/var/spool/slurm/d/job347275/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/Cvirg/Bismark_genome/ (absolute path is '/gscratch/srlab/strigg/data/Cvirg/Bismark_genome/)' FastQ format assumed (by default) Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181004'): /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_10_s1_R1.fastq.gz /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_10_s1_R2.fastq.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/srlab/strigg/analyses/20181004/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/srlab/strigg/analyses/20181004 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 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/Cvirg/FASTQS/18-04-07/zr2096_10_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_10_s1_R2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_10_s1_R1.fastq.gz to zr2096_10_s1_R1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_10_s1_R1.fastq.gz to zr2096_10_s1_R1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_10_s1_R1.fastq.gz (17717127 sequences in total) Writing a C -> T converted version of the input file zr2096_10_s1_R2.fastq.gz to zr2096_10_s1_R2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_10_s1_R2.fastq.gz to zr2096_10_s1_R2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_10_s1_R2.fastq.gz (17717127 sequences in total) Input files are zr2096_10_s1_R1.fastq.gz_C_to_T.fastq and zr2096_10_s1_R1.fastq.gz_G_to_A.fastq and zr2096_10_s1_R2.fastq.gz_C_to_T.fastq and zr2096_10_s1_R2.fastq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ with the specified options: -q --score-min L,0,-1.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 100 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_10_s1_R1.fastq.gz_C_to_T.fastq and zr2096_10_s1_R2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 100 --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:2:1101:1232:2155_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 GTTATATATAATTGTATTAATTATAAAAAATATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATTTATTATTAAAAATATTAAATATATTATTTTA BBBBBFFFFFFFFFFFFFFBFFFFFFFFFFFFF#################################<>> Writing bisulfite mapping results to zr2096_10_s1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_10_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_10_s1_R2.fastq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far 17717127 reads; of these: 17717127 (100.00%) were paired; of these: 14731694 (83.15%) aligned concordantly 0 times 1198366 (6.76%) aligned concordantly exactly 1 time 1787067 (10.09%) aligned concordantly >1 times 16.85% overall alignment rate 17717127 reads; of these: 17717127 (100.00%) were paired; of these: 14735800 (83.17%) aligned concordantly 0 times 1191785 (6.73%) aligned concordantly exactly 1 time 1789542 (10.10%) aligned concordantly >1 times 16.83% overall alignment rate 17717127 reads; of these: 17717127 (100.00%) were paired; of these: 14633322 (82.59%) aligned concordantly 0 times 1230502 (6.95%) aligned concordantly exactly 1 time 1853303 (10.46%) aligned concordantly >1 times 17.41% overall alignment rate 17717127 reads; of these: 17717127 (100.00%) were paired; of these: 14627627 (82.56%) aligned concordantly 0 times 1238819 (6.99%) aligned concordantly exactly 1 time 1850681 (10.45%) aligned concordantly >1 times 17.44% overall alignment rate Processed 17717127 sequences in total Successfully deleted the temporary files zr2096_10_s1_R1.fastq.gz_C_to_T.fastq, zr2096_10_s1_R1.fastq.gz_G_to_A.fastq, zr2096_10_s1_R2.fastq.gz_C_to_T.fastq and zr2096_10_s1_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 17717127 Number of paired-end alignments with a unique best hit: 6293704 Mapping efficiency: 35.5% Sequence pairs with no alignments under any condition: 9714892 Sequence pairs did not map uniquely: 1708531 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: 1601646 ((converted) top strand) GA/CT/CT: 1537591 (complementary to (converted) top strand) GA/CT/GA: 1548913 (complementary to (converted) bottom strand) CT/GA/GA: 1605554 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 232453732 Total methylated C's in CpG context: 22151409 Total methylated C's in CHG context: 1632227 Total methylated C's in CHH context: 5841216 Total methylated C's in Unknown context: 707839 Total unmethylated C's in CpG context: 10405571 Total unmethylated C's in CHG context: 50198281 Total unmethylated C's in CHH context: 142225028 Total unmethylated C's in Unknown context: 2858024 C methylated in CpG context: 68.0% C methylated in CHG context: 3.1% C methylated in CHH context: 3.9% C methylated in unknown context (CN or CHN): 19.9% Bismark completed in 0d 3h 11m 59s ==================== 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/Cvirg/Bismark_genome/ (absolute path is '/gscratch/srlab/strigg/data/Cvirg/Bismark_genome/)' FastQ format assumed (by default) Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181004'): /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_1_s1_R1.fastq.gz /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_1_s1_R2.fastq.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/srlab/strigg/analyses/20181004/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/srlab/strigg/analyses/20181004 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 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/Cvirg/FASTQS/18-04-07/zr2096_1_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_1_s1_R2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_1_s1_R1.fastq.gz to zr2096_1_s1_R1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_1_s1_R1.fastq.gz to zr2096_1_s1_R1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_1_s1_R1.fastq.gz (28982766 sequences in total) Writing a C -> T converted version of the input file zr2096_1_s1_R2.fastq.gz to zr2096_1_s1_R2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_1_s1_R2.fastq.gz to zr2096_1_s1_R2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_1_s1_R2.fastq.gz (28982766 sequences in total) Input files are zr2096_1_s1_R1.fastq.gz_C_to_T.fastq and zr2096_1_s1_R1.fastq.gz_G_to_A.fastq and zr2096_1_s1_R2.fastq.gz_C_to_T.fastq and zr2096_1_s1_R2.fastq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ with the specified options: -q --score-min L,0,-1.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 100 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_1_s1_R1.fastq.gz_C_to_T.fastq and zr2096_1_s1_R2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 100 --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1249:2156_1:N:0:CGATGT/1 99 NC_035780.1_CT_converted 65371909 6 100M = 65372013 204 GAGTTTTTTTGATTATTTGTTGTTTGTTGTTTGTTTGNNNNTNNNTNNGTTTGTTTGTTTGTTTGTTTGTTTGTAAATTTTTTATATTTTTATTTTTTTT BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF####<###<##<<>> Writing bisulfite mapping results to zr2096_1_s1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_1_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_1_s1_R2.fastq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1309:7531:24389_1:N:0:CGATGT NC_035781.1 2 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far 28982766 reads; of these: 28982766 (100.00%) were paired; of these: 26795705 (92.45%) aligned concordantly 0 times 868964 (3.00%) aligned concordantly exactly 1 time 1318097 (4.55%) aligned concordantly >1 times 7.55% overall alignment rate 28982766 reads; of these: 28982766 (100.00%) were paired; of these: 26794629 (92.45%) aligned concordantly 0 times 872103 (3.01%) aligned concordantly exactly 1 time 1316034 (4.54%) aligned concordantly >1 times 7.55% overall alignment rate 28982766 reads; of these: 28982766 (100.00%) were paired; of these: 26807213 (92.49%) aligned concordantly 0 times 864348 (2.98%) aligned concordantly exactly 1 time 1311205 (4.52%) aligned concordantly >1 times 7.51% overall alignment rate 28982766 reads; of these: 28982766 (100.00%) were paired; of these: 26802656 (92.48%) aligned concordantly 0 times 869086 (3.00%) aligned concordantly exactly 1 time 1311024 (4.52%) aligned concordantly >1 times 7.52% overall alignment rate Processed 28982766 sequences in total Successfully deleted the temporary files zr2096_1_s1_R1.fastq.gz_C_to_T.fastq, zr2096_1_s1_R1.fastq.gz_G_to_A.fastq, zr2096_1_s1_R2.fastq.gz_C_to_T.fastq and zr2096_1_s1_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 28982766 Number of paired-end alignments with a unique best hit: 4521752 Mapping efficiency: 15.6% Sequence pairs with no alignments under any condition: 23239578 Sequence pairs did not map uniquely: 1221436 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1135164 ((converted) top strand) GA/CT/CT: 1123470 (complementary to (converted) top strand) GA/CT/GA: 1130861 (complementary to (converted) bottom strand) CT/GA/GA: 1132256 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 163653583 Total methylated C's in CpG context: 14475033 Total methylated C's in CHG context: 1101550 Total methylated C's in CHH context: 4900521 Total methylated C's in Unknown context: 581418 Total unmethylated C's in CpG context: 6611427 Total unmethylated C's in CHG context: 33757094 Total unmethylated C's in CHH context: 102807958 Total unmethylated C's in Unknown context: 2347522 C methylated in CpG context: 68.6% C methylated in CHG context: 3.2% C methylated in CHH context: 4.5% C methylated in unknown context (CN or CHN): 19.9% Bismark completed in 0d 3h 59m 30s ==================== 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/Cvirg/Bismark_genome/ (absolute path is '/gscratch/srlab/strigg/data/Cvirg/Bismark_genome/)' FastQ format assumed (by default) Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181004'): /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_2_s1_R1.fastq.gz /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_2_s1_R2.fastq.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/srlab/strigg/analyses/20181004/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/srlab/strigg/analyses/20181004 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 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/Cvirg/FASTQS/18-04-07/zr2096_2_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_2_s1_R2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_2_s1_R1.fastq.gz to zr2096_2_s1_R1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_2_s1_R1.fastq.gz to zr2096_2_s1_R1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_2_s1_R1.fastq.gz (30798582 sequences in total) Writing a C -> T converted version of the input file zr2096_2_s1_R2.fastq.gz to zr2096_2_s1_R2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_2_s1_R2.fastq.gz to zr2096_2_s1_R2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_2_s1_R2.fastq.gz (30798582 sequences in total) Input files are zr2096_2_s1_R1.fastq.gz_C_to_T.fastq and zr2096_2_s1_R1.fastq.gz_G_to_A.fastq and zr2096_2_s1_R2.fastq.gz_C_to_T.fastq and zr2096_2_s1_R2.fastq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ with the specified options: -q --score-min L,0,-1.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 100 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_2_s1_R1.fastq.gz_C_to_T.fastq and zr2096_2_s1_R2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 100 --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1148:2157_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 TTTTTTATTAAAATTTATTATTTTAAAAATAAAAATTNNNNTNNNTTTTATTATTTTTTTTAATATTTTTTAATATAATTAAATAATAAAAAAAATTAAT BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF####<###<<>> Writing bisulfite mapping results to zr2096_2_s1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_2_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_2_s1_R2.fastq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1105:2702:79279_1:N:0:TGACCA NC_035781.1 2 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far 30798582 reads; of these: 30798582 (100.00%) were paired; of these: 26905585 (87.36%) aligned concordantly 0 times 1494416 (4.85%) aligned concordantly exactly 1 time 2398581 (7.79%) aligned concordantly >1 times 12.64% overall alignment rate 30798582 reads; of these: 30798582 (100.00%) were paired; of these: 26894665 (87.32%) aligned concordantly 0 times 1504452 (4.88%) aligned concordantly exactly 1 time 2399465 (7.79%) aligned concordantly >1 times 12.68% overall alignment rate 30798582 reads; of these: 30798582 (100.00%) were paired; of these: 26967228 (87.56%) aligned concordantly 0 times 1477645 (4.80%) aligned concordantly exactly 1 time 2353709 (7.64%) aligned concordantly >1 times 12.44% overall alignment rate 30798582 reads; of these: 30798582 (100.00%) were paired; of these: 26979967 (87.60%) aligned concordantly 0 times 1466940 (4.76%) aligned concordantly exactly 1 time 2351675 (7.64%) aligned concordantly >1 times 12.40% overall alignment rate Processed 30798582 sequences in total Successfully deleted the temporary files zr2096_2_s1_R1.fastq.gz_C_to_T.fastq, zr2096_2_s1_R1.fastq.gz_G_to_A.fastq, zr2096_2_s1_R2.fastq.gz_C_to_T.fastq and zr2096_2_s1_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 30798582 Number of paired-end alignments with a unique best hit: 7879875 Mapping efficiency: 25.6% Sequence pairs with no alignments under any condition: 20682061 Sequence pairs did not map uniquely: 2236646 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1988714 ((converted) top strand) GA/CT/CT: 1934508 (complementary to (converted) top strand) GA/CT/GA: 1961754 (complementary to (converted) bottom strand) CT/GA/GA: 1994898 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 282047529 Total methylated C's in CpG context: 25969563 Total methylated C's in CHG context: 1938729 Total methylated C's in CHH context: 9023855 Total methylated C's in Unknown context: 934954 Total unmethylated C's in CpG context: 11825530 Total unmethylated C's in CHG context: 61284539 Total unmethylated C's in CHH context: 172005313 Total unmethylated C's in Unknown context: 3930167 C methylated in CpG context: 68.7% C methylated in CHG context: 3.1% C methylated in CHH context: 5.0% C methylated in unknown context (CN or CHN): 19.2% Bismark completed in 0d 4h 54m 27s ==================== 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/Cvirg/Bismark_genome/ (absolute path is '/gscratch/srlab/strigg/data/Cvirg/Bismark_genome/)' FastQ format assumed (by default) Input files to be analysed (in current folder '/gscratch/srlab/strigg/analyses/20181004'): /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_3_s1_R1.fastq.gz /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_3_s1_R2.fastq.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/srlab/strigg/analyses/20181004/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/srlab/strigg/analyses/20181004 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 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/Cvirg/FASTQS/18-04-07/zr2096_3_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_3_s1_R2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_3_s1_R1.fastq.gz to zr2096_3_s1_R1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_3_s1_R1.fastq.gz to zr2096_3_s1_R1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_3_s1_R1.fastq.gz (29892002 sequences in total) Writing a C -> T converted version of the input file zr2096_3_s1_R2.fastq.gz to zr2096_3_s1_R2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_3_s1_R2.fastq.gz to zr2096_3_s1_R2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_3_s1_R2.fastq.gz (29892002 sequences in total) Input files are zr2096_3_s1_R1.fastq.gz_C_to_T.fastq and zr2096_3_s1_R1.fastq.gz_G_to_A.fastq and zr2096_3_s1_R2.fastq.gz_C_to_T.fastq and zr2096_3_s1_R2.fastq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ with the specified options: -q --score-min L,0,-1.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 100 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_3_s1_R1.fastq.gz_C_to_T.fastq and zr2096_3_s1_R2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 100 --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1059:2153_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 TNTTTTAAAATAATTTAAATAATTTTATATAAATNNNNNNNNNNNNNNNTATTTAAATTAAAAATTTAAATAAATTTTTTTAATTATTTATTGTTTAATG B#<>> Writing bisulfite mapping results to zr2096_3_s1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_3_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_3_s1_R2.fastq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1211:16930:36708_1:N:0:ACAGTG NC_007175.2 17151 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far