Total methylated C's in CpG context: 60 Total methylated C's in CHG context: 48 Total methylated C's in CHH context: 307 Total methylated C's in Unknown context: 52 Total unmethylated C's in CpG context: 2553 Total unmethylated C's in CHG context: 2535 Total unmethylated C's in CHH context: 10165 Total unmethylated C's in Unknown context: 279 C methylated in CpG context: 2.3% C methylated in CHG context: 1.9% C methylated in CHH context: 2.9% C methylated in unknown context (CN or CHN): 15.7% Bismark completed in 0d 0h 0m 39s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.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/20190806_100K_Calig_test/AS-1_I60/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz to Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz to Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz to Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz to Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 TNATTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTGTTTTTTTTAGGAAGTGTTAGGTATAATTTTGTTTGGTATAAAATAAATAAAGGATTAATTTTATTTTATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TCCACAATTCCAAACAACTCACTAAACTACCACCCAACTAAACAAATAATAAAATTAAACACAATACTTTCCATATCAATATTTCTTTCCTCAACATTTTTAATCAAAAAATAACCTTCAAACTCAATAATATAAAATAAATAACTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 CNACTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTATTTTTTTTAAAAAATATTAAATATAATTTTATTTAATATAAAATAAATAAAAAATTAATTTTATTTTATAAATTATTTATTTTATATTATTAAATTTAAAAATTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TTTATAATTTTAAATAATTTATTAAATTATTATTTAATTAAATAAATAATAAAATTAAATATAATATTTTTTATATTAATATTTTTTTTTTTAATATTTTTAATTAAAAAATAATTTTTAAATTTAATAATATAAAATAAATAATTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 CNACTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTATTTTTTTTAAAAAATATTAAATATAATTTTATTTAATATAAAATAAATAAAAAATTAATTTTATTTTATAAATTATTTATTTTATATTATTAAATTTAAAAATTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TTTATAATTTTAAATAATTTATTAAATTATTATTTAATTAAATAAATAATAAAATTAAATATAATATTTTTTATATTAATATTTTTTTTTTTAATATTTTTAATTAAAAAATAATTTTTAAATTTAATAATATAAAATAAATAATTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 TNATTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTGTTTTTTTTAGGAAGTGTTAGGTATAATTTTGTTTGGTATAAAATAAATAAAGGATTAATTTTATTTTATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TCCACAATTCCAAACAACTCACTAAACTACCACCCAACTAAACAAATAATAAAATTAAACACAATACTTTCCATATCAATATTTCTTTCCTCAACATTTTTAATCAAAAAATAACCTTCAAACTCAATAATATAAAATAAATAACTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F1_S20_L002_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99571 (99.57%) aligned concordantly 0 times 109 (0.11%) aligned concordantly exactly 1 time 320 (0.32%) aligned concordantly >1 times 0.43% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99677 (99.68%) aligned concordantly 0 times 68 (0.07%) aligned concordantly exactly 1 time 255 (0.26%) aligned concordantly >1 times 0.32% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99594 (99.59%) aligned concordantly 0 times 85 (0.09%) aligned concordantly exactly 1 time 321 (0.32%) aligned concordantly >1 times 0.41% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99670 (99.67%) aligned concordantly 0 times 75 (0.07%) aligned concordantly exactly 1 time 255 (0.26%) aligned concordantly >1 times 0.33% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 545 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99137 Sequence pairs did not map uniquely: 318 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 165 ((converted) top strand) GA/CT/CT: 109 (complementary to (converted) top strand) GA/CT/GA: 129 (complementary to (converted) bottom strand) CT/GA/GA: 142 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 24909 Total methylated C's in CpG context: 80 Total methylated C's in CHG context: 89 Total methylated C's in CHH context: 478 Total methylated C's in Unknown context: 59 Total unmethylated C's in CpG context: 3702 Total unmethylated C's in CHG context: 3994 Total unmethylated C's in CHH context: 16566 Total unmethylated C's in Unknown context: 421 C methylated in CpG context: 2.1% C methylated in CHG context: 2.2% C methylated in CHH context: 2.8% C methylated in unknown context (CN or CHN): 12.3% Bismark completed in 0d 0h 0m 38s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.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/20190806_100K_Calig_test/AS-1_I60/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz to Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz to Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz to Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz to Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANTTGAATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTCTTATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANCTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTTTTATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANCTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTTTTATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANTTGAATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTCTTATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F2_S22_L001_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100000100.00 reads; of these:% ) were paired; of these: 100000 (99802 (99.80%) aligned concordantly 0 times 100.00 %42) were paired; of these: ( 0.04 %99804) aligned concordantly exactly 1 time ( 99.80 %156) aligned concordantly 0 times ( 0.16 %36) aligned concordantly >1 times ( 0.040.20%%) aligned concordantly exactly 1 time overall alignment rate 160 (0.16%) aligned concordantly >1 times 0.20% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99787 (99.79%) aligned concordantly 0 times 41 (0.04%) aligned concordantly exactly 1 time 172 (0.17%) aligned concordantly >1 times 0.21% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99797 (99.80%) aligned concordantly 0 times 35 (0.04%) aligned concordantly exactly 1 time 168 (0.17%) aligned concordantly >1 times 0.20% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 291 Mapping efficiency: 0.3% Sequence pairs with no alignments under any condition: 99540 Sequence pairs did not map uniquely: 169 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 67 ((converted) top strand) GA/CT/CT: 80 (complementary to (converted) top strand) GA/CT/GA: 72 (complementary to (converted) bottom strand) CT/GA/GA: 72 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 13567 Total methylated C's in CpG context: 41 Total methylated C's in CHG context: 35 Total methylated C's in CHH context: 297 Total methylated C's in Unknown context: 28 Total unmethylated C's in CpG context: 2204 Total unmethylated C's in CHG context: 2280 Total unmethylated C's in CHH context: 8710 Total unmethylated C's in Unknown context: 225 C methylated in CpG context: 1.8% C methylated in CHG context: 1.5% C methylated in CHH context: 3.3% C methylated in unknown context (CN or CHN): 11.1% Bismark completed in 0d 0h 0m 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.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/20190806_100K_Calig_test/AS-1_I60/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz to Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz to Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz to Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz to Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 77 * 0 0 * * 0 0 ANATAATTTATAAAAATTTAATTTTTATTTTTTTTAATTTTATTTTAATTTTTTTATTTTTTAAAAATAATATATTAAATTTAATAAATATATTTTAGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 141 * 0 0 * * 0 0 CCTAAAATATATTTATTAAATTTAATATATTATTTTTAAAAAATAAAAAAATTAAAATAAAATTAAAAAAAATAAAAATTAAATTTTTATAAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 99 Cr_scaffold0000004_GA_converted 20587397 0 41M1D58M = 20587397 -100 ANACAATCCACAAAAACCTAATTTCTACCTTCCCTAACTCCACCCTAACCTCTCCACCCTCCAAAAATAACACACTAAATTCAATAAATATATTTTAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-45 XS:i:-45 XN:i:0 XM:i:7 XO:i:1 XG:i:1 NM:i:8 MD:Z:1C1A16C1C18^T47A7T1C0 YS:i:-44 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 147 Cr_scaffold0000004_GA_converted 20587397 0 41M1D58M = 20587397 -100 ACACAATCCACAAAAACCTAATTTCTACCTTCCCTAACTCCACCCTAACCTCTCCACCCTCCAAAAATAACACACTAAATTCAATAAATATATTTTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-44 XS:i:-44 XN:i:0 XM:i:6 XO:i:1 XG:i:1 NM:i:7 MD:Z:3A16C1C18^T47A7T1C0 YS:i:-45 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 83 Cr_scaffold0000009_CT_converted 11629674 0 88M1I10M = 11629674 -98 TTTAAAATATATTTATTGAATTTAGTGTGTTATTTTTGGAGGGTGGAGAGGTTAGGGTGGAGTTAGGGAAGGTAGAAATTAGGTTTTTGTGGATTGTNT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-39 XS:i:-39 XN:i:0 XM:i:6 XO:i:1 XG:i:1 NM:i:7 MD:Z:0G1A7T67G15T1G1 YS:i:-38 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 163 Cr_scaffold0000009_CT_converted 11629674 0 88M1I10M = 11629674 -98 TTTAAAATATATTTATTGAATTTAGTGTGTTATTTTTGGAGGGTGGAGAGGTTAGGGTGGAGTTAGGGAAGGTAGAAATTAGGTTTTTGTGGATTGTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-38 XS:i:-38 XN:i:0 XM:i:5 XO:i:1 XG:i:1 NM:i:6 MD:Z:0G1A7T67G15T3 YS:i:-39 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 77 * 0 0 * * 0 0 ANATAATTTATAAAAATTTAATTTTTATTTTTTTTAATTTTATTTTAATTTTTTTATTTTTTAAAAATAATATATTAAATTTAATAAATATATTTTAGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 141 * 0 0 * * 0 0 CCTAAAATATATTTATTAAATTTAATATATTATTTTTAAAAAATAAAAAAATTAAAATAAAATTAAAAAAAATAAAAATTAAATTTTTATAAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F2_S22_L002_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99960 (99.96%) aligned concordantly 0 times 11 (0.01%) aligned concordantly exactly 1 time 29 (0.03%) aligned concordantly >1 times 0.04% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99957 (99.96%) aligned concordantly 0 times 13 (0.01%) aligned concordantly exactly 1 time 30 (0.03%) aligned concordantly >1 times 0.04% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99954 (99.95%) aligned concordantly 0 times100000 reads; of these: 10 (1000000.01 (%) aligned concordantly exactly 1 time 36 (100.000.04%%) were paired; of these:) aligned concordantly >1 times 0.0599955% ( overall alignment rate99.95 %) aligned concordantly 0 times 11 (0.01%) aligned concordantly exactly 1 time 34 (0.03%) aligned concordantly >1 times 0.04% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 77 Mapping efficiency: 0.1% Sequence pairs with no alignments under any condition: 99897 Sequence pairs did not map uniquely: 26 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 23 ((converted) top strand) GA/CT/CT: 15 (complementary to (converted) top strand) GA/CT/GA: 19 (complementary to (converted) bottom strand) CT/GA/GA: 20 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 3256 Total methylated C's in CpG context: 18 Total methylated C's in CHG context: 24 Total methylated C's in CHH context: 121 Total methylated C's in Unknown context: 7 Total unmethylated C's in CpG context: 496 Total unmethylated C's in CHG context: 504 Total unmethylated C's in CHH context: 2093 Total unmethylated C's in Unknown context: 77 C methylated in CpG context: 3.5% C methylated in CHG context: 4.5% C methylated in CHH context: 5.5% C methylated in unknown context (CN or CHN): 8.3% Bismark completed in 0d 0h 0m 36s ==================== Bismark run complete ==================== /var/spool/slurm/d/job1155861/slurm_script: line 88: 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.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 Created output directory /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test/AS-1.2_I60/! Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test/AS-1.2_I60/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz to Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz to Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz to Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz to Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 TNTTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 CNCCAATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AATAAAATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 CNCCAATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AATAAAATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 TNTTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F1_S20_L001_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 10000099733 reads; of these: ( 99.73 %100000) aligned concordantly 0 times ( 68 (0.07%100.00) aligned concordantly exactly 1 time% ) were paired; of these: 199 (996790.20 (%99.68) aligned concordantly >1 times% ) aligned concordantly 0 times0.27 % overall alignment rate67 (0.07%) aligned concordantly exactly 1 time 254 (0.25%) aligned concordantly >1 times 0.32% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99697 (99.70%) aligned concordantly 0 times 50 (0.05%) aligned concordantly exactly 1 time 253 (0.25%) aligned concordantly >1 times 0.30% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99757 (99.76%) aligned concordantly 0 times 52 (0.05%) aligned concordantly exactly 1 time 191 (0.19%) aligned concordantly >1 times 0.24% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 449 Mapping efficiency: 0.4% Sequence pairs with no alignments under any condition: 99351 Sequence pairs did not map uniquely: 200 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 130 ((converted) top strand) GA/CT/CT: 110 (complementary to (converted) top strand) GA/CT/GA: 102 (complementary to (converted) bottom strand) CT/GA/GA: 107 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 19082 Total methylated C's in CpG context: 91 Total methylated C's in CHG context: 88 Total methylated C's in CHH context: 652 Total methylated C's in Unknown context: 89 Total unmethylated C's in CpG context: 3005 Total unmethylated C's in CHG context: 2970 Total unmethylated C's in CHH context: 12276 Total unmethylated C's in Unknown context: 412 C methylated in CpG context: 2.9% C methylated in CHG context: 2.9% C methylated in CHH context: 5.0% C methylated in unknown context (CN or CHN): 17.8% Bismark completed in 0d 0h 0m 40s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.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/20190806_100K_Calig_test/AS-1.2_I60/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz to Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz to Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz to Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz to Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 99 Cr_scaffold0000017_CT_converted 13255753 0 6M2I15M3I11M4D42M3D5M1I59M2I4M = 13255862 248 TNATTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTGTTTTTTTTAGGAAGTGTTAGGTATAATTTTGTTTGGTATAAAATAAATAAAGGATTAATTTTATTTTATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF AS:i:-172 XN:i:0 XM:i:17 XO:i:6 XG:i:15 NM:i:32 MD:Z:1A10G1G0A7A0A0A6^GTTG12T0T25A2^TTT3G7T1T17G3G8G11G11 YS:i:-177 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 147 Cr_scaffold0000017_CT_converted 13255862 0 61M1I47M10I17M1D13M = 13255753 -248 ATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTTTTGATTAAAAATGTTGAGGAAAGAAATATTGATATGGAAAGTATTGTGTTTAATTTTATTATTTGTTTAGTTGGGTGGTAGTTTAGTGAGTTGTTTGGAATTGTGGA :FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFF:F,FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFF:F AS:i:-177 XN:i:0 XM:i:21 XO:i:3 XG:i:12 NM:i:33 MD:Z:3G3G8G11G8T2A2G8T13T8A0A1T3A0T31G0A1A0T5^A8A0A0A2 YS:i:-172 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 CNACTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTATTTTTTTTAAAAAATATTAAATATAATTTTATTTAATATAAAATAAATAAAAAATTAATTTTATTTTATAAATTATTTATTTTATATTATTAAATTTAAAAATTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TTTATAATTTTAAATAATTTATTAAATTATTATTTAATTAAATAAATAATAAAATTAAATATAATATTTTTTATATTAATATTTTTTTTTTTAATATTTTTAATTAAAAAATAATTTTTAAATTTAATAATATAAAATAAATAATTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 CNACTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTATTTTTTTTAAAAAATATTAAATATAATTTTATTTAATATAAAATAAATAAAAAATTAATTTTATTTTATAAATTATTTATTTTATATTATTAAATTTAAAAATTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TTTATAATTTTAAATAATTTATTAAATTATTATTTAATTAAATAAATAATAAAATTAAATATAATATTTTTTATATTAATATTTTTTTTTTTAATATTTTTAATTAAAAAATAATTTTTAAATTTAATAATATAAAATAAATAATTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 TNATTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTGTTTTTTTTAGGAAGTGTTAGGTATAATTTTGTTTGGTATAAAATAAATAAAGGATTAATTTTATTTTATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TCCACAATTCCAAACAACTCACTAAACTACCACCCAACTAAACAAATAATAAAATTAAACACAATACTTTCCATATCAATATTTCTTTCCTCAACATTTTTAATCAAAAAATAACCTTCAAACTCAATAATATAAAATAAATAACTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F1_S20_L002_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99606 (99.61%) aligned concordantly 0 times 87 (0.09%) aligned concordantly exactly 1 time 307 (0.31%) aligned concordantly >1 times 0.39% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99470100000 ( reads; of these:99.47 % ) aligned concordantly 0 times100000 ( 126 (0.13%100.00) aligned concordantly exactly 1 time% ) were paired; of these: 404 (996030.40 (%99.60) aligned concordantly >1 times% ) aligned concordantly 0 times0.53 % overall alignment rate87 (0.09%) aligned concordantly exactly 1 time 310 (0.31%) aligned concordantly >1 times 0.40% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99485 (99.48%) aligned concordantly 0 times 111 (0.11%) aligned concordantly exactly 1 time 404 (0.40%) aligned concordantly >1 times 0.52% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 705 Mapping efficiency: 0.7% Sequence pairs with no alignments under any condition: 98948 Sequence pairs did not map uniquely: 347 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 205 ((converted) top strand) GA/CT/CT: 147 (complementary to (converted) top strand) GA/CT/GA: 151 (complementary to (converted) bottom strand) CT/GA/GA: 202 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 30854 Total methylated C's in CpG context: 121 Total methylated C's in CHG context: 134 Total methylated C's in CHH context: 1011 Total methylated C's in Unknown context: 103 Total unmethylated C's in CpG context: 4542 Total unmethylated C's in CHG context: 4883 Total unmethylated C's in CHH context: 20163 Total unmethylated C's in Unknown context: 668 C methylated in CpG context: 2.6% C methylated in CHG context: 2.7% C methylated in CHH context: 4.8% C methylated in unknown context (CN or CHN): 13.4% Bismark completed in 0d 0h 0m 40s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.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/20190806_100K_Calig_test/AS-1.2_I60/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz to Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz to Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz to Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz to Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANTTGAATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTCTTATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 99 Cr_scaffold0000013_GA_converted 2386443 0 7M2I1M1I23M1D11M1I20M = 2386443 -63 ANCTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF AS:i:-78 XN:i:0 XM:i:8 XO:i:4 XG:i:5 NM:i:13 MD:Z:0C0A11A2T5T1C6^C1C26T2 YS:i:-77 YT:Z:CP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 147 Cr_scaffold0000013_GA_converted 2386443 0 7M2I1M1I23M1D11M1I20M = 2386443 -63 AACTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA FFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-77 XN:i:0 XM:i:7 XO:i:4 XG:i:5 NM:i:12 MD:Z:0C12A2T5T1C6^C1C26T2 YS:i:-78 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANCTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTTTTATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANTTGAATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTCTTATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F2_S22_L001_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99751 (99.75%) aligned concordantly 0 times 51 (0.05%) aligned concordantly exactly 1 time 198 (0.20%) aligned concordantly >1 times 0.25% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99729 (99.73%) aligned concordantly 0 times 58 (0.06%) aligned concordantly exactly 1 time 213 (0.21%) aligned concordantly >1 times 0.27% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99740 (99.74%) aligned concordantly 0 times 50 (0.05%) aligned concordantly exactly 1 time 210 (0.21%) aligned concordantly >1 times 0.26% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99744 (99.74%) aligned concordantly 0 times 59 (0.06%) aligned concordantly exactly 1 time 197 (0.20%) aligned concordantly >1 times 0.26% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 427 Mapping efficiency: 0.4% Sequence pairs with no alignments under any condition: 99396 Sequence pairs did not map uniquely: 177 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 105 ((converted) top strand) GA/CT/CT: 116 (complementary to (converted) top strand) GA/CT/GA: 102 (complementary to (converted) bottom strand) CT/GA/GA: 104 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 18109 Total methylated C's in CpG context: 73 Total methylated C's in CHG context: 85 Total methylated C's in CHH context: 864 Total methylated C's in Unknown context: 74 Total unmethylated C's in CpG context: 2843 Total unmethylated C's in CHG context: 2916 Total unmethylated C's in CHH context: 11328 Total unmethylated C's in Unknown context: 438 C methylated in CpG context: 2.5% C methylated in CHG context: 2.8% C methylated in CHH context: 7.1% C methylated in unknown context (CN or CHN): 14.5% Bismark completed in 0d 0h 0m 37s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.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/20190806_100K_Calig_test/AS-1.2_I60/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz to Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz to Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz to Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz to Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 77 * 0 0 * * 0 0 ANATAATTTATAAAAATTTAATTTTTATTTTTTTTAATTTTATTTTAATTTTTTTATTTTTTAAAAATAATATATTAAATTTAATAAATATATTTTAGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 141 * 0 0 * * 0 0 CCTAAAATATATTTATTAAATTTAATATATTATTTTTAAAAAATAAAAAAATTAAAATAAAATTAAAAAAAATAAAAATTAAATTTTTATAAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 99 Cr_scaffold0000004_GA_converted 20587397 2 41M1D58M = 20587397 -100 ANACAATCCACAAAAACCTAATTTCTACCTTCCCTAACTCCACCCTAACCTCTCCACCCTCCAAAAATAACACACTAAATTCAATAAATATATTTTAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-45 XS:i:-47 XN:i:0 XM:i:7 XO:i:1 XG:i:1 NM:i:8 MD:Z:1C1A16C1C18^T47A7T1C0 YS:i:-44 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 147 Cr_scaffold0000004_GA_converted 20587397 2 41M1D58M = 20587397 -100 ACACAATCCACAAAAACCTAATTTCTACCTTCCCTAACTCCACCCTAACCTCTCCACCCTCCAAAAATAACACACTAAATTCAATAAATATATTTTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-44 XS:i:-46 XN:i:0 XM:i:6 XO:i:1 XG:i:1 NM:i:7 MD:Z:3A16C1C18^T47A7T1C0 YS:i:-45 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 83 Cr_scaffold0000005_CT_converted 29732770 1 58M1D41M = 29732770 -100 TTTAAAATATATTTATTGAATTTAGTGTGTTATTTTTGGAGGGTGGAGAGGTTAGGGTGGAGTTAGGGAAGGTAGAAATTAGGTTTTTGTGGATTGTNT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-39 XS:i:-39 XN:i:0 XM:i:6 XO:i:1 XG:i:1 NM:i:7 MD:Z:0G0G8T47^A20G16T1G1 YS:i:-38 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 163 Cr_scaffold0000005_CT_converted 29732770 1 58M1D41M = 29732770 -100 TTTAAAATATATTTATTGAATTTAGTGTGTTATTTTTGGAGGGTGGAGAGGTTAGGGTGGAGTTAGGGAAGGTAGAAATTAGGTTTTTGTGGATTGTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-38 XS:i:-38 XN:i:0 XM:i:5 XO:i:1 XG:i:1 NM:i:6 MD:Z:0G0G8T47^A20G16T3 YS:i:-39 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 77 * 0 0 * * 0 0 ANATAATTTATAAAAATTTAATTTTTATTTTTTTTAATTTTATTTTAATTTTTTTATTTTTTAAAAATAATATATTAAATTTAATAAATATATTTTAGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 141 * 0 0 * * 0 0 CCTAAAATATATTTATTAAATTTAATATATTATTTTTAAAAAATAAAAAAATTAAAATAAAATTAAAAAAAATAAAAATTAAATTTTTATAAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F2_S22_L002_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99932 (99.93%) aligned concordantly 0 times 26 (0.03%) aligned concordantly exactly 1 time 42 (0.04%) aligned concordantly >1 times 0.07% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99939 (99.94%) aligned concordantly 0 times 14 (0.01%) aligned concordantly exactly 1 time 47 (0.05%) aligned concordantly >1 times 0.06% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99923 (99.92%) aligned concordantly 0 times 22 (0.02%) aligned concordantly exactly 1 time 55 (0.06%) aligned concordantly >1 times 0.08% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99921 (99.92%) aligned concordantly 0 times 21 (0.02%) aligned concordantly exactly 1 time 58 (0.06%) aligned concordantly >1 times 0.08% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 141 Mapping efficiency: 0.1% Sequence pairs with no alignments under any condition: 99821 Sequence pairs did not map uniquely: 38 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 40 ((converted) top strand) GA/CT/CT: 29 (complementary to (converted) top strand) GA/CT/GA: 34 (complementary to (converted) bottom strand) CT/GA/GA: 38 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 5343 Total methylated C's in CpG context: 27 Total methylated C's in CHG context: 40 Total methylated C's in CHH context: 365 Total methylated C's in Unknown context: 34 Total unmethylated C's in CpG context: 777 Total unmethylated C's in CHG context: 785 Total unmethylated C's in CHH context: 3349 Total unmethylated C's in Unknown context: 156 C methylated in CpG context: 3.4% C methylated in CHG context: 4.8% C methylated in CHH context: 9.8% C methylated in unknown context (CN or CHN): 17.9% Bismark completed in 0d 0h 0m 37s ==================== Bismark run complete ==================== /var/spool/slurm/d/job1155861/slurm_script: line 104: 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.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 Created output directory /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test/AS-2/! Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test/AS-2/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz to Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz to Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L001_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz to Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz to Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L001_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 TNTTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 99 Cr_scaffold0000010_GA_converted 17798310 2 4M1I5M1I19M1D3M1D13M4I14M5I23M2D9M = 17798310 -94 CNCCAATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-159 XS:i:-167 XN:i:0 XM:i:14 XO:i:7 XG:i:15 NM:i:29 MD:Z:1T0A11T0A3A0A1A5^A3^C5A0A1A12C0C1C25^TC6T2 YS:i:-164 YT:Z:CP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 147 Cr_scaffold0000010_GA_converted 17798310 2 4M1I5M1I19M1D3M1D13M4I14M5I23M2D9M = 17798310 -94 CACCAATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT FFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-164 XS:i:-169 XN:i:0 XM:i:14 XO:i:7 XG:i:15 NM:i:29 MD:Z:1T0A11T0A3A0A1A5^A3^C5A0A1A12C0C1C25^TC6T2 YS:i:-159 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 83 Cr_scaffold0000016_CT_converted 6162686 2 14M6I30M2I6M1I11M13I6M1I1M2I8M = 6162686 -76 AATAAAATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGNG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF#F AS:i:-160 XS:i:-167 XN:i:0 XM:i:10 XO:i:6 XG:i:25 NM:i:35 MD:Z:0G7T10A1G24A8G2G5G8T0T1 YS:i:-159 YT:Z:CP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 163 Cr_scaffold0000016_CT_converted 6162686 2 14M6I30M2I6M1I11M13I6M1I1M2I8M = 6162686 -76 AATAAAATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF AS:i:-159 XS:i:-166 XN:i:0 XM:i:9 XO:i:6 XG:i:25 NM:i:34 MD:Z:0G7T10A1G24A8G2G5G8T2 YS:i:-160 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 TNTTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F1_S20_L001_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L001_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 15125 (15.12%) aligned concordantly 0 times 4284 (4.28%) aligned concordantly exactly 1 time 80591 (80.59%) aligned concordantly >1 times 84.88% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 15048 (15.05%) aligned concordantly 0 times 4300 (4.30%) aligned concordantly exactly 1 time 80652 (80.65%) aligned concordantly >1 times 84.95% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 16042 (16.04%) aligned concordantly 0 times 5126 (5.13%) aligned concordantly exactly 1 time 78832 (78.83%) aligned concordantly >1 times 83.96% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 16270 (16.27%) aligned concordantly 0 times 5044 (5.04%) aligned concordantly exactly 1 time 78686 (78.69%) aligned concordantly >1 times 83.73% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F1_S20_L001_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 90189 Mapping efficiency: 90.2% Sequence pairs with no alignments under any condition: 327 Sequence pairs did not map uniquely: 9484 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 23556 ((converted) top strand) GA/CT/CT: 21209 (complementary to (converted) top strand) GA/CT/GA: 21654 (complementary to (converted) bottom strand) CT/GA/GA: 23770 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2928311 Total methylated C's in CpG context: 32593 Total methylated C's in CHG context: 33493 Total methylated C's in CHH context: 425643 Total methylated C's in Unknown context: 82804 Total unmethylated C's in CpG context: 315888 Total unmethylated C's in CHG context: 319754 Total unmethylated C's in CHH context: 1800940 Total unmethylated C's in Unknown context: 245433 C methylated in CpG context: 9.4% C methylated in CHG context: 9.5% C methylated in CHH context: 19.1% C methylated in unknown context (CN or CHN): 25.2% Bismark completed in 0d 0h 2m 21s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.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/20190806_100K_Calig_test/AS-2/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz to Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz to Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L002_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz to Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz to Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_L002_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 99 Cr_scaffold0000017_CT_converted 13255753 2 6M2I15M3I11M4D42M3D5M1I59M2I4M = 13255862 248 TNATTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTGTTTTTTTTAGGAAGTGTTAGGTATAATTTTGTTTGGTATAAAATAAATAAAGGATTAATTTTATTTTATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF AS:i:-172 XS:i:-188 XN:i:0 XM:i:17 XO:i:6 XG:i:15 NM:i:32 MD:Z:1A10G1G0A7A0A0A6^GTTG12T0T25A2^TTT3G7T1T17G3G8G11G11 YS:i:-177 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 147 Cr_scaffold0000017_CT_converted 13255862 2 61M1I47M10I17M1D13M = 13255753 -248 ATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTTTTGATTAAAAATGTTGAGGAAAGAAATATTGATATGGAAAGTATTGTGTTTAATTTTATTATTTGTTTAGTTGGGTGGTAGTTTAGTGAGTTGTTTGGAATTGTGGA :FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFF:F,FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFF:F AS:i:-177 XS:i:-191 XN:i:0 XM:i:21 XO:i:3 XG:i:12 NM:i:33 MD:Z:3G3G8G11G8T2A2G8T13T8A0A1T3A0T31G0A1A0T5^A8A0A0A2 YS:i:-172 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 99 Cr_scaffold0000009_GA_converted 18144523 2 14M1I13M4I3M1D13M3I11M1I4M2D8M1I9M3I21M1D19M2I2M2I9M1I6M = 18144547 148 CNACTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTATTTTTTTTAAAAAATATTAAATATAATTTTATTTAATATAAAATAAATAAAAAATTAATTTTATTTTATAAATTATTTATTTTATATTATTAAATTTAAAAATTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF AS:i:-247 XS:i:-238 XN:i:0 XM:i:21 XO:i:12 XG:i:22 NM:i:43 MD:Z:0A0T1T1C2A0A5C8A0C1A2^T8A9T9^TT25A0T9A1^T1T0T11A11T0T0C7 YS:i:-221 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 147 Cr_scaffold0000009_GA_converted 18144547 2 11M1I10M2I24M4I4M9I3M1I5M3I36M3I2M2I9M1D13M1I6M = 18144523 -148 ATAAATTATTTATTTTATATTATTAAATTTAAAAATTATTTTTTAATTAAAAATATTAAAAAAAAAAATATTAATATAAAAAATATTATATTTAATTTTATTATTTATTTAATTAAATAATAATTTAATAAATTATTTAAAATTATAAA :FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFF:F,FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFF:F AS:i:-221 XS:i:-232 XN:i:0 XM:i:15 XO:i:10 XG:i:27 NM:i:42 MD:Z:1C3A6A4T9T5A8T18T5T28T5T1^C1T3T3T8T0 YS:i:-247 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 83 Cr_scaffold0000010_CT_converted 17678162 2 6M5I5M3I1M1I17M1D24M3I8M1I9M2D4M1I11M3I13M1D2M4I12M1D1M2D4M1I11M = 17678147 -150 AAAATAATTTTTAAATTTAATAATATAAAATAAATAATTTATAAAATAAAATTAATTTTTTATTTATTTTATATTAAATAAAATTATATTTAATATTTTTTAAAAAAAATAAAATTTAAAAATAAATTAAAAAAAATTAAAAAATAGTNG FFFFFFF,F::FFFFF,FFF:FFFFFFFFF,F:FFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFF,FFFFFFFFFFFFFFF,F:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-242 XS:i:-274 XN:i:0 XM:i:15 XO:i:14 XG:i:29 NM:i:44 MD:Z:7G9T11^A0A0A2T9A0T25^AT9A9T8^A2T1G0T8^G1^TT11T1T0A0 YS:i:-230 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 163 Cr_scaffold0000010_CT_converted 17678147 2 9M1D1M1D8M1D9M9I36M3I4M9I4M1I3M4I25M2I10M1I11M = 17678162 150 TTTATAATTTTAAATAATTTATTAAATTATTATTTAATTAAATAAATAATAAAATTAAATATAATATTTTTTATATTAATATTTTTTTTTTTAATATTTTTAATTAAAAAATAATTTTTAAATTTAATAATATAAAATAAATAATTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: AS:i:-230 XS:i:-253 XN:i:0 XM:i:14 XO:i:10 XG:i:32 NM:i:46 MD:Z:0A8^A1^A4A3^A1G1A30A5A18A6T1T5A9A4T6T3G1 YS:i:-242 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 83 Cr_scaffold0000005_GA_converted 11405066 2 3M2I56M1I4M2I38M1D2M1D9M4I7M7I15M = 11404966 -236 AAAATAACCTTCAAACTCAATAATATAAAATAAATAACTTATAAAATAAAATTAATCCTTTATTTATTTTATACCAAACAAAATTATACCTAACACTTCCTAAAAAAAACAAAATTTAAAAATAAATTAAAAAAAATTAAAAAATAATNA FFFFFFF,F::FFFFF,FFF:FFFFFFFFF,F:FFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFF,FFFFFFFFFFFFFFF,F:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-150 XS:i:-164 XN:i:0 XM:i:11 XO:i:7 XG:i:18 NM:i:29 MD:Z:11C11A12C26A0A29A6^C2^T2T0T14C7T2T1 YS:i:-188 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 163 Cr_scaffold0000005_GA_converted 11404966 2 9M1I6M3I5M3I5M3I5M1D24M1I5M1D79M = 11405066 236 TCCACAATTCCAAACAACTCACTAAACTACCACCCAACTAAACAAATAATAAAATTAAACACAATACTTTCCATATCAATATTTCTTTCCTCAACATTTTTAATCAAAAAATAACCTTCAAACTCAATAATATAAAATAAATAACTTAT F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF: AS:i:-188 XS:i:-195 XN:i:0 XM:i:19 XO:i:7 XG:i:13 NM:i:32 MD:Z:2T0T0T5T6A12^C2A22T3^A2T6A1A3C4C5A8C2T2A8C11A12C3 YS:i:-150 YT:Z:CP >>> Writing bisulfite mapping results to Sealice_F1_S20_L002_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F1_S20_L002_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 15233 (15.23%) aligned concordantly 0 times 4288 (4.29%) aligned concordantly exactly 1 time 80479 (80.48%) aligned concordantly >1 times 84.77% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 14977 (14.98%) aligned concordantly 0 times 4411 (4.41%) aligned concordantly exactly 1 time 80612 (80.61%) aligned concordantly >1 times 85.02% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 16278 (16.28%) aligned concordantly 0 times 5127 (5.13%) aligned concordantly exactly 1 time 78595 (78.59%) aligned concordantly >1 times 83.72% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 16290 (16.29%) aligned concordantly 0 times 5157 (5.16%) aligned concordantly exactly 1 time 78553 (78.55%) aligned concordantly >1 times 83.71% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F1_S20_L002_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 90064 Mapping efficiency: 90.1% Sequence pairs with no alignments under any condition: 355 Sequence pairs did not map uniquely: 9581 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 23560 ((converted) top strand) GA/CT/CT: 21293 (complementary to (converted) top strand) GA/CT/GA: 21479 (complementary to (converted) bottom strand) CT/GA/GA: 23732 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2935405 Total methylated C's in CpG context: 33388 Total methylated C's in CHG context: 33870 Total methylated C's in CHH context: 428501 Total methylated C's in Unknown context: 82770 Total unmethylated C's in CpG context: 316242 Total unmethylated C's in CHG context: 320619 Total unmethylated C's in CHH context: 1802785 Total unmethylated C's in Unknown context: 244912 C methylated in CpG context: 9.5% C methylated in CHG context: 9.6% C methylated in CHH context: 19.2% C methylated in unknown context (CN or CHN): 25.3% Bismark completed in 0d 0h 2m 21s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.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/20190806_100K_Calig_test/AS-2/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz to Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz to Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L001_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz to Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz to Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L001_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANTTGAATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTCTTATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 99 Cr_scaffold0000008_GA_converted 25054400 2 7M2I1M1I34M2I19M = 25054400 -61 ANCTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF AS:i:-79 XS:i:-82 XN:i:0 XM:i:9 XO:i:3 XG:i:5 NM:i:14 MD:Z:1A9A2A2A3A3T1T0T26C5 YS:i:-78 YT:Z:CP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 147 Cr_scaffold0000008_GA_converted 25054400 2 7M2I1M1I34M2I19M = 25054400 -61 AACTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA FFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-78 XS:i:-81 XN:i:0 XM:i:8 XO:i:3 XG:i:5 NM:i:13 MD:Z:11A2A2A3A3T1T0T26C5 YS:i:-79 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 83 Cr_scaffold0000007_CT_converted 26587162 2 34M1I13M1I17M = 26587162 -64 TTTTTTATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGNT FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-59 XS:i:-68 XN:i:0 XM:i:8 XO:i:2 XG:i:2 NM:i:10 MD:Z:6T23T9T11A0T6G0T0T1 YS:i:-58 YT:Z:CP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 163 Cr_scaffold0000007_CT_converted 26587162 2 34M1I13M1I17M = 26587162 -64 TTTTTTATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF AS:i:-58 XS:i:-69 XN:i:0 XM:i:7 XO:i:2 XG:i:2 NM:i:9 MD:Z:6T23T9T11A0T6G0T2 YS:i:-59 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANTTGAATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTCTTATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F2_S22_L001_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L001_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 20863 (20.86%) aligned concordantly 0 times 4708 (4.71%) aligned concordantly exactly 1 time 74429 (74.43%) aligned concordantly >1 times 79.14% overall alignment rate 100000100000 reads; of these: reads; of these: 100000100000 ( (100.00100.00%%) were paired; of these:) were paired; of these: 2351423633 ( (23.5123.63%%) aligned concordantly 0 times) aligned concordantly 0 times 50374711 ( (5.044.71%%) aligned concordantly exactly 1 time) aligned concordantly exactly 1 time 7144971656 ( (71.4571.66%%) aligned concordantly >1 times) aligned concordantly >1 times 76.4976.37%% overall alignment rate overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 21010 (21.01%) aligned concordantly 0 times 4693 (4.69%) aligned concordantly exactly 1 time 74297 (74.30%) aligned concordantly >1 times 78.99% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F2_S22_L001_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 90500 Mapping efficiency: 90.5% Sequence pairs with no alignments under any condition: 935 Sequence pairs did not map uniquely: 8565 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 23355 ((converted) top strand) GA/CT/CT: 21820 (complementary to (converted) top strand) GA/CT/GA: 22244 (complementary to (converted) bottom strand) CT/GA/GA: 23081 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2761255 Total methylated C's in CpG context: 34116 Total methylated C's in CHG context: 34007 Total methylated C's in CHH context: 495998 Total methylated C's in Unknown context: 98140 Total unmethylated C's in CpG context: 282603 Total unmethylated C's in CHG context: 284042 Total unmethylated C's in CHH context: 1630489 Total unmethylated C's in Unknown context: 247130 C methylated in CpG context: 10.8% C methylated in CHG context: 10.7% C methylated in CHH context: 23.3% C methylated in unknown context (CN or CHN): 28.4% Bismark completed in 0d 0h 2m 13s ==================== 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/Caligus/GENOMES/ (absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)' 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/20190806_100K_Calig_test'): /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.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/20190806_100K_Calig_test/AS-2/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig_test Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz to Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz to Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L002_R1_001_trimmed.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz Writing a C -> T converted version of the input file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz to Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz to Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_L002_R2_001_trimmed.fq.gz (100001 sequences in total) Input files are Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 99 Cr_scaffold0000009_CT_converted 19439767 2 11M4I4M1I26M2I11M2D6M1D5M1I2M1I8M1I2M2I12M = 19439767 -90 ANATAATTTATAAAAATTTAATTTTTATTTTTTTTAATTTTATTTTAATTTTTTTATTTTTTAAAAATAATATATTAAATTTAATAAATATATTTTAGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-139 XS:i:-150 XN:i:0 XM:i:9 XO:i:9 XG:i:15 NM:i:24 MD:Z:1G2T4T5T36^AA6^T3T6G11A4A0A0 YS:i:-144 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 147 Cr_scaffold0000009_CT_converted 19439767 2 11M4I4M1I26M2I11M2D6M1D5M1I2M1I8M1I2M2I12M = 19439767 -90 ATATAATTTATAAAAATTTAATTTTTATTTTTTTTAATTTTATTTTAATTTTTTTATTTTTTAAAAATAATATATTAAATTTAATAAATATATTTTAGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-144 XS:i:-152 XN:i:0 XM:i:9 XO:i:9 XG:i:15 NM:i:24 MD:Z:1G2T4T5T36^AA6^T3T6G11A4A0A0 YS:i:-139 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 99 Cr_scaffold0000004_GA_converted 20587397 6 41M1D58M = 20587397 -100 ANACAATCCACAAAAACCTAATTTCTACCTTCCCTAACTCCACCCTAACCTCTCCACCCTCCAAAAATAACACACTAAATTCAATAAATATATTTTAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-45 XS:i:-47 XN:i:0 XM:i:7 XO:i:1 XG:i:1 NM:i:8 MD:Z:1C1A16C1C18^T47A7T1C0 YS:i:-44 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 147 Cr_scaffold0000004_GA_converted 20587397 6 41M1D58M = 20587397 -100 ACACAATCCACAAAAACCTAATTTCTACCTTCCCTAACTCCACCCTAACCTCTCCACCCTCCAAAAATAACACACTAAATTCAATAAATATATTTTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-44 XS:i:-46 XN:i:0 XM:i:6 XO:i:1 XG:i:1 NM:i:7 MD:Z:3A16C1C18^T47A7T1C0 YS:i:-45 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 83 Cr_scaffold0000005_CT_converted 29732770 1 58M1D41M = 29732770 -100 TTTAAAATATATTTATTGAATTTAGTGTGTTATTTTTGGAGGGTGGAGAGGTTAGGGTGGAGTTAGGGAAGGTAGAAATTAGGTTTTTGTGGATTGTNT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-39 XS:i:-39 XN:i:0 XM:i:6 XO:i:1 XG:i:1 NM:i:7 MD:Z:0G0G8T47^A20G16T1G1 YS:i:-38 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 163 Cr_scaffold0000005_CT_converted 29732770 1 58M1D41M = 29732770 -100 TTTAAAATATATTTATTGAATTTAGTGTGTTATTTTTGGAGGGTGGAGAGGTTAGGGTGGAGTTAGGGAAGGTAGAAATTAGGTTTTTGTGGATTGTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-38 XS:i:-38 XN:i:0 XM:i:5 XO:i:1 XG:i:1 NM:i:6 MD:Z:0G0G8T47^A20G16T3 YS:i:-39 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 83 Cr_scaffold0000013_GA_converted 18701787 0 7M3I10M1D42M1I22M1D4M1I3M2I4M = 18701787 -97 CCTAAAATATATTTATTAAATTTAATATATTATTTTTAAAAAATAAAAAAATTAAAATAAAATTAAAAAAAATAAAAATTAAATTTTTATAAATTATNT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-130 XS:i:-153 XN:i:0 XM:i:13 XO:i:6 XG:i:9 NM:i:22 MD:Z:2A10A3^C7A1A0A2A0A0A11C4A6T24^C0A8T1 YS:i:-134 YT:Z:CP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 163 Cr_scaffold0000013_GA_converted 18701787 0 7M3I10M1D42M1I22M1D14M = 18701787 -97 CCTAAAATATATTTATTAAATTTAATATATTATTTTTAAAAAATAAAAAAATTAAAATAAAATTAAAAAAAATAAAAATTAAATTTTTATAAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-134 XS:i:-156 XN:i:0 XM:i:16 XO:i:4 XG:i:6 NM:i:22 MD:Z:2A10A3^C7A1A0A2A0A0A11C4A6T24^C0A3A5T0A1A0 YS:i:-130 YT:Z:CP >>> Writing bisulfite mapping results to Sealice_F2_S22_L002_R1_001_trimmed_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R1_001_trimmed.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/Sealice_F2_S22_L002_R2_001_trimmed.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 23543 (10000023.54 reads; of these:% ) aligned concordantly 0 times 100000 (4845 (4.84%) aligned concordantly exactly 1 time100.00 % ) were paired; of these:71612 ( 71.6123419% () aligned concordantly >1 times23.42 %76.46) aligned concordantly 0 times% overall alignment rate 4865 (4.87%) aligned concordantly exactly 1 time 71716 (71.72%) aligned concordantly >1 times 76.58% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 21108 (21.11%) aligned concordantly 0 times 4728 (4.73%) aligned concordantly exactly 1 time 74164 (74.16%) aligned concordantly >1 times 78.89% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 21105 (21.11%) aligned concordantly 0 times 4786 (4.79%) aligned concordantly exactly 1 time 74109 (74.11%) aligned concordantly >1 times 78.89% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_C_to_T.fastq, Sealice_F2_S22_L002_R1_001_trimmed.fq.gz_G_to_A.fastq, Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001_trimmed.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 90518 Mapping efficiency: 90.5% Sequence pairs with no alignments under any condition: 910 Sequence pairs did not map uniquely: 8572 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 23164 ((converted) top strand) GA/CT/CT: 22146 (complementary to (converted) top strand) GA/CT/GA: 22275 (complementary to (converted) bottom strand) CT/GA/GA: 22933 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2764624 Total methylated C's in CpG context: 34261 Total methylated C's in CHG context: 34341 Total methylated C's in CHH context: 495188 Total methylated C's in Unknown context: 98728 Total unmethylated C's in CpG context: 281572 Total unmethylated C's in CHG context: 283317 Total unmethylated C's in CHH context: 1635945 Total unmethylated C's in Unknown context: 248911 C methylated in CpG context: 10.8% C methylated in CHG context: 10.8% C methylated in CHH context: 23.2% C methylated in unknown context (CN or CHN): 28.4% Bismark completed in 0d 0h 2m 14s ==================== Bismark run complete ==================== /var/spool/slurm/d/job1155861/slurm_script: line 121: !cat: command not found /var/spool/slurm/d/job1155861/slurm_script: line 125: !cat: command not found grep: conflicting matchers specified /var/spool/slurm/d/job1155861/slurm_script: line 130: !cat: command not found grep: conflicting matchers specified /var/spool/slurm/d/job1155861/slurm_script: line 135: !cat: command not found grep: conflicting matchers specified /var/spool/slurm/d/job1155861/slurm_script: line 140: !cat: command not found grep: conflicting matchers specified /var/spool/slurm/d/job1155861/slurm_script: line 145: !cat: command not found grep: conflicting matchers specified /var/spool/slurm/d/job1155861/slurm_script: line 152: !paste: command not found