/var/spool/slurm/d/job394229/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: 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 17717127 reads; of these: 17717127 (17717127 reads; of these:100.00 % ) were paired; of these:17717127 ( 14735800 (83.17100.00%%) aligned concordantly 0 times) were paired; of these: 119178514633322 ( (6.7382.59%%) aligned concordantly exactly 1 time) aligned concordantly 0 times 17895421230502 ( (10.106.95%%) aligned concordantly >1 times) aligned concordantly exactly 1 time 16.83 %1853303 overall alignment rate ( 10.46%) aligned concordantly >1 times 17.41% overall alignment rate 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 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 34m 55s ==================== 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: 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 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 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 4h 32m 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/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: 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 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: 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 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 5h 29m 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/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 Processed 29000000 sequence pairs so far 29892002 reads; of these: 29892002 (100.00%) were paired; of these: 24787198 (82.92%) aligned concordantly 0 times 1930600 (6.46%) aligned concordantly exactly 1 time 3174204 (10.62%) aligned concordantly >1 times 17.08% overall alignment rate 29892002 reads; of these: 29892002 (100.00%) were paired; of these: 24864720 (83.18%) aligned concordantly 0 times 1902020 (6.36%) aligned concordantly exactly 1 time 3125262 (10.46%) aligned concordantly >1 times 16.82% overall alignment rate 29892002 reads; of these: 29892002 (100.00%) were paired; of these: 24802420 (82.97%) aligned concordantly 0 times 1914624 (6.41%) aligned concordantly exactly 1 time 3174958 (10.62%) aligned concordantly >1 times 17.03% overall alignment rate 29892002 reads; of these: 29892002 (100.00%) were paired; of these: 24849341 (83.13%) aligned concordantly 0 times 1918185 (6.42%) aligned concordantly exactly 1 time 3124476 (10.45%) aligned concordantly >1 times 16.87% overall alignment rate Processed 29892002 sequences in total Successfully deleted the temporary files zr2096_3_s1_R1.fastq.gz_C_to_T.fastq, zr2096_3_s1_R1.fastq.gz_G_to_A.fastq, zr2096_3_s1_R2.fastq.gz_C_to_T.fastq and zr2096_3_s1_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29892002 Number of paired-end alignments with a unique best hit: 10170153 Mapping efficiency: 34.0% Sequence pairs with no alignments under any condition: 16789874 Sequence pairs did not map uniquely: 2931975 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: 2554767 ((converted) top strand) GA/CT/CT: 2514160 (complementary to (converted) top strand) GA/CT/GA: 2537491 (complementary to (converted) bottom strand) CT/GA/GA: 2563734 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 380186993 Total methylated C's in CpG context: 41316176 Total methylated C's in CHG context: 2588230 Total methylated C's in CHH context: 9338662 Total methylated C's in Unknown context: 1160192 Total unmethylated C's in CpG context: 13734426 Total unmethylated C's in CHG context: 82498352 Total unmethylated C's in CHH context: 230711147 Total unmethylated C's in Unknown context: 4951346 C methylated in CpG context: 75.1% C methylated in CHG context: 3.0% C methylated in CHH context: 3.9% C methylated in unknown context (CN or CHN): 19.0% Bismark completed in 0d 6h 7m 14s ==================== 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_4_s1_R1.fastq.gz /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_4_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_4_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_4_s1_R2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_4_s1_R1.fastq.gz to zr2096_4_s1_R1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_4_s1_R1.fastq.gz to zr2096_4_s1_R1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_4_s1_R1.fastq.gz (24341968 sequences in total) Writing a C -> T converted version of the input file zr2096_4_s1_R2.fastq.gz to zr2096_4_s1_R2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_4_s1_R2.fastq.gz to zr2096_4_s1_R2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_4_s1_R2.fastq.gz (24341968 sequences in total) Input files are zr2096_4_s1_R1.fastq.gz_C_to_T.fastq and zr2096_4_s1_R1.fastq.gz_G_to_A.fastq and zr2096_4_s1_R2.fastq.gz_C_to_T.fastq and zr2096_4_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_4_s1_R1.fastq.gz_C_to_T.fastq and zr2096_4_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:1:1101:1343:2133_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 NGATTAGTGTATAGTGGTTGTTATGGAAATTAGNNNNNNNNNNNNNNNNNNNNNNNNNTGNANTNTTTTTATTAGAATTGTTAAGGTTTATTTGATTTAT #<>> Writing bisulfite mapping results to zr2096_4_s1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_4_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_4_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 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2213:19455:71351_1:N:0:GCCAAT NC_035780.1 2 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 24341968 reads; of these: 24341968 (100.00%) were paired; of these: 20587212 (84.57%) aligned concordantly 0 times 1473219 (6.05%) aligned concordantly exactly 1 time 2281537 (9.37%) aligned concordantly >1 times 15.43% overall alignment rate 24341968 reads; of these: 24341968 (100.00%) were paired; of these: 20759122 (85.28%) aligned concordantly 0 times 1410966 (5.80%) aligned concordantly exactly 1 time 2171880 (8.92%) aligned concordantly >1 times 14.72% overall alignment rate 24341968 reads; of these: 24341968 (100.00%) were paired; of these: 20583981 (84.56%) aligned concordantly 0 times 1481581 (6.09%) aligned concordantly exactly 1 time 2276406 (9.35%) aligned concordantly >1 times 15.44% overall alignment rate 24341968 reads; of these: 24341968 (100.00%) were paired; of these: 20754491 (85.26%) aligned concordantly 0 times 1417676 (5.82%) aligned concordantly exactly 1 time 2169801 (8.91%) aligned concordantly >1 times 14.74% overall alignment rate Processed 24341968 sequences in total Successfully deleted the temporary files zr2096_4_s1_R1.fastq.gz_C_to_T.fastq, zr2096_4_s1_R1.fastq.gz_G_to_A.fastq, zr2096_4_s1_R2.fastq.gz_C_to_T.fastq and zr2096_4_s1_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24341968 Number of paired-end alignments with a unique best hit: 7587323 Mapping efficiency: 31.2% Sequence pairs with no alignments under any condition: 14662643 Sequence pairs did not map uniquely: 2092002 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: 1946078 ((converted) top strand) GA/CT/CT: 1835678 (complementary to (converted) top strand) GA/CT/GA: 1856529 (complementary to (converted) bottom strand) CT/GA/GA: 1949037 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 268056140 Total methylated C's in CpG context: 21938186 Total methylated C's in CHG context: 1744867 Total methylated C's in CHH context: 7735389 Total methylated C's in Unknown context: 834133 Total unmethylated C's in CpG context: 12374431 Total unmethylated C's in CHG context: 56852641 Total unmethylated C's in CHH context: 167410626 Total unmethylated C's in Unknown context: 3707185 C methylated in CpG context: 63.9% C methylated in CHG context: 3.0% C methylated in CHH context: 4.4% C methylated in unknown context (CN or CHN): 18.4% Bismark completed in 0d 4h 40m 7s ==================== 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_5_s1_R1.fastq.gz /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_5_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_5_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_5_s1_R2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_5_s1_R1.fastq.gz to zr2096_5_s1_R1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_5_s1_R1.fastq.gz to zr2096_5_s1_R1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_5_s1_R1.fastq.gz (31778715 sequences in total) Writing a C -> T converted version of the input file zr2096_5_s1_R2.fastq.gz to zr2096_5_s1_R2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_5_s1_R2.fastq.gz to zr2096_5_s1_R2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_5_s1_R2.fastq.gz (31778715 sequences in total) Input files are zr2096_5_s1_R1.fastq.gz_C_to_T.fastq and zr2096_5_s1_R1.fastq.gz_G_to_A.fastq and zr2096_5_s1_R2.fastq.gz_C_to_T.fastq and zr2096_5_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_5_s1_R1.fastq.gz_C_to_T.fastq and zr2096_5_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:1:1101:1218:2142_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 NAATAAAATATTATTTAAATTTTATTATTTATANNNNNNNNNNNNNNNNNNATTNTTTTTATTATATATATAAAATTATTTTAAAATTATTATATTTTTT #<>> Writing bisulfite mapping results to zr2096_5_s1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_5_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_5_s1_R2.fastq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1106:7388:36641_1:N:0:CAGATC NC_007175.2 17151 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1110:3486:24661_1:N:0:CAGATC NC_035780.1 3 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:1:1212:5557:13434_1:N:0:CAGATC NC_007175.2 17165 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1216:10289:18419_1:N:0:CAGATC NC_035780.1 3 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1305:7699:42587_1:N:0:CAGATC NC_007175.2 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 Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far 31778715 reads; of these: 31778715 (100.00%) were paired; of these: 26675600 (83.94%) aligned concordantly 0 times 2044971 (6.44%) aligned concordantly exactly 1 time 3058144 (9.62%) aligned concordantly >1 times 16.06% overall alignment rate 31778715 reads; of these: 31778715 (100.00%) were paired; of these: 26978095 (84.89%) aligned concordantly 0 times 1913499 (6.02%) aligned concordantly exactly 1 time 2887121 (9.09%) aligned concordantly >1 times 15.11% overall alignment rate 31778715 reads; of these: 31778715 (100.00%) were paired; of these: 26669929 (83.92%) aligned concordantly 0 times 2042587 (6.43%) aligned concordantly exactly 1 time 3066199 (9.65%) aligned concordantly >1 times 16.08% overall alignment rate 31778715 reads; of these: 31778715 (100.00%) were paired; of these: 26986488 (84.92%) aligned concordantly 0 times 1913870 (6.02%) aligned concordantly exactly 1 time 2878357 (9.06%) aligned concordantly >1 times 15.08% overall alignment rate Processed 31778715 sequences in total Successfully deleted the temporary files zr2096_5_s1_R1.fastq.gz_C_to_T.fastq, zr2096_5_s1_R1.fastq.gz_G_to_A.fastq, zr2096_5_s1_R2.fastq.gz_C_to_T.fastq and zr2096_5_s1_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 31778715 Number of paired-end alignments with a unique best hit: 10309461 Mapping efficiency: 32.4% Sequence pairs with no alignments under any condition: 18728694 Sequence pairs did not map uniquely: 2740560 Sequence pairs which were discarded because genomic sequence could not be extracted: 5 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2677514 ((converted) top strand) GA/CT/CT: 2476905 (complementary to (converted) top strand) GA/CT/GA: 2486673 (complementary to (converted) bottom strand) CT/GA/GA: 2668364 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 370441524 Total methylated C's in CpG context: 30590802 Total methylated C's in CHG context: 2478038 Total methylated C's in CHH context: 10020162 Total methylated C's in Unknown context: 1213895 Total unmethylated C's in CpG context: 15985714 Total unmethylated C's in CHG context: 76625684 Total unmethylated C's in CHH context: 234741124 Total unmethylated C's in Unknown context: 5096608 C methylated in CpG context: 65.7% C methylated in CHG context: 3.1% C methylated in CHH context: 4.1% C methylated in unknown context (CN or CHN): 19.2% Bismark completed in 0d 6h 17m 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/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_6_s1_R1.fastq.gz /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_6_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_6_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_6_s1_R2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_6_s1_R1.fastq.gz to zr2096_6_s1_R1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_6_s1_R1.fastq.gz to zr2096_6_s1_R1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_6_s1_R1.fastq.gz (24237290 sequences in total) Writing a C -> T converted version of the input file zr2096_6_s1_R2.fastq.gz to zr2096_6_s1_R2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_6_s1_R2.fastq.gz to zr2096_6_s1_R2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_6_s1_R2.fastq.gz (24237290 sequences in total) Input files are zr2096_6_s1_R1.fastq.gz_C_to_T.fastq and zr2096_6_s1_R1.fastq.gz_G_to_A.fastq and zr2096_6_s1_R2.fastq.gz_C_to_T.fastq and zr2096_6_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_6_s1_R1.fastq.gz_C_to_T.fastq and zr2096_6_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:1:1101:1093:2134_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 NTTATTAAATTTAATTTTATTATTAAATAAAAANNNNNNNNNNNNNNNNNNNNNNANNTANANAAATATTAATTAAATATTTTTAAAATAATAAATTTAA #<>> Writing bisulfite mapping results to zr2096_6_s1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_6_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_6_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 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2210:9560:37512_1:N:0:CTTGTA NC_035780.1 2 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2214:11172:10265_1:N:0:CTTGTA NC_035780.1 3 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 24237290 reads; of these: 24237290 (100.00%) were paired; of these: 20627389 (85.11%) aligned concordantly 0 times 1409153 (5.81%) aligned concordantly exactly 1 time 2200748 (9.08%) aligned concordantly >1 times 14.89% overall alignment rate 24237290 reads; of these: 24237290 (100.00%) were paired; of these: 20625437 (85.10%) aligned concordantly 0 times 1416059 (5.84%) aligned concordantly exactly 1 time 2195794 (9.06%) aligned concordantly >1 times 14.90% overall alignment rate 24237290 reads; of these: 24237290 (100.00%) were paired; of these: 20266410 (83.62%) aligned concordantly 0 times 1550789 (6.40%) aligned concordantly exactly 1 time 2420091 (9.98%) aligned concordantly >1 times 16.38% overall alignment rate 24237290 reads; of these: 24237290 (100.00%) were paired; of these: 20271204 (83.64%) aligned concordantly 0 times 1543300 (6.37%) aligned concordantly exactly 1 time 2422786 (10.00%) aligned concordantly >1 times 16.36% overall alignment rate Processed 24237290 sequences in total Successfully deleted the temporary files zr2096_6_s1_R1.fastq.gz_C_to_T.fastq, zr2096_6_s1_R1.fastq.gz_G_to_A.fastq, zr2096_6_s1_R2.fastq.gz_C_to_T.fastq and zr2096_6_s1_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24237290 Number of paired-end alignments with a unique best hit: 7735314 Mapping efficiency: 31.9% Sequence pairs with no alignments under any condition: 14340992 Sequence pairs did not map uniquely: 2160984 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2038524 ((converted) top strand) GA/CT/CT: 1822720 (complementary to (converted) top strand) GA/CT/GA: 1834457 (complementary to (converted) bottom strand) CT/GA/GA: 2039611 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 275523644 Total methylated C's in CpG context: 25657852 Total methylated C's in CHG context: 1838651 Total methylated C's in CHH context: 7806415 Total methylated C's in Unknown context: 911519 Total unmethylated C's in CpG context: 10345208 Total unmethylated C's in CHG context: 58273355 Total unmethylated C's in CHH context: 171602163 Total unmethylated C's in Unknown context: 3902421 C methylated in CpG context: 71.3% C methylated in CHG context: 3.1% C methylated in CHH context: 4.4% C methylated in unknown context (CN or CHN): 18.9% Bismark completed in 0d 4h 46m 50s ==================== 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_7_s1_R1.fastq.gz /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_7_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_7_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_7_s1_R2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_7_s1_R1.fastq.gz to zr2096_7_s1_R1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_7_s1_R1.fastq.gz to zr2096_7_s1_R1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_7_s1_R1.fastq.gz (29534746 sequences in total) Writing a C -> T converted version of the input file zr2096_7_s1_R2.fastq.gz to zr2096_7_s1_R2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_7_s1_R2.fastq.gz to zr2096_7_s1_R2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_7_s1_R2.fastq.gz (29534746 sequences in total) Input files are zr2096_7_s1_R1.fastq.gz_C_to_T.fastq and zr2096_7_s1_R1.fastq.gz_G_to_A.fastq and zr2096_7_s1_R2.fastq.gz_C_to_T.fastq and zr2096_7_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_7_s1_R1.fastq.gz_C_to_T.fastq and zr2096_7_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:1:1101:1132:2189_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 AAAAAAATGATTATTATGATGAATTTAAATATTAATAATAAAATTTAAAAAAAATATAAATGTTAAATATTAAATTTTTTAAAAAATGATTATGG BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 141 * 0 0 * * 0 0 CCATAATCATTTTTTAAAAAATTTAATATTTAACATTTATATTTTTTTTAAATTTTATTATTAATATTTAAATTCATCATAATAATCATTTTTTT BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFBBFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr2096_7_s1_R1.fastq.gz_G_to_A.fastq and zr2096_7_s1_R2.fastq.gz_C_to_T.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:1:1101:1132:2189_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 AAAAAAACAACTACTACAACAAATTCAAATATTAATAACAAAATTTAAAAAAAACATAAACATTAAATATCAAATTCTTCAAAAAACAATTACAA BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 141 * 0 0 * * 0 0 TTGTAATTGTTTTTTGAAGAATTTGATATTTAATGTTTATGTTTTTTTTAAATTTTGTTATTAATATTTGAATTTGTTGTAGTAGTTGTTTTTTT BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFBBFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr2096_7_s1_R1.fastq.gz_G_to_A.fastq and zr2096_7_s1_R2.fastq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 100 --maxins 500 --nofw)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 AAAAAAACAACTACTACAACAAATTCAAATATTAATAACAAAATTTAAAAAAAACATAAACATTAAATATCAAATTCTTCAAAAAACAATTACAA BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 141 * 0 0 * * 0 0 TTGTAATTGTTTTTTGAAGAATTTGATATTTAATGTTTATGTTTTTTTTAAATTTTGTTATTAATATTTGAATTTGTTGTAGTAGTTGTTTTTTT BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFBBFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr2096_7_s1_R1.fastq.gz_C_to_T.fastq and zr2096_7_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 --nofw)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 AAAAAAATGATTATTATGATGAATTTAAATATTAATAATAAAATTTAAAAAAAATATAAATGTTAAATATTAAATTTTTTAAAAAATGATTATGG BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 141 * 0 0 * * 0 0 CCATAATCATTTTTTAAAAAATTTAATATTTAACATTTATATTTTTTTTAAATTTTATTATTAATATTTAAATTCATCATAATAATCATTTTTTT BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFBBFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr2096_7_s1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_7_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_7_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 Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1302:9910:66096_1:N:0:ATCACG NC_007175.2 17146 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 29534746 reads; of these: 29534746 (100.00%) were paired; of these: 24705391 (83.65%) aligned concordantly 0 times 1973907 (6.68%) aligned concordantly exactly 1 time 2855448 (9.67%) aligned concordantly >1 times 16.35% overall alignment rate 29534746 reads; of these: 29534746 (100.00%) were paired; of these: 24574019 (83.20%) aligned concordantly 0 times 2025909 (6.86%) aligned concordantly exactly 1 time 2934818 (9.94%) aligned concordantly >1 times 16.80% overall alignment rate 29534746 reads; of these: 29534746 (100.00%) were paired; of these: 24568456 (83.18%) aligned concordantly 0 times 2031264 (6.88%) aligned concordantly exactly 1 time 2935026 (9.94%) aligned concordantly >1 times 16.82% overall alignment rate 29534746 reads; of these: 29534746 (100.00%) were paired; of these: 24702423 (83.64%) aligned concordantly 0 times 1978480 (6.70%) aligned concordantly exactly 1 time 2853843 (9.66%) aligned concordantly >1 times 16.36% overall alignment rate Processed 29534746 sequences in total Successfully deleted the temporary files zr2096_7_s1_R1.fastq.gz_C_to_T.fastq, zr2096_7_s1_R1.fastq.gz_G_to_A.fastq, zr2096_7_s1_R2.fastq.gz_C_to_T.fastq and zr2096_7_s1_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29534746 Number of paired-end alignments with a unique best hit: 10263536 Mapping efficiency: 34.8% Sequence pairs with no alignments under any condition: 16560814 Sequence pairs did not map uniquely: 2710396 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: 2605817 ((converted) top strand) GA/CT/CT: 2517619 (complementary to (converted) top strand) GA/CT/GA: 2532159 (complementary to (converted) bottom strand) CT/GA/GA: 2607940 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 369380706 Total methylated C's in CpG context: 32900574 Total methylated C's in CHG context: 2617073 Total methylated C's in CHH context: 9978987 Total methylated C's in Unknown context: 1167787 Total unmethylated C's in CpG context: 13974627 Total unmethylated C's in CHG context: 78100593 Total unmethylated C's in CHH context: 231808852 Total unmethylated C's in Unknown context: 4963777 C methylated in CpG context: 70.2% C methylated in CHG context: 3.2% C methylated in CHH context: 4.1% C methylated in unknown context (CN or CHN): 19.0% Bismark completed in 0d 5h 54m 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/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_8_s1_R1.fastq.gz /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_8_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_8_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_8_s1_R2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_8_s1_R1.fastq.gz to zr2096_8_s1_R1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_8_s1_R1.fastq.gz to zr2096_8_s1_R1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_8_s1_R1.fastq.gz (29761837 sequences in total) Writing a C -> T converted version of the input file zr2096_8_s1_R2.fastq.gz to zr2096_8_s1_R2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_8_s1_R2.fastq.gz to zr2096_8_s1_R2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_8_s1_R2.fastq.gz (29761837 sequences in total) Input files are zr2096_8_s1_R1.fastq.gz_C_to_T.fastq and zr2096_8_s1_R1.fastq.gz_G_to_A.fastq and zr2096_8_s1_R2.fastq.gz_C_to_T.fastq and zr2096_8_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_8_s1_R1.fastq.gz_C_to_T.fastq and zr2096_8_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:1:1101:1281:2170_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 TAATTTAAAATTAAAAAATTTATTAAATTTATTATTATTTNTTATTTTTTATAAAAGAAAATAGAGAGAGAGAGAGAGAGAGAGAGAG BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#<>> Writing bisulfite mapping results to zr2096_8_s1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_8_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_8_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 Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1208:16282:90212_1:N:0:TTAGGC NC_007175.2 3 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1303:16780:7528_1:N:0:TTAGGC NC_007175.2 17147 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 Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2207:4579:62082_1:N:0:TTATGC NC_007175.2 17151 Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2303:6577:56043_1:N:0:TTAGGC NC_007175.2 17160 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2315:4342:46624_1:N:0:TTAGGC NC_007175.2 17177 29761837 reads; of these: 29761837 (100.00%) were paired; of these: 25549847 (85.85%) aligned concordantly 0 times 1738884 (5.84%) aligned concordantly exactly 1 time 2473106 (8.31%) aligned concordantly >1 times 14.15% overall alignment rate 29761837 reads; of these: 29761837 (100.00%) were paired; of these: 25563157 (85.89%) aligned concordantly 0 times 1730596 (5.81%) aligned concordantly exactly 1 time 2468084 (8.29%) aligned concordantly >1 times 14.11% overall alignment rate 29761837 reads; of these: 29761837 (100.00%) were paired; of these: 25404596 (85.36%) aligned concordantly 0 times 1799055 (6.04%) aligned concordantly exactly 1 time 2558186 (8.60%) aligned concordantly >1 times 14.64% overall alignment rate 29761837 reads; of these: 29761837 (100.00%) were paired; of these: 25395445 (85.33%) aligned concordantly 0 times 1803830 (6.06%) aligned concordantly exactly 1 time 2562562 (8.61%) aligned concordantly >1 times 14.67% overall alignment rate Processed 29761837 sequences in total Successfully deleted the temporary files zr2096_8_s1_R1.fastq.gz_C_to_T.fastq, zr2096_8_s1_R1.fastq.gz_G_to_A.fastq, zr2096_8_s1_R2.fastq.gz_C_to_T.fastq and zr2096_8_s1_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29761837 Number of paired-end alignments with a unique best hit: 9031924 Mapping efficiency: 30.3% Sequence pairs with no alignments under any condition: 18352667 Sequence pairs did not map uniquely: 2377246 Sequence pairs which were discarded because genomic sequence could not be extracted: 5 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2310227 ((converted) top strand) GA/CT/CT: 2208932 (complementary to (converted) top strand) GA/CT/GA: 2211243 (complementary to (converted) bottom strand) CT/GA/GA: 2301517 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 319685131 Total methylated C's in CpG context: 25081844 Total methylated C's in CHG context: 2220090 Total methylated C's in CHH context: 9298556 Total methylated C's in Unknown context: 1029157 Total unmethylated C's in CpG context: 13629344 Total unmethylated C's in CHG context: 67667514 Total unmethylated C's in CHH context: 201787783 Total unmethylated C's in Unknown context: 4326319 C methylated in CpG context: 64.8% C methylated in CHG context: 3.2% C methylated in CHH context: 4.4% C methylated in unknown context (CN or CHN): 19.2% Bismark completed in 0d 5h 33m 34s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools' Reference genome folder provided is /gscratch/srlab/strigg/data/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_9_s1_R1.fastq.gz /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_9_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_9_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_9_s1_R2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_9_s1_R1.fastq.gz to zr2096_9_s1_R1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_9_s1_R1.fastq.gz to zr2096_9_s1_R1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_9_s1_R1.fastq.gz (32636231 sequences in total) Writing a C -> T converted version of the input file zr2096_9_s1_R2.fastq.gz to zr2096_9_s1_R2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_9_s1_R2.fastq.gz to zr2096_9_s1_R2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_9_s1_R2.fastq.gz (32636231 sequences in total) Input files are zr2096_9_s1_R1.fastq.gz_C_to_T.fastq and zr2096_9_s1_R1.fastq.gz_G_to_A.fastq and zr2096_9_s1_R2.fastq.gz_C_to_T.fastq and zr2096_9_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_9_s1_R1.fastq.gz_C_to_T.fastq and zr2096_9_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:2:1101:1135:2128_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 NATTAAATAAAAAATAATAAATAATAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTATAGG #/<<>> Writing bisulfite mapping results to zr2096_9_s1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_9_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_9_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 Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:2:1214:4921:70468_1:N:0:ACTTGA NC_007175.2 17151 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 Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:2:2115:8608:86171_1:N:0:ACTTGA NC_007175.2 17165 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 Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far 32636231 reads; of these: 32636231 (100.00%) were paired; of these: 28019024 (85.85%) aligned concordantly 0 times 1851888 (5.67%) aligned concordantly exactly 1 time 2765319 (8.47%) aligned concordantly >1 times 14.15% overall alignment rate 32636231 reads; of these: 32636231 (100.00%) were paired; of these: 27267138 (83.55%) aligned concordantly 0 times32636231 reads; of these: 2152780 (326362316.60 (%) aligned concordantly exactly 1 time 3216313 (100.009.86%%) were paired; of these:) aligned concordantly >1 times 16.4527259692% ( overall alignment rate83.53 %) aligned concordantly 0 times 2167713 (6.64%) aligned concordantly exactly 1 time 3208826 (9.83%) aligned concordantly >1 times 16.47% overall alignment rate 32636231 reads; of these: 32636231 (100.00%) were paired; of these: 28024144 (85.87%) aligned concordantly 0 times 1862195 (5.71%) aligned concordantly exactly 1 time 2749892 (8.43%) aligned concordantly >1 times 14.13% overall alignment rate Processed 32636231 sequences in total Successfully deleted the temporary files zr2096_9_s1_R1.fastq.gz_C_to_T.fastq, zr2096_9_s1_R1.fastq.gz_G_to_A.fastq, zr2096_9_s1_R2.fastq.gz_C_to_T.fastq and zr2096_9_s1_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 32636231 Number of paired-end alignments with a unique best hit: 10389383 Mapping efficiency: 31.8% Sequence pairs with no alignments under any condition: 19378195 Sequence pairs did not map uniquely: 2868653 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2817892 ((converted) top strand) GA/CT/CT: 2366113 (complementary to (converted) top strand) GA/CT/GA: 2380610 (complementary to (converted) bottom strand) CT/GA/GA: 2824766 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 393776621 Total methylated C's in CpG context: 40612390 Total methylated C's in CHG context: 2982484 Total methylated C's in CHH context: 10534650 Total methylated C's in Unknown context: 1349020 Total unmethylated C's in CpG context: 13936979 Total unmethylated C's in CHG context: 84223643 Total unmethylated C's in CHH context: 241486475 Total unmethylated C's in Unknown context: 5462880 C methylated in CpG context: 74.5% C methylated in CHG context: 3.4% C methylated in CHH context: 4.2% C methylated in unknown context (CN or CHN): 19.8% Bismark completed in 0d 6h 25m 50s ==================== Bismark run complete ==================== /var/spool/slurm/d/job394229/slurm_script: line 38: fg: no job control Now testing Bismark result file /gscratch/srlab/strigg/analyses/20181004/zr2096_10_s1_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_10_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_10_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/" Now testing Bismark result file /gscratch/srlab/strigg/analyses/20181004/zr2096_1_s1_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_1_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_1_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/" Now testing Bismark result file /gscratch/srlab/strigg/analyses/20181004/zr2096_2_s1_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_2_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_2_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/" Now testing Bismark result file /gscratch/srlab/strigg/analyses/20181004/zr2096_3_s1_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_3_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_3_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/" Now testing Bismark result file /gscratch/srlab/strigg/analyses/20181004/zr2096_4_s1_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_4_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_4_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/" Now testing Bismark result file /gscratch/srlab/strigg/analyses/20181004/zr2096_5_s1_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_5_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_5_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/" Now testing Bismark result file /gscratch/srlab/strigg/analyses/20181004/zr2096_6_s1_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_6_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_6_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/" Now testing Bismark result file /gscratch/srlab/strigg/analyses/20181004/zr2096_7_s1_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_7_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_7_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/" Now testing Bismark result file /gscratch/srlab/strigg/analyses/20181004/zr2096_8_s1_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_8_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_8_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/" Now testing Bismark result file /gscratch/srlab/strigg/analyses/20181004/zr2096_9_s1_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_9_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_9_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/" /var/spool/slurm/d/job394229/slurm_script: line 47: !cat: command not found /var/spool/slurm/d/job394229/slurm_script: line 51: !sed: command not found /var/spool/slurm/d/job394229/slurm_script: line 56: fg: no job control xargs: samtools: No such file or directory /var/spool/slurm/d/job394229/slurm_script: line 61: -o: command not found