Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-103_S27_L005_R1_001_val_1.fq.gz to EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-103_S27_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-103_S27_L005_R2_001_val_2.fq.gz to EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-103_S27_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1512:1956_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 NGTTTATATGTATGTATTATATTTGTGTAGGTATTGTATTTGATAAGGAT #<<>> Writing bisulfite mapping results to EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99776 (99.78%) aligned concordantly 0 times 224 (0.22%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.22% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99598 (99.60%) aligned concordantly 0 times 402 (0.40%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.40% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 626 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99374 Sequence pairs did not map uniquely: 0 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: 402 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 224 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 27210 Total methylated C's in CpG context: 69 Total methylated C's in CHG context: 210 Total methylated C's in CHH context: 82 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 7706 Total unmethylated C's in CHG context: 7606 Total unmethylated C's in CHH context: 11537 Total unmethylated C's in Unknown context: 6 C methylated in CpG context: 0.9% C methylated in CHG context: 2.7% C methylated in CHH context: 0.7% C methylated in unknown context (CN or CHN): 25.0% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-104_S28_L005_R1_001_val_1.fq.gz to EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-104_S28_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-104_S28_L005_R2_001_val_2.fq.gz to EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-104_S28_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1112:1988_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 NGGTGGTAGTTATTAAGTATGTATATGTATTAAAAATTGAAATGAAAAATTATTTTATTAGTTTTTGAAATATTTTGGTATTATATTTAGAGGTGTTTGTG #<>> Writing bisulfite mapping results to EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100000100.00 reads; of these:% ) were paired; of these: 100000 (99829 (99.83%) aligned concordantly 0 times 100.00 %171) were paired; of these: ( 0.17 %99659) aligned concordantly exactly 1 time ( 99.66 %0) aligned concordantly 0 times ( 0.00 %341) aligned concordantly >1 times ( 0.340.17%%) aligned concordantly exactly 1 time overall alignment rate 0 (0.00%) aligned concordantly >1 times 0.34% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 512 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99488 Sequence pairs did not map uniquely: 0 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: 341 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 171 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 21465 Total methylated C's in CpG context: 67 Total methylated C's in CHG context: 184 Total methylated C's in CHH context: 76 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 6109 Total unmethylated C's in CHG context: 5946 Total unmethylated C's in CHH context: 9083 Total unmethylated C's in Unknown context: 6 C methylated in CpG context: 1.1% C methylated in CHG context: 3.0% C methylated in CHH context: 0.8% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-111_S29_L005_R1_001_val_1.fq.gz to EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-111_S29_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-111_S29_L005_R2_001_val_2.fq.gz to EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-111_S29_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1222:1965_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 NTGATGAGTGATTTATAATGTTTTGTAGGTTTATTAAAAGATTGTGTTTGTGTTTGTAATTTTTTTGATATATTGTTAATTAAAGTTGGGATGGTTGGATT #<>> Writing bisulfite mapping results to EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 10000099880 reads; of these: ( 99.88 %100000) aligned concordantly 0 times ( 120 (0.12100.00%%) aligned concordantly exactly 1 time) were paired; of these: 099780 ( (0.0099.78%%) aligned concordantly >1 times) aligned concordantly 0 times 0.12 %220 overall alignment rate ( 0.22%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.22% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 340 Mapping efficiency: 0.3% Sequence pairs with no alignments under any condition: 99660 Sequence pairs did not map uniquely: 0 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: 220 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 120 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 13846 Total methylated C's in CpG context: 37 Total methylated C's in CHG context: 114 Total methylated C's in CHH context: 34 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 3990 Total unmethylated C's in CHG context: 3772 Total unmethylated C's in CHH context: 5899 Total unmethylated C's in Unknown context: 1 C methylated in CpG context: 0.9% C methylated in CHG context: 2.9% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 66.7% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-113_S30_L005_R1_001_val_1.fq.gz to EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-113_S30_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-113_S30_L005_R2_001_val_2.fq.gz to EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-113_S30_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1442:1956_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 NTAGTATTTTTATTAGAAGAATTAGAAATATTAGTAATAGTAAATTATTAGGTAGTGATAATATTGTAAATGAGTAATTAAAGTATTTATTATATGTGATG #>> Writing bisulfite mapping results to EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99513 (99.51%) aligned concordantly 0 times 487 (0.49%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.49% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99750 (99.75%) aligned concordantly 0 times 250 (0.25%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.25% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 737 Mapping efficiency: 0.7% Sequence pairs with no alignments under any condition: 99263 Sequence pairs did not map uniquely: 0 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: 487 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 250 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 29996 Total methylated C's in CpG context: 81 Total methylated C's in CHG context: 261 Total methylated C's in CHH context: 100 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 8622 Total unmethylated C's in CHG context: 8210 Total unmethylated C's in CHH context: 12722 Total unmethylated C's in Unknown context: 3 C methylated in CpG context: 0.9% C methylated in CHG context: 3.1% C methylated in CHH context: 0.8% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-119_S31_L005_R1_001_val_1.fq.gz to EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-119_S31_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-119_S31_L005_R2_001_val_2.fq.gz to EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-119_S31_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1132:1973_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 NTGGTGAAAATTTTGAAAATTGTTTAATAATGGTGTAAAATATTAATTTATATATTATTTTAGTAATTAGGGTGAAATATTTTGAAAGTAAGA #<>> Writing bisulfite mapping results to EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these:100000 reads; of these: 98783 (100000 (98.78%) aligned concordantly 0 times100.00 % ) were paired; of these:1217 ( 1.2299392% () aligned concordantly exactly 1 time99.39 % ) aligned concordantly 0 times0 ( 0.00608% () aligned concordantly >1 times0.61 %1.22) aligned concordantly exactly 1 time% overall alignment rate 0 (0.00%) aligned concordantly >1 times 0.61% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 1825 Mapping efficiency: 1.8% Sequence pairs with no alignments under any condition: 98175 Sequence pairs did not map uniquely: 0 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: 1217 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 608 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 78115 Total methylated C's in CpG context: 207 Total methylated C's in CHG context: 655 Total methylated C's in CHH context: 232 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 22679 Total unmethylated C's in CHG context: 22265 Total unmethylated C's in CHH context: 32077 Total unmethylated C's in Unknown context: 30 C methylated in CpG context: 0.9% C methylated in CHG context: 2.9% C methylated in CHH context: 0.7% C methylated in unknown context (CN or CHN): 6.2% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-120_S32_L005_R1_001_val_1.fq.gz to EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-120_S32_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-120_S32_L005_R2_001_val_2.fq.gz to EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-120_S32_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1140:1995_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 NGTATTTGGTTATATTTTAATATTAAATTTTGATTAAAATAGTTGTTGAAAATTGATTAGTATTATTTAGGAAGTATAGAAGTGTTAATATAAAGTTAATT #<>> Writing bisulfite mapping results to EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99662 (99.66100000% reads; of these:) aligned concordantly 0 times 100000338 ( (0.34%) aligned concordantly exactly 1 time 100.000% () were paired; of these:0.00 % ) aligned concordantly >1 times99829 (0.3499.83%% overall alignment rate) aligned concordantly 0 times 171 (0.17%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.17% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 509 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99491 Sequence pairs did not map uniquely: 0 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: 338 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 171 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 20623 Total methylated C's in CpG context: 66 Total methylated C's in CHG context: 185 Total methylated C's in CHH context: 72 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 5916 Total unmethylated C's in CHG context: 5838 Total unmethylated C's in CHH context: 8546 Total unmethylated C's in Unknown context: 4 C methylated in CpG context: 1.1% C methylated in CHG context: 3.1% C methylated in CHH context: 0.8% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-127_S33_L005_R1_001_val_1.fq.gz to EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-127_S33_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-127_S33_L005_R2_001_val_2.fq.gz to EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-127_S33_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1259:1963_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 NTATTTATTTTTATATATTATTAAAAATTTATATTTTTATTATTAAAAATATAAATTTATATATTATTAATAATTTATTTTTATATTTTATTAATAAT #<>> Writing bisulfite mapping results to EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99685 (99.69%) aligned concordantly 0 times 315 (0.32%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.32% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99843 (99.84%) aligned concordantly 0 times 157 (0.16%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.16% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 472 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99528 Sequence pairs did not map uniquely: 0 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: 315 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 157 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19671 Total methylated C's in CpG context: 43 Total methylated C's in CHG context: 178 Total methylated C's in CHH context: 51 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 5723 Total unmethylated C's in CHG context: 5518 Total unmethylated C's in CHH context: 8158 Total unmethylated C's in Unknown context: 2 C methylated in CpG context: 0.7% C methylated in CHG context: 3.1% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 50.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-128_S34_L005_R1_001_val_1.fq.gz to EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-128_S34_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-128_S34_L005_R2_001_val_2.fq.gz to EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-128_S34_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1617:1971_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 NGAGATTATTTAATATAGATATGTGTTTAAGGTTTTGGTAGATATTGTTAATTATGATTATTGAGGTTATTTAATATAGATATGTTTTAAAGGTTTGG #<<>> Writing bisulfite mapping results to EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99894 (99.89%) aligned concordantly 0 times 106 (0.11%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.11% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99791 (99.79%) aligned concordantly 0 times 209 (0.21%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.21% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 315 Mapping efficiency: 0.3% Sequence pairs with no alignments under any condition: 99685 Sequence pairs did not map uniquely: 0 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: 209 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 106 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 12689 Total methylated C's in CpG context: 52 Total methylated C's in CHG context: 128 Total methylated C's in CHH context: 39 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 3637 Total unmethylated C's in CHG context: 3467 Total unmethylated C's in CHH context: 5366 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 1.4% C methylated in CHG context: 3.6% C methylated in CHH context: 0.7% Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-135_S35_L005_R1_001_val_1.fq.gz to EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-135_S35_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-135_S35_L005_R2_001_val_2.fq.gz to EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-135_S35_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1469:1995_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 NTGTATTTGTTATATTTTTAAAATAAATTAAAATTTTAATTATTTGTTTATTTTGTTTTTTTGGAATTTTGAGTGTATATGTATTATATAATTTATT #<>> Writing bisulfite mapping results to EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99736 (99.74%) aligned concordantly 0 times 264 (0.26%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.26% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99862 (99.86%) aligned concordantly 0 times 138 (0.14%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.14% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 402 Mapping efficiency: 0.4% Sequence pairs with no alignments under any condition: 99598 Sequence pairs did not map uniquely: 0 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: 264 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 138 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 15423 Total methylated C's in CpG context: 51 Total methylated C's in CHG context: 204 Total methylated C's in CHH context: 41 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 4476 Total unmethylated C's in CHG context: 4350 Total unmethylated C's in CHH context: 6301 Total unmethylated C's in Unknown context: 4 C methylated in CpG context: 1.1% C methylated in CHG context: 4.5% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-136_S36_L005_R1_001_val_1.fq.gz to EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-136_S36_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-136_S36_L005_R2_001_val_2.fq.gz to EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-136_S36_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1242:1980_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 NATGGTTGGATTATTTTATAGTTAAAATATTATGAGGTGTATTGATTGTTTTATTTTGAGATGTTGTGTAGATATTGTTTTAATGGGGTGTAGTGTTTTT #<>> Writing bisulfite mapping results to EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99637 (99.64%) aligned concordantly 0 times 363 (0.36%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.36% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99786 (99.79%) aligned concordantly 0 times 214 (0.21%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.21% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 577 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99423 Sequence pairs did not map uniquely: 0 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: 363 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 214 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 22626 Total methylated C's in CpG context: 70 Total methylated C's in CHG context: 248 Total methylated C's in CHH context: 67 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 6254 Total unmethylated C's in CHG context: 6148 Total unmethylated C's in CHH context: 9839 Total unmethylated C's in Unknown context: 2 C methylated in CpG context: 1.1% C methylated in CHG context: 3.9% C methylated in CHH context: 0.7% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-143_S37_L005_R1_001_val_1.fq.gz to EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-143_S37_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-143_S37_L005_R2_001_val_2.fq.gz to EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-143_S37_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1205:1956_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 NGAAGGAAAATGAATTGATAGTATTATAAGGTTTAAATTTGTTATTATTTTTATAATTTGTATTATTTTTATTATTATGTTATATTTTTATAAATAAATTT #<>> Writing bisulfite mapping results to EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99520 (99.52%100000) aligned concordantly 0 times reads; of these: 480100000 ( (0.48%) aligned concordantly exactly 1 time 0100.00 (%0.00) were paired; of these:% ) aligned concordantly >1 times 997520.48 (%99.75 overall alignment rate% ) aligned concordantly 0 times 248 (0.25%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.25% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 728 Mapping efficiency: 0.7% Sequence pairs with no alignments under any condition: 99272 Sequence pairs did not map uniquely: 0 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: 480 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 248 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 29662 Total methylated C's in CpG context: 77 Total methylated C's in CHG context: 262 Total methylated C's in CHH context: 84 Total methylated C's in Unknown context: 4 Total unmethylated C's in CpG context: 8359 Total unmethylated C's in CHG context: 8219 Total unmethylated C's in CHH context: 12661 Total unmethylated C's in Unknown context: 1 C methylated in CpG context: 0.9% C methylated in CHG context: 3.1% C methylated in CHH context: 0.7% C methylated in unknown context (CN or CHN): 80.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-145_S38_L005_R1_001_val_1.fq.gz to EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-145_S38_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-145_S38_L005_R2_001_val_2.fq.gz to EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-145_S38_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1386:1965_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 NTGGGTAAGTAAAGATATAATATTGTAAGTATTATTATGTATATAAGTTTTATATTTTTTTTTTGAGGGTTGAAGTGTTATTATTTTGATATATATT #<>> Writing bisulfite mapping results to EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99842 (99.84%) aligned concordantly 0 times 158 (0.16%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.16% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99697 (99.70%) aligned concordantly 0 times 303 (0.30%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.30% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 461 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99539 Sequence pairs did not map uniquely: 0 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: 303 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 158 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19052 Total methylated C's in CpG context: 66 Total methylated C's in CHG context: 200 Total methylated C's in CHH context: 68 Total methylated C's in Unknown context: 4 Total unmethylated C's in CpG context: 5564 Total unmethylated C's in CHG context: 5129 Total unmethylated C's in CHH context: 8025 Total unmethylated C's in Unknown context: 9 C methylated in CpG context: 1.2% C methylated in CHG context: 3.8% C methylated in CHH context: 0.8% C methylated in unknown context (CN or CHN): 30.8% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-151_S2_L002_R1_001_val_1.fq.gz to EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-151_S2_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-151_S2_L002_R2_001_val_2.fq.gz to EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-151_S2_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1928:2248_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 TAGTAGAGGTTTATATGTATTTATGTTTGGTTAGAAAAGGTTTATATGTATTTATGTTTGGTTAGTAGAGGTTTATATGTATTTATGTTTGGTTA BBBBBFFBFFBBFBBBBFFF/B/FBBF>> Writing bisulfite mapping results to EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99579 (99.58%) aligned concordantly 0 times 421 (0.42%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.42% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99800 (99.80%) aligned concordantly 0 times 200 (0.20%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.20% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 621 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99379 Sequence pairs did not map uniquely: 0 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: 421 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 200 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 24525 Total methylated C's in CpG context: 75 Total methylated C's in CHG context: 309 Total methylated C's in CHH context: 104 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 6962 Total unmethylated C's in CHG context: 6893 Total unmethylated C's in CHH context: 10182 Total unmethylated C's in Unknown context: 2 C methylated in CpG context: 1.1% C methylated in CHG context: 4.3% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-152_S3_L002_R1_001_val_1.fq.gz to EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-152_S3_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-152_S3_L002_R2_001_val_2.fq.gz to EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-152_S3_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1155:2233_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 AATGGNTATGAAAATGTAATAAAGGAAGAGATATGAAAATGTAATAAAGGAANATTTATGANAATGTATTGTGGGAAGTGATATGAAAATGTAATATG BBBBB#B>> Writing bisulfite mapping results to EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99843 (99.84%) aligned concordantly 0 times 157 (0.16%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.16% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99688 (99.69%) aligned concordantly 0 times 312 (0.31%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.31% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 469 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99531 Sequence pairs did not map uniquely: 0 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: 312 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 157 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19248 Total methylated C's in CpG context: 48 Total methylated C's in CHG context: 198 Total methylated C's in CHH context: 87 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 5447 Total unmethylated C's in CHG context: 5293 Total unmethylated C's in CHH context: 8175 Total unmethylated C's in Unknown context: 1 C methylated in CpG context: 0.9% C methylated in CHG context: 3.6% C methylated in CHH context: 1.1% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-153_S4_L002_R1_001_val_1.fq.gz to EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-153_S4_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-153_S4_L002_R2_001_val_2.fq.gz to EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-153_S4_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1785:2231_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 TGTTGNGATATATAATTGAAAATTGTTGAAAGTGTTATTAAATATAATGTAATAATAAATGATAAAGGGATGTAATGTTGTATATTAATTATTAT BBBBB#BBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:2:2207:1785:2231_2:N:0:TTAGGC/2 141 * 0 0 * * 0 0 ATANNNNNNNNNNNNNNNNNNNNNNNNNNNNTNNNATTTATTATTACATTATATTTAATAACACTTTCAACAATTTTCAATTATATATCACAACA BBB############################B###BB<>> Writing bisulfite mapping results to EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99795 (99.80%) aligned concordantly 0 times 205 (0.20%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.20% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99568 (99.57%) aligned concordantly 0 times 432 (0.43%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.43% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 637 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99363 Sequence pairs did not map uniquely: 0 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: 432 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 205 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 26175 Total methylated C's in CpG context: 100 Total methylated C's in CHG context: 289 Total methylated C's in CHH context: 159 Total methylated C's in Unknown context: 12 Total unmethylated C's in CpG context: 7435 Total unmethylated C's in CHG context: 7145 Total unmethylated C's in CHH context: 11047 Total unmethylated C's in Unknown context: 5 C methylated in CpG context: 1.3% C methylated in CHG context: 3.9% C methylated in CHH context: 1.4% C methylated in unknown context (CN or CHN): 70.6% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-154_S5_L002_R1_001_val_1.fq.gz to EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-154_S5_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-154_S5_L002_R2_001_val_2.fq.gz to EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-154_S5_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:2191:2242_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 ATGTANATTAAGAGTTAAATTATGTAGATGTAGATTAAAAGTTAAATTATGTATAGGTAGATTAAGAGTTAAATTAAGTAGATGTAGATTAAGAGTTTAAT BBBBB#>> Writing bisulfite mapping results to EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99736 (99.74%) aligned concordantly 0 times 264 (0.26%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.26% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99435 (99.44%) aligned concordantly 0 times 565 (0.56%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.56% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 829 Mapping efficiency: 0.8% Sequence pairs with no alignments under any condition: 99171 Sequence pairs did not map uniquely: 0 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: 565 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 264 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 33555 Total methylated C's in CpG context: 112 Total methylated C's in CHG context: 380 Total methylated C's in CHH context: 145 Total methylated C's in Unknown context: 5 Total unmethylated C's in CpG context: 9663 Total unmethylated C's in CHG context: 9316 Total unmethylated C's in CHH context: 13939 Total unmethylated C's in Unknown context: 15 C methylated in CpG context: 1.1% C methylated in CHG context: 3.9% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 25.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-159_S6_L002_R1_001_val_1.fq.gz to EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-159_S6_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-159_S6_L002_R2_001_val_2.fq.gz to EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-159_S6_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1469:2230_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 GGTTANTGAAGTGTATATAGTTATATTGTAAATTAATGGTTGAGTGAGTTTTNTTTTTTATTAGGTAATATTTTAAGGGAATGGTTGTTTGTAAATATTGG BBBBB#BBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFF#<>> Writing bisulfite mapping results to EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz 100000100000 reads; of these: reads; of these: 100000100000 ( (100.00100.00%%) were paired; of these:) were paired; of these: 9965099862 ( (99.6599.86%%) aligned concordantly 0 times) aligned concordantly 0 times 350138 ( (0.350.14%%) aligned concordantly exactly 1 time) aligned concordantly exactly 1 time 00 ( (0.000.00%%) aligned concordantly >1 times) aligned concordantly >1 times 0.350.14%% overall alignment rate overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 488 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99512 Sequence pairs did not map uniquely: 0 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: 350 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 138 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19125 Total methylated C's in CpG context: 72 Total methylated C's in CHG context: 192 Total methylated C's in CHH context: 85 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 5542 Total unmethylated C's in CHG context: 5229 Total unmethylated C's in CHH context: 8005 Total unmethylated C's in Unknown context: 4 C methylated in CpG context: 1.3% C methylated in CHG context: 3.5% C methylated in CHH context: 1.1% C methylated in unknown context (CN or CHN): 33.3% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-160_S7_L002_R1_001_val_1.fq.gz to EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-160_S7_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-160_S7_L002_R2_001_val_2.fq.gz to EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-160_S7_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1522:2231_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 GTATGNGTAATTAGGTGATTTTTTTTGATTTGATGTAGTTAGTGGATTGGGAATTGGTAA BBBBB#BBBFFBFFFFFFFFFFFFFFB/>> Writing bisulfite mapping results to EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99390 (99.39%) aligned concordantly 0 times 610 (0.61%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.61% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 98785 (98.78%) aligned concordantly 0 times 1215 (1.22%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 1.22% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 1825 Mapping efficiency: 1.8% Sequence pairs with no alignments under any condition: 98175 Sequence pairs did not map uniquely: 0 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: 1215 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 610 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 67790 Total methylated C's in CpG context: 214 Total methylated C's in CHG context: 788 Total methylated C's in CHH context: 347 Total methylated C's in Unknown context: 8 Total unmethylated C's in CpG context: 19193 Total unmethylated C's in CHG context: 18392 Total unmethylated C's in CHH context: 28856 Total unmethylated C's in Unknown context: 24 C methylated in CpG context: 1.1% C methylated in CHG context: 4.1% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 25.0% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-161_S8_L002_R1_001_val_1.fq.gz to EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-161_S8_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-161_S8_L002_R2_001_val_2.fq.gz to EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-161_S8_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:2010:2229_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TGATANGTAGTATATGGTGTATGATATAGTA BBBBB#>> Writing bisulfite mapping results to EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99630 (99.63%) aligned concordantly 0 times 370 (0.37%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.37% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99783 (99.78%) aligned concordantly 0 times 217 (0.22%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.22% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 587 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99413 Sequence pairs did not map uniquely: 0 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: 370 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 217 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 22950 Total methylated C's in CpG context: 98 Total methylated C's in CHG context: 237 Total methylated C's in CHH context: 100 Total methylated C's in Unknown context: 5 Total unmethylated C's in CpG context: 6548 Total unmethylated C's in CHG context: 6286 Total unmethylated C's in CHH context: 9681 Total unmethylated C's in Unknown context: 4 C methylated in CpG context: 1.5% C methylated in CHG context: 3.6% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 55.6% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-162_S9_L002_R1_001_val_1.fq.gz to EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-162_S9_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-162_S9_L002_R2_001_val_2.fq.gz to EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-162_S9_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1238:2233_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 TGTTANTTATTTTAAAATTTGTTGATAAATTGTTTATTTTTAGGATAGTTTTTTTAGATATTGTTTTTTTTTGGTTTGAAAGGGTTATGAATAGTTTTTTT BBBBB#>> Writing bisulfite mapping results to EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99804 (99.80%) aligned concordantly 0 times 196 (0.20%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.20% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99581 (99.58%) aligned concordantly 0 times 419 (0.42%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.42% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 615 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99385 Sequence pairs did not map uniquely: 0 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: 419 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 196 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 22576 Total methylated C's in CpG context: 83 Total methylated C's in CHG context: 302 Total methylated C's in CHH context: 127 Total methylated C's in Unknown context: 4 Total unmethylated C's in CpG context: 6495 Total unmethylated C's in CHG context: 6133 Total unmethylated C's in CHH context: 9436 Total unmethylated C's in Unknown context: 6 C methylated in CpG context: 1.3% C methylated in CHG context: 4.7% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 40.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-167_S10_L002_R1_001_val_1.fq.gz to EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-167_S10_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-167_S10_L002_R2_001_val_2.fq.gz to EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-167_S10_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1666:2232_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 TTGAANTTGTTGATTTATATGGGGATATGAATAATAAGTTTAATATTTAAGATGGAGAAGAAATAAGTGTAGAATTTTGGATAAAGGATAATTAAGTTAAT BBBBB#BBFFFFFF>> Writing bisulfite mapping results to EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99716 (99.72%) aligned concordantly 0 times 284 (0.28%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.28% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99503 (99.50%) aligned concordantly 0 times 497 (0.50%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.50% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 781 Mapping efficiency: 0.8% Sequence pairs with no alignments under any condition: 99219 Sequence pairs did not map uniquely: 0 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: 497 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 284 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 36053 Total methylated C's in CpG context: 189 Total methylated C's in CHG context: 367 Total methylated C's in CHH context: 300 Total methylated C's in Unknown context: 5 Total unmethylated C's in CpG context: 10550 Total unmethylated C's in CHG context: 10313 Total unmethylated C's in CHH context: 14334 Total unmethylated C's in Unknown context: 13 C methylated in CpG context: 1.8% C methylated in CHG context: 3.4% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 27.8% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-168_S11_L002_R1_001_val_1.fq.gz to EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-168_S11_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-168_S11_L002_R2_001_val_2.fq.gz to EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-168_S11_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1424:2239_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 GTGATNTATAATGTATTATTGAAAGTTAATAGTTTATTTAAGTTTTTGGTATTTTTTGATTTAGGTTTAATTATTTTGTTATGTGGGTTTGTGATTTG BBBBB#B>> Writing bisulfite mapping results to EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99818 (99.82%) aligned concordantly 0 times 182 (0.18%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.18% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99603 (99.60%) aligned concordantly 0 times 397 (0.40%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.40% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 579 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99421 Sequence pairs did not map uniquely: 0 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: 397 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 182 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 23642 Total methylated C's in CpG context: 71 Total methylated C's in CHG context: 251 Total methylated C's in CHH context: 126 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 6804 Total unmethylated C's in CHG context: 6632 Total unmethylated C's in CHH context: 9758 Total unmethylated C's in Unknown context: 7 C methylated in CpG context: 1.0% C methylated in CHG context: 3.6% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 22.2% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-169_S12_L002_R1_001_val_1.fq.gz to EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-169_S12_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-169_S12_L002_R2_001_val_2.fq.gz to EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-169_S12_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1452:2231_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 TGGTANGAGGTTGTGTGATTAGTATAAAGGTGTTTAGAGTTATTAAGTGGATTGGATTGGAGTTTGGATTGGTTTTGTATTAATAAAAGTGTTTTTTTTGT BBBBB#<>> Writing bisulfite mapping results to EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99780 (99.78%) aligned concordantly 0 times 220 (0.22%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.22% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99898 (99.90%) aligned concordantly 0 times 102 (0.10%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.10% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 322 Mapping efficiency: 0.3% Sequence pairs with no alignments under any condition: 99678 Sequence pairs did not map uniquely: 0 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: 220 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 102 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 12209 Total methylated C's in CpG context: 55 Total methylated C's in CHG context: 153 Total methylated C's in CHH context: 62 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 3518 Total unmethylated C's in CHG context: 3274 Total unmethylated C's in CHH context: 5147 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 1.5% C methylated in CHG context: 4.5% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 100.0% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-170_S13_L002_R1_001_val_1.fq.gz to EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-170_S13_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-170_S13_L002_R2_001_val_2.fq.gz to EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-170_S13_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:2244:2228_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 TTGTTNAGTTTGTTTAAGTTATTTTGATTTGTTAAAAAATATGGTAG BBBBB#<>> Writing bisulfite mapping results to EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz 100000100000 reads; of these: reads; of these: 100000100000 ( (100.00100.00%%) were paired; of these:) were paired; of these: 9968799849 ( (99.6999.85%%) aligned concordantly 0 times) aligned concordantly 0 times 313151 ( (0.310.15%%) aligned concordantly exactly 1 time) aligned concordantly exactly 1 time 00 ( (0.000.00%%) aligned concordantly >1 times) aligned concordantly >1 times 0.310.15%% overall alignment rate overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 464 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99536 Sequence pairs did not map uniquely: 0 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: 313 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 151 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 16764 Total methylated C's in CpG context: 51 Total methylated C's in CHG context: 230 Total methylated C's in CHH context: 80 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 4862 Total unmethylated C's in CHG context: 4524 Total unmethylated C's in CHH context: 7017 Total unmethylated C's in Unknown context: 4 C methylated in CpG context: 1.0% C methylated in CHG context: 4.8% C methylated in CHH context: 1.1% C methylated in unknown context (CN or CHN): 33.3% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-175_S14_L003_R1_001_val_1.fq.gz to EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-175_S14_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-175_S14_L003_R2_001_val_2.fq.gz to EPI-175_S14_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-175_S14_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-175_S14_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-175_S14_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:1436:2247_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 AAGAANATGTGTTTGTATGTTGGAAGTTTGTTTAGTGTGG BBBBB#>> Writing bisulfite mapping results to EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99457100000 ( reads; of these:99.46 % ) aligned concordantly 0 times100000 ( 543 (0.54%100.00) aligned concordantly exactly 1 time% ) were paired; of these: 0 (997510.00 (%99.75) aligned concordantly >1 times% ) aligned concordantly 0 times0.54 % overall alignment rate249 (0.25%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.25% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-175_S14_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 792 Mapping efficiency: 0.8% Sequence pairs with no alignments under any condition: 99208 Sequence pairs did not map uniquely: 0 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: 543 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 249 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 32529 Total methylated C's in CpG context: 85 Total methylated C's in CHG context: 351 Total methylated C's in CHH context: 128 Total methylated C's in Unknown context: 4 Total unmethylated C's in CpG context: 9343 Total unmethylated C's in CHG context: 8875 Total unmethylated C's in CHH context: 13747 Total unmethylated C's in Unknown context: 5 C methylated in CpG context: 0.9% C methylated in CHG context: 3.8% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 44.4% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-176_S15_L003_R1_001_val_1.fq.gz to EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-176_S15_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-176_S15_L003_R2_001_val_2.fq.gz to EPI-176_S15_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-176_S15_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-176_S15_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-176_S15_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4405:2246_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 TGTGGNGTAGATGAAGATGTTTGATATGTTGTAGAATATGTAGTTGTAGAGTGTTATTGTGAAGGTGATGTATGTTGTTATTATTGAGAG BBBBB#B>> Writing bisulfite mapping results to EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99235 (99.23%) aligned concordantly 0 times 765 (0.77%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.77% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99611 (99.61%) aligned concordantly 0 times 389 (0.39%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.39% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-176_S15_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 1154 Mapping efficiency: 1.2% Sequence pairs with no alignments under any condition: 98846 Sequence pairs did not map uniquely: 0 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: 765 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 389 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 47248 Total methylated C's in CpG context: 158 Total methylated C's in CHG context: 516 Total methylated C's in CHH context: 187 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 13283 Total unmethylated C's in CHG context: 12806 Total unmethylated C's in CHH context: 20298 Total unmethylated C's in Unknown context: 24 C methylated in CpG context: 1.2% C methylated in CHG context: 3.9% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-181_S16_L003_R1_001_val_1.fq.gz to EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-181_S16_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-181_S16_L003_R2_001_val_2.fq.gz to EPI-181_S16_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-181_S16_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-181_S16_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-181_S16_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:3117:2249_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 GTTAGNGTTTAAAATATATGTATATTGAATATGTAGTAATTATATAGATAAAGTTTTATTGGTTATAAAATAGGGATGTTTTTAGTTTTGTTGAGTAT BBBBB#>> Writing bisulfite mapping results to EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99850 (99.85%) aligned concordantly 0 times 150 (0.15%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.15% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99730 (99.73%) aligned concordantly 0 times 270 (0.27%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.27% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-181_S16_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 420 Mapping efficiency: 0.4% Sequence pairs with no alignments under any condition: 99580 Sequence pairs did not map uniquely: 0 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: 270 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 150 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 17504 Total methylated C's in CpG context: 57 Total methylated C's in CHG context: 146 Total methylated C's in CHH context: 66 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 4851 Total unmethylated C's in CHG context: 4794 Total unmethylated C's in CHH context: 7590 Total unmethylated C's in Unknown context: 5 C methylated in CpG context: 1.2% C methylated in CHG context: 3.0% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-182_S17_L003_R1_001_val_1.fq.gz to EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-182_S17_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-182_S17_L003_R2_001_val_2.fq.gz to EPI-182_S17_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-182_S17_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-182_S17_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-182_S17_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:2786:2250_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 TGATTNTATTATGGAAATATTGTTTAGTTTAGTAGAAATATTTTTTGGAGTTGTTGTGA BBBBB#<>> Writing bisulfite mapping results to EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99838 (99.84%) aligned concordantly 0 times 162 (0.16%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.16% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99696 (99.70%) aligned concordantly 0 times 304 (0.30%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.30% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-182_S17_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 466 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99534 Sequence pairs did not map uniquely: 0 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: 304 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 162 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19438 Total methylated C's in CpG context: 57 Total methylated C's in CHG context: 189 Total methylated C's in CHH context: 75 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 5560 Total unmethylated C's in CHG context: 5249 Total unmethylated C's in CHH context: 8308 Total unmethylated C's in Unknown context: 2 C methylated in CpG context: 1.0% C methylated in CHG context: 3.5% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-184_S18_L003_R1_001_val_1.fq.gz to EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-184_S18_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-184_S18_L003_R2_001_val_2.fq.gz to EPI-184_S18_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-184_S18_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-184_S18_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-184_S18_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:2159:2247_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 GAATANGGAAATGGGTAGGATGTAGGTTATAAAGGAAATTGGGTTAATAATGTGAATAGAGAAATGGGTAGGAGGTAGGTTATAAAGGAAATTGGGT BBBBB#B>> Writing bisulfite mapping results to EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99838 (99.84%) aligned concordantly 0 times 162 (0.16%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.16% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99705 (99.70%) aligned concordantly 0 times 295 (0.29%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.29% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-184_S18_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 457 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99543 Sequence pairs did not map uniquely: 0 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: 295 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 162 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 17774 Total methylated C's in CpG context: 57 Total methylated C's in CHG context: 191 Total methylated C's in CHH context: 84 Total methylated C's in Unknown context: 1 Total unmethylated C's in CpG context: 4960 Total unmethylated C's in CHG context: 4864 Total unmethylated C's in CHH context: 7618 Total unmethylated C's in Unknown context: 3 C methylated in CpG context: 1.1% C methylated in CHG context: 3.8% C methylated in CHH context: 1.1% C methylated in unknown context (CN or CHN): 25.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-185_S19_L003_R1_001_val_1.fq.gz to EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-185_S19_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-185_S19_L003_R2_001_val_2.fq.gz to EPI-185_S19_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-185_S19_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-185_S19_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-185_S19_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4218:2247_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 GGGGANGGAGAGTTATAGGTAGTTGTAGTGGATATGTTGTGGGATTGAGGATGTTGTGTTGTGTTTTATGGTTTTGGGTTGTTGTTGTAGAGTTGAATTTG BBBBB#B>> Writing bisulfite mapping results to EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99832 (99.83%) aligned concordantly 0 times 168 (0.17%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.17% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99669 (99.67%) aligned concordantly 0 times 331 (0.33%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.33% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-185_S19_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 499 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99501 Sequence pairs did not map uniquely: 0 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: 331 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 168 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19174 Total methylated C's in CpG context: 89 Total methylated C's in CHG context: 196 Total methylated C's in CHH context: 77 Total methylated C's in Unknown context: 8 Total unmethylated C's in CpG context: 5395 Total unmethylated C's in CHG context: 5101 Total unmethylated C's in CHH context: 8316 Total unmethylated C's in Unknown context: 7 C methylated in CpG context: 1.6% C methylated in CHG context: 3.7% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 53.3% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-187_S20_L003_R1_001_val_1.fq.gz to EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-187_S20_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-187_S20_L003_R2_001_val_2.fq.gz to EPI-187_S20_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-187_S20_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-187_S20_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-187_S20_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:5270:2246_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TAATANATAATTATTTTAGATAATAAGGTTGGAAAAATTGTTGAAATATGGGTTTATTTTTTGTTTTATTGTTTGTAAATTTAGTGTTGAGTTATTGT BBBBB#BBBFFFFFFFFBFFFFFFBBFFF>> Writing bisulfite mapping results to EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99886 (99.89%) aligned concordantly 0 times 114 (0.11%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.11% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99708 (99.71%) aligned concordantly 0 times 292 (0.29%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.29% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-187_S20_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 406 Mapping efficiency: 0.4% Sequence pairs with no alignments under any condition: 99594 Sequence pairs did not map uniquely: 0 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: 292 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 114 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 16344 Total methylated C's in CpG context: 69 Total methylated C's in CHG context: 186 Total methylated C's in CHH context: 69 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 4667 Total unmethylated C's in CHG context: 4576 Total unmethylated C's in CHH context: 6777 Total unmethylated C's in Unknown context: 3 C methylated in CpG context: 1.5% C methylated in CHG context: 3.9% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 40.0% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-188_S21_L003_R1_001_val_1.fq.gz to EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-188_S21_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-188_S21_L003_R2_001_val_2.fq.gz to EPI-188_S21_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-188_S21_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-188_S21_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-188_S21_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:6853:2249_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 AGTTGNGGGTAAGAGAGAGTTTTTTTGGAAAATTTTGATATTTTAAAAGTTAAATAATGTATTATAGTAAGTTTTATAGTGTATGAGGGG BBBBB#>> Writing bisulfite mapping results to EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99621 (99.62%) aligned concordantly 0 times 379 (0.38%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.38% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99819 (99.82%) aligned concordantly 0 times 181 (0.18%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.18% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-188_S21_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 560 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99440 Sequence pairs did not map uniquely: 0 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: 379 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 181 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19403 Total methylated C's in CpG context: 84 Total methylated C's in CHG context: 229 Total methylated C's in CHH context: 87 Total methylated C's in Unknown context: 13 Total unmethylated C's in CpG context: 5516 Total unmethylated C's in CHG context: 5264 Total unmethylated C's in CHH context: 8223 Total unmethylated C's in Unknown context: 8 C methylated in CpG context: 1.5% C methylated in CHG context: 4.2% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 61.9% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-193_S22_L003_R1_001_val_1.fq.gz to EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-193_S22_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-193_S22_L003_R2_001_val_2.fq.gz to EPI-193_S22_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-193_S22_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-193_S22_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-193_S22_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:3001:2249_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 ATTGTNTATAATTTTGGTATAGTTTTATGTAGTTGGGGATATTTAGGGATATTGTATATAATTTTGGTATAGTTTTGTAAAGTTAGGGATATTTAGGG /B/BB#//>> Writing bisulfite mapping results to EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99820 (99.82%) aligned concordantly 0 times 180 (0.18%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.18% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99648 (99.65%) aligned concordantly 0 times 352 (0.35%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.35% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-193_S22_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 532 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99468 Sequence pairs did not map uniquely: 0 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: 352 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 180 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19364 Total methylated C's in CpG context: 79 Total methylated C's in CHG context: 239 Total methylated C's in CHH context: 84 Total methylated C's in Unknown context: 5 Total unmethylated C's in CpG context: 5478 Total unmethylated C's in CHG context: 5399 Total unmethylated C's in CHH context: 8085 Total unmethylated C's in Unknown context: 5 C methylated in CpG context: 1.4% C methylated in CHG context: 4.2% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 50.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-194_S23_L003_R1_001_val_1.fq.gz to EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-194_S23_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-194_S23_L003_R2_001_val_2.fq.gz to EPI-194_S23_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-194_S23_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-194_S23_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-194_S23_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4438:2247_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 TTAGTNATTAAGGGGTTGTGTGTTTGAATTTTTTGTTTGGTAATAGTTTTTGTGATGATTGATATATGATATTGTGTTTTATTATTATTTGTTTTTTA BBBBB#BBB>> Writing bisulfite mapping results to EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99815 (99.81%) aligned concordantly 0 times 185 (0.18%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.18% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99577 (99.58%) aligned concordantly 0 times 423 (0.42%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.42% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-194_S23_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 608 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99392 Sequence pairs did not map uniquely: 0 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: 423 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 185 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 24315 Total methylated C's in CpG context: 90 Total methylated C's in CHG context: 279 Total methylated C's in CHH context: 102 Total methylated C's in Unknown context: 3 Total unmethylated C's in CpG context: 7146 Total unmethylated C's in CHG context: 6537 Total unmethylated C's in CHH context: 10161 Total unmethylated C's in Unknown context: 12 C methylated in CpG context: 1.2% C methylated in CHG context: 4.1% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 20.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-199_S24_L003_R1_001_val_1.fq.gz to EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-199_S24_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-199_S24_L003_R2_001_val_2.fq.gz to EPI-199_S24_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-199_S24_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-199_S24_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-199_S24_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:3720:2249_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 ATTAGNTTTTTATATTTAAGGAGATTGAGAGATATATTGTGAATTTTGAAAGAAAATTGAAAGAGGTTATTGAAGAAAGAGGTATGTG BBBBB#BB>> Writing bisulfite mapping results to EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99835 (99.83%) aligned concordantly 0 times 165 (0.17%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.17% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99677 (99.68%) aligned concordantly 0 times 323 (0.32%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.32% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-199_S24_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 488 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99512 Sequence pairs did not map uniquely: 0 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: 323 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 165 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 17466 Total methylated C's in CpG context: 65 Total methylated C's in CHG context: 190 Total methylated C's in CHH context: 74 Total methylated C's in Unknown context: 4 Total unmethylated C's in CpG context: 4904 Total unmethylated C's in CHG context: 4687 Total unmethylated C's in CHH context: 7546 Total unmethylated C's in Unknown context: 5 C methylated in CpG context: 1.3% C methylated in CHG context: 3.9% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 44.4% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-200_S25_L003_R1_001_val_1.fq.gz to EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-200_S25_L003_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-200_S25_L003_R2_001_val_2.fq.gz to EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-200_S25_L003_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4688:2247_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 GTATGNTGTTTATGTGTTTTAGAGGTGGAGTATTGGATTAATGATAA BBBBB#BBFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:3:1107:4688:2247_2:N:0:CTTGTA/2 141 * 0 0 * * 0 0 TTANCANNNNNNNNNNNNNNNNNCTNTNNNNNACATAAACACCATAC BBB#BB#################B<#B#####BBBFFFFFFFFFFFF YT:Z:UP YF:Z:NS Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4688:2247_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 GTATGNTGTTTATGTGTTTTAGAGGTGGAGTATTGGATTAATGATAA BBBBB#BBFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:3:1107:4688:2247_2:N:0:CTTGTA/2 141 * 0 0 * * 0 0 TTANCANNNNNNNNNNNNNNNNNCTNTNNNNNACATAAACACCATAC BBB#BB#################B<#B#####BBBFFFFFFFFFFFF YT:Z:UP YF:Z:NS >>> Writing bisulfite mapping results to EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99850 (99.85%) aligned concordantly 0 times 150 (0.15%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.15% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99678 (99.68%) aligned concordantly 0 times 322 (0.32%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.32% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 472 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99528 Sequence pairs did not map uniquely: 0 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: 322 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 150 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 16786 Total methylated C's in CpG context: 54 Total methylated C's in CHG context: 226 Total methylated C's in CHH context: 92 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 4640 Total unmethylated C's in CHG context: 4649 Total unmethylated C's in CHH context: 7125 Total unmethylated C's in Unknown context: 7 C methylated in CpG context: 1.2% C methylated in CHG context: 4.6% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 22.2% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-205_S26_L004_R1_001_val_1.fq.gz to EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-205_S26_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-205_S26_L004_R2_001_val_2.fq.gz to EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-205_S26_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1391:2218_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 GATGTAGGTTGTGGTTGATGGAGAAATATTGGAAGTAGTATTTGT BBBBB/FFFFFFFFFFFFFFFFFFFF>> Writing bisulfite mapping results to EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99827 (99.83%) aligned concordantly 0 times 173 (0.17%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.17% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99668 (99.67%) aligned concordantly 0 times 332 (0.33%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.33% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 505 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99495 Sequence pairs did not map uniquely: 0 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: 332 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 173 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 17949 Total methylated C's in CpG context: 78 Total methylated C's in CHG context: 205 Total methylated C's in CHH context: 78 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 5146 Total unmethylated C's in CHG context: 4965 Total unmethylated C's in CHH context: 7477 Total unmethylated C's in Unknown context: 2 C methylated in CpG context: 1.5% C methylated in CHG context: 4.0% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 50.0% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-206_S27_L004_R1_001_val_1.fq.gz to EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-206_S27_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-206_S27_L004_R2_001_val_2.fq.gz to EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-206_S27_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1645:2233_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 TTATATGAGGTGGTGGTTATATTTTGATTTAATTTGAGGTTTTTTTTATTAATATGATTGG BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF>> Writing bisulfite mapping results to EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99654 (99.65%) aligned concordantly 0 times 346 (0.35%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.35% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99833 (99.83%) aligned concordantly 0 times 167 (0.17%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.17% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 513 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99487 Sequence pairs did not map uniquely: 0 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: 346 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 167 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 17988 Total methylated C's in CpG context: 68 Total methylated C's in CHG context: 201 Total methylated C's in CHH context: 83 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 5111 Total unmethylated C's in CHG context: 4998 Total unmethylated C's in CHH context: 7527 Total unmethylated C's in Unknown context: 13 C methylated in CpG context: 1.3% C methylated in CHG context: 3.9% C methylated in CHH context: 1.1% C methylated in unknown context (CN or CHN): 13.3% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-208_S28_L004_R1_001_val_1.fq.gz to EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-208_S28_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-208_S28_L004_R2_001_val_2.fq.gz to EPI-208_S28_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-208_S28_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-208_S28_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-208_S28_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1156:2191_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 ATGTTTTATTTTTTAGANATAATAGGTTAANNNTNTNNNNTGTAGTATTTAGNGGTTNGNNNGGAAGAGTATATGTTTGAATTTTAGTTATTTAGGTATTT BBBBBFF>> Writing bisulfite mapping results to EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99288 (99.29%) aligned concordantly 0 times 712 (0.71%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.71% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99626 (99.63%) aligned concordantly 0 times 374 (0.37%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.37% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-208_S28_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 1086 Mapping efficiency: 1.1% Sequence pairs with no alignments under any condition: 98914 Sequence pairs did not map uniquely: 0 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: 712 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 374 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 36315 Total methylated C's in CpG context: 174 Total methylated C's in CHG context: 481 Total methylated C's in CHH context: 183 Total methylated C's in Unknown context: 1 Total unmethylated C's in CpG context: 10494 Total unmethylated C's in CHG context: 10189 Total unmethylated C's in CHH context: 14794 Total unmethylated C's in Unknown context: 3 C methylated in CpG context: 1.6% C methylated in CHG context: 4.5% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 25.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-209_S29_L004_R1_001_val_1.fq.gz to EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-209_S29_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-209_S29_L004_R2_001_val_2.fq.gz to EPI-209_S29_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-209_S29_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-209_S29_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-209_S29_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1317:2220_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 TAAAGGTATTGGATTAGTTATTGTTGTATGAGTAAAGAATGTATATAATAAATATGATTTTAAATAGTTTTAGTTGATATATTAGGT BB>> Writing bisulfite mapping results to EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99544 (99.54%) aligned concordantly 0 times 456 (0.46%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.46% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99816 (99.82%) aligned concordantly 0 times 184 (0.18%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.18% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-209_S29_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 640 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99360 Sequence pairs did not map uniquely: 0 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: 456 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 184 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 24643 Total methylated C's in CpG context: 93 Total methylated C's in CHG context: 308 Total methylated C's in CHH context: 71 Total methylated C's in Unknown context: 4 Total unmethylated C's in CpG context: 7101 Total unmethylated C's in CHG context: 6882 Total unmethylated C's in CHH context: 10188 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 1.3% C methylated in CHG context: 4.3% C methylated in CHH context: 0.7% C methylated in unknown context (CN or CHN): 100.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-214_S30_L004_R1_001_val_1.fq.gz to EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-214_S30_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-214_S30_L004_R2_001_val_2.fq.gz to EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-214_S30_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1228:2242_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 TAAGATGTATTTTTATAGTATAATGAAGTATATTTATTTTT BBBBBFFFFFFFFFFFFFFFFBBFFBFFFFFFFFFBFFFFF YT:Z:UP D00743:144:CAAWNANXX:4:2315:1228:2242_2:N:0:ACAGTG/2 141 * 0 0 * * 0 0 AAAAATAAATATACTTCATTATACTATAAAAATACATCTTA BBBFFFFFBF>> Writing bisulfite mapping results to EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99577 (99.58%) aligned concordantly 0 times 422 (0.42%) aligned concordantly exactly 1 time 1 (0.00%) aligned concordantly >1 times 0.42% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99799 (99.80%) aligned concordantly 0 times 201 (0.20%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.20% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 624 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99376 Sequence pairs did not map uniquely: 0 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: 423 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 201 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 24470 Total methylated C's in CpG context: 77 Total methylated C's in CHG context: 243 Total methylated C's in CHH context: 99 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 6942 Total unmethylated C's in CHG context: 6758 Total unmethylated C's in CHH context: 10351 Total unmethylated C's in Unknown context: 9 C methylated in CpG context: 1.1% C methylated in CHG context: 3.5% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 18.2% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-215_S31_L004_R1_001_val_1.fq.gz to EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-215_S31_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-215_S31_L004_R2_001_val_2.fq.gz to EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-215_S31_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1539:2240_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 ATGGTAGTAGAGTGTTGGATTAATATTGGGGTTTGTATGTTTGAGTGTATGGTTTAGTAGTAGAGTGTTGGATTAATATTGGGGGTTGTATGTTTGAGTGT BBBBBFF>> Writing bisulfite mapping results to EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99506 (99.51%) aligned concordantly 0 times 494 (0.49%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.49% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99805 (99.81%) aligned concordantly 0 times 195 (0.20%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.20% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 689 Mapping efficiency: 0.7% Sequence pairs with no alignments under any condition: 99311 Sequence pairs did not map uniquely: 0 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: 494 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 195 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 23984 Total methylated C's in CpG context: 80 Total methylated C's in CHG context: 340 Total methylated C's in CHH context: 102 Total methylated C's in Unknown context: 8 Total unmethylated C's in CpG context: 7002 Total unmethylated C's in CHG context: 6800 Total unmethylated C's in CHH context: 9660 Total unmethylated C's in Unknown context: 5 C methylated in CpG context: 1.1% C methylated in CHG context: 4.8% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 61.5% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-220_S32_L004_R1_001_val_1.fq.gz to EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-220_S32_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-220_S32_L004_R2_001_val_2.fq.gz to EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-220_S32_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1490:2220_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TTTTTTGGTTGTTGTATGGTGTTGTTGTATAGTGTTGTGGTGTTGTTGTATGGTGTTGGTATATGGTGTTGTGGTGTTATGTATGGTGTTGTGGTGTTGGT BBBBBFFFFFFBFFFFFFF/BFFFFFBF/FFFFFFFFFFFBF>> Writing bisulfite mapping results to EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99720 (99.72%) aligned concordantly 0 times 280 (0.28%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.28% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99871 (99.87%) aligned concordantly 0 times 129 (0.13%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.13% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 409 Mapping efficiency: 0.4% Sequence pairs with no alignments under any condition: 99591 Sequence pairs did not map uniquely: 0 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: 280 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 129 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 15161 Total methylated C's in CpG context: 59 Total methylated C's in CHG context: 153 Total methylated C's in CHH context: 87 Total methylated C's in Unknown context: 4 Total unmethylated C's in CpG context: 4243 Total unmethylated C's in CHG context: 4218 Total unmethylated C's in CHH context: 6401 Total unmethylated C's in Unknown context: 3 C methylated in CpG context: 1.4% C methylated in CHG context: 3.5% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 57.1% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-221_S33_L004_R1_001_val_1.fq.gz to EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-221_S33_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-221_S33_L004_R2_001_val_2.fq.gz to EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-221_S33_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1412:2190_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 ATTTTNTGTTTTATGTTTTATTTTTATTTTAGTGTTTGAAAAAATTTTGGAGAAAGGTAGATATTTTTTAGTGGTTGTAAAAAATATAAGTTGGATTG BBBBB#BBBBFFFFFFFFFFFFFFFFFFFFFBF7FFFFF>> Writing bisulfite mapping results to EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99836 (99.84%) aligned concordantly 0 times 164 (0.16%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.16% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99695 (99.69%) aligned concordantly 0 times 305 (0.30%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.30% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 469 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99531 Sequence pairs did not map uniquely: 0 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: 305 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 164 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 16654 Total methylated C's in CpG context: 60 Total methylated C's in CHG context: 210 Total methylated C's in CHH context: 68 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 4765 Total unmethylated C's in CHG context: 4711 Total unmethylated C's in CHH context: 6840 Total unmethylated C's in Unknown context: 11 C methylated in CpG context: 1.2% C methylated in CHG context: 4.3% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-226_S34_L004_R1_001_val_1.fq.gz to EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-226_S34_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-226_S34_L004_R2_001_val_2.fq.gz to EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-226_S34_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1168:2235_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 TTATATTATATTTTATANTGTGTAAAGTTGTNGTTAAGTGATTTATATTTGTNGTATTTTNNTTGTTATTGTTTATATAGTGGG BBBBBFFFFFFFFFFBF#BB>> Writing bisulfite mapping results to EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99779 (99.78%) aligned concordantly 0 times 221 (0.22%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.22% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99900 (99.90%) aligned concordantly 0 times 100 (0.10%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.10% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 321 Mapping efficiency: 0.3% Sequence pairs with no alignments under any condition: 99679 Sequence pairs did not map uniquely: 0 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: 221 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 100 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 12469 Total methylated C's in CpG context: 26 Total methylated C's in CHG context: 152 Total methylated C's in CHH context: 66 Total methylated C's in Unknown context: 4 Total unmethylated C's in CpG context: 3625 Total unmethylated C's in CHG context: 3431 Total unmethylated C's in CHH context: 5169 Total unmethylated C's in Unknown context: 4 C methylated in CpG context: 0.7% C methylated in CHG context: 4.2% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 50.0% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-227_S35_L004_R1_001_val_1.fq.gz to EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-227_S35_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-227_S35_L004_R2_001_val_2.fq.gz to EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-227_S35_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1203:2205_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 TTTGTTTTTTTTTATATATAAATTATTAATTAAATAATTTAATTTTGTAAAANTTGTAAAANTATATAAATATTTATGTATTATTTTAATATTTTATAGTT BBBBB>> Writing bisulfite mapping results to EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99877 (99.88%) aligned concordantly 0 times 123 (0.12%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.12% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99730 (99.73%) aligned concordantly 0 times 270 (0.27%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.27% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 393 Mapping efficiency: 0.4% Sequence pairs with no alignments under any condition: 99607 Sequence pairs did not map uniquely: 0 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: 270 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 123 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 14367 Total methylated C's in CpG context: 59 Total methylated C's in CHG context: 207 Total methylated C's in CHH context: 57 Total methylated C's in Unknown context: 7 Total unmethylated C's in CpG context: 4210 Total unmethylated C's in CHG context: 3866 Total unmethylated C's in CHH context: 5968 Total unmethylated C's in Unknown context: 1 C methylated in CpG context: 1.4% C methylated in CHG context: 5.1% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 87.5% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-229_S36_L004_R1_001_val_1.fq.gz to EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-229_S36_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-229_S36_L004_R2_001_val_2.fq.gz to EPI-229_S36_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-229_S36_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-229_S36_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-229_S36_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1979:2198_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 TGTATAGTATAGTTTAGTGTTGTGGTTAGTTTTAATATAGAAATATTAATTTTAATTTAATGTGATGTATTTAGAAAGTTTTAGAAAGTTTGTGGTAG B/BBBFFFF>> Writing bisulfite mapping results to EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99765 (99.77%) aligned concordantly 0 times 235 (0.23%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.23% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99529 (99.53%) aligned concordantly 0 times 471 (0.47%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.47% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-229_S36_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 706 Mapping efficiency: 0.7% Sequence pairs with no alignments under any condition: 99294 Sequence pairs did not map uniquely: 0 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: 471 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 235 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 25788 Total methylated C's in CpG context: 64 Total methylated C's in CHG context: 359 Total methylated C's in CHH context: 92 Total methylated C's in Unknown context: 3 Total unmethylated C's in CpG context: 7416 Total unmethylated C's in CHG context: 7161 Total unmethylated C's in CHH context: 10696 Total unmethylated C's in Unknown context: 10 C methylated in CpG context: 0.9% C methylated in CHG context: 4.8% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 23.1% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-230_S37_L004_R1_001_val_1.fq.gz to EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-230_S37_L004_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-230_S37_L004_R2_001_val_2.fq.gz to EPI-230_S37_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-230_S37_L004_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-230_S37_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-230_S37_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1161:2210_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 ATTTTGTATATGGTATANATTTAGTTTGATTNNTNANATNGGTGAATGATGTNGTATATNNNTTGTTTGATTGGTAAAATGGGTGAATGATGTTATATATG BBBBBFFFFFFFFFFFF#B<>> Writing bisulfite mapping results to EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99759 (99.76%) aligned concordantly 0 times 241 (0.24%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.24% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99531 (99.53%) aligned concordantly 0 times 469 (0.47%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.47% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-230_S37_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 710 Mapping efficiency: 0.7% Sequence pairs with no alignments under any condition: 99290 Sequence pairs did not map uniquely: 0 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: 469 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 241 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 27134 Total methylated C's in CpG context: 92 Total methylated C's in CHG context: 316 Total methylated C's in CHH context: 74 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 7884 Total unmethylated C's in CHG context: 7379 Total unmethylated C's in CHH context: 11389 Total unmethylated C's in Unknown context: 4 C methylated in CpG context: 1.2% C methylated in CHG context: 4.1% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 33.3% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-41_S38_L005_R1_001_val_1.fq.gz to EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-41_S38_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-41_S38_L005_R2_001_val_2.fq.gz to EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-41_S38_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1186:2238_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 GTAGTNTTGGTTGGAATATATATTGTATTGTTATTTGTATTTGGTATATAAGNGGTATNGTNGTTGGTGTTTGGTGTGTAAGTAGTATTGTTGTTGGAGTT BBBBB#>> Writing bisulfite mapping results to EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99553 (99.55%) aligned concordantly 0 times 447 (0.45%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.45% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99830 (99.83%) aligned concordantly 0 times 170 (0.17%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.17% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 617 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99383 Sequence pairs did not map uniquely: 0 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: 447 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 170 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 22262 Total methylated C's in CpG context: 66 Total methylated C's in CHG context: 257 Total methylated C's in CHH context: 106 Total methylated C's in Unknown context: 9 Total unmethylated C's in CpG context: 6651 Total unmethylated C's in CHG context: 6218 Total unmethylated C's in CHH context: 8964 Total unmethylated C's in Unknown context: 4 C methylated in CpG context: 1.0% C methylated in CHG context: 4.0% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 69.2% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-42_S39_L005_R1_001_val_1.fq.gz to EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-42_S39_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-42_S39_L005_R2_001_val_2.fq.gz to EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-42_S39_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1597:2224_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 AGGTANTATGATGTGATGATGGGGTATGATGTGAAGATGGG BBBBB#BBFFFFFFFFFFFFFFFFBFFBFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:5:1107:1597:2224_2:N:0:CGATGT/2 141 * 0 0 * * 0 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNCCT ####################################<#<>> Writing bisulfite mapping results to EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100000 reads; of these:100.00 % ) were paired; of these:100000 ( 99864 (99.86%100.00) aligned concordantly 0 times% ) were paired; of these: 136 (996150.14 (%99.61) aligned concordantly exactly 1 time% ) aligned concordantly 0 times 0 (3850.00 (%0.39) aligned concordantly >1 times% ) aligned concordantly exactly 1 time0.14 % overall alignment rate0 (0.00%) aligned concordantly >1 times 0.39% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 521 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99479 Sequence pairs did not map uniquely: 0 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: 385 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 136 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 18303 Total methylated C's in CpG context: 55 Total methylated C's in CHG context: 232 Total methylated C's in CHH context: 88 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 5528 Total unmethylated C's in CHG context: 5252 Total unmethylated C's in CHH context: 7148 Total unmethylated C's in Unknown context: 3 C methylated in CpG context: 1.0% C methylated in CHG context: 4.2% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-43_S40_L005_R1_001_val_1.fq.gz to EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-43_S40_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-43_S40_L005_R2_001_val_2.fq.gz to EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-43_S40_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1481:2240_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 TTTTAATATTAATATATTAAAATATAAAATTTTTATAATTATAATATATATAAATATTATAATATTAATATATTAATATAAAAATTTTATATAATTATAAT BBBBBFF>> Writing bisulfite mapping results to EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99417 (99.42%) aligned concordantly 0 times 583 (0.58%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.58% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99742 (99.74%) aligned concordantly 0 times 258 (0.26%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.26% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 841 Mapping efficiency: 0.8% Sequence pairs with no alignments under any condition: 99159 Sequence pairs did not map uniquely: 0 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: 583 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 258 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 29803 Total methylated C's in CpG context: 102 Total methylated C's in CHG context: 354 Total methylated C's in CHH context: 94 Total methylated C's in Unknown context: 3 Total unmethylated C's in CpG context: 8642 Total unmethylated C's in CHG context: 8293 Total unmethylated C's in CHH context: 12318 Total unmethylated C's in Unknown context: 13 C methylated in CpG context: 1.2% C methylated in CHG context: 4.1% C methylated in CHH context: 0.8% C methylated in unknown context (CN or CHN): 18.8% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104b'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 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/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-44_S41_L005_R1_001_val_1.fq.gz to EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-44_S41_L005_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-44_S41_L005_R2_001_val_2.fq.gz to EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-44_S41_L005_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1348:2233_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 AATTTNGGTGTATAGTTTAAGTTAGGAAAGTTTTTTTTATTAAATTGTTTTGTTATGTTTAAATAGATATTTTTTTGGTAGTAT BBBBB#/B>> Writing bisulfite mapping results to EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99808 (99.81%) aligned concordantly 0 times 192 (0.19%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.19% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99530 (99.53%) aligned concordantly 0 times 470 (0.47%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.47% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 662 Mapping efficiency: 0.7% Sequence pairs with no alignments under any condition: 99338 Sequence pairs did not map uniquely: 0 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: 470 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 192 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 22316 Total methylated C's in CpG context: 61 Total methylated C's in CHG context: 289 Total methylated C's in CHH context: 87 Total methylated C's in Unknown context: 4 Total unmethylated C's in CpG context: 6526 Total unmethylated C's in CHG context: 6229 Total unmethylated C's in CHH context: 9124 Total unmethylated C's in Unknown context: 2 C methylated in CpG context: 0.9% C methylated in CHG context: 4.4% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 66.7% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Processing paired-end Bismark output file(s) (SAM format): EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam: 626 Total number duplicated alignments removed: 15 (2.40%) Duplicated alignments were found at: 11 different position(s) Total count of deduplicated leftover sequences: 611 (97.60% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam: 512 Total number duplicated alignments removed: 15 (2.93%) Duplicated alignments were found at: 12 different position(s) Total count of deduplicated leftover sequences: 497 (97.07% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam: 340 Total number duplicated alignments removed: 16 (4.71%) Duplicated alignments were found at: 11 different position(s) Total count of deduplicated leftover sequences: 324 (95.29% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam: 737 Total number duplicated alignments removed: 44 (5.97%) Duplicated alignments were found at: 33 different position(s) Total count of deduplicated leftover sequences: 693 (94.03% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam: 1825 Total number duplicated alignments removed: 84 (4.60%) Duplicated alignments were found at: 67 different position(s) Total count of deduplicated leftover sequences: 1741 (95.40% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam: 509 Total number duplicated alignments removed: 24 (4.72%) Duplicated alignments were found at: 17 different position(s) Total count of deduplicated leftover sequences: 485 (95.28% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam: 472 Total number duplicated alignments removed: 18 (3.81%) Duplicated alignments were found at: 13 different position(s) Total count of deduplicated leftover sequences: 454 (96.19% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam: 315 Total number duplicated alignments removed: 13 (4.13%) Duplicated alignments were found at: 11 different position(s) Total count of deduplicated leftover sequences: 302 (95.87% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam: 402 Total number duplicated alignments removed: 20 (4.98%) Duplicated alignments were found at: 16 different position(s) Total count of deduplicated leftover sequences: 382 (95.02% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam: 577 Total number duplicated alignments removed: 26 (4.51%) Duplicated alignments were found at: 21 different position(s) Total count of deduplicated leftover sequences: 551 (95.49% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam: 728 Total number duplicated alignments removed: 33 (4.53%) Duplicated alignments were found at: 26 different position(s) Total count of deduplicated leftover sequences: 695 (95.47% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam: 461 Total number duplicated alignments removed: 23 (4.99%) Duplicated alignments were found at: 17 different position(s) Total count of deduplicated leftover sequences: 438 (95.01% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam: 621 Total number duplicated alignments removed: 67 (10.79%) Duplicated alignments were found at: 42 different position(s) Total count of deduplicated leftover sequences: 554 (89.21% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam: 469 Total number duplicated alignments removed: 40 (8.53%) Duplicated alignments were found at: 31 different position(s) Total count of deduplicated leftover sequences: 429 (91.47% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam: 637 Total number duplicated alignments removed: 28 (4.40%) Duplicated alignments were found at: 21 different position(s) Total count of deduplicated leftover sequences: 609 (95.60% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam: 829 Total number duplicated alignments removed: 95 (11.46%) Duplicated alignments were found at: 55 different position(s) Total count of deduplicated leftover sequences: 734 (88.54% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam: 488 Total number duplicated alignments removed: 36 (7.38%) Duplicated alignments were found at: 29 different position(s) Total count of deduplicated leftover sequences: 452 (92.62% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam: 1825 Total number duplicated alignments removed: 285 (15.62%) Duplicated alignments were found at: 159 different position(s) Total count of deduplicated leftover sequences: 1540 (84.38% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam: 587 Total number duplicated alignments removed: 54 (9.20%) Duplicated alignments were found at: 38 different position(s) Total count of deduplicated leftover sequences: 533 (90.80% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam: 615 Total number duplicated alignments removed: 38 (6.18%) Duplicated alignments were found at: 31 different position(s) Total count of deduplicated leftover sequences: 577 (93.82% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam: 781 Total number duplicated alignments removed: 3 (0.38%) Duplicated alignments were found at: 3 different position(s) Total count of deduplicated leftover sequences: 778 (99.62% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam: 579 Total number duplicated alignments removed: 34 (5.87%) Duplicated alignments were found at: 27 different position(s) Total count of deduplicated leftover sequences: 545 (94.13% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam: 322 Total number duplicated alignments removed: 16 (4.97%) Duplicated alignments were found at: 12 different position(s) Total count of deduplicated leftover sequences: 306 (95.03% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam: 464 Total number duplicated alignments removed: 18 (3.88%) Duplicated alignments were found at: 15 different position(s) Total count of deduplicated leftover sequences: 446 (96.12% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam: 792 Total number duplicated alignments removed: 91 (11.49%) Duplicated alignments were found at: 61 different position(s) Total count of deduplicated leftover sequences: 701 (88.51% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam: 1154 Total number duplicated alignments removed: 130 (11.27%) Duplicated alignments were found at: 81 different position(s) Total count of deduplicated leftover sequences: 1024 (88.73% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam: 420 Total number duplicated alignments removed: 16 (3.81%) Duplicated alignments were found at: 14 different position(s) Total count of deduplicated leftover sequences: 404 (96.19% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam: 466 Total number duplicated alignments removed: 27 (5.79%) Duplicated alignments were found at: 23 different position(s) Total count of deduplicated leftover sequences: 439 (94.21% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam: 457 Total number duplicated alignments removed: 27 (5.91%) Duplicated alignments were found at: 20 different position(s) Total count of deduplicated leftover sequences: 430 (94.09% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam: 499 Total number duplicated alignments removed: 35 (7.01%) Duplicated alignments were found at: 28 different position(s) Total count of deduplicated leftover sequences: 464 (92.99% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam: 406 Total number duplicated alignments removed: 37 (9.11%) Duplicated alignments were found at: 26 different position(s) Total count of deduplicated leftover sequences: 369 (90.89% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam: 560 Total number duplicated alignments removed: 30 (5.36%) Duplicated alignments were found at: 26 different position(s) Total count of deduplicated leftover sequences: 530 (94.64% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam: 532 Total number duplicated alignments removed: 46 (8.65%) Duplicated alignments were found at: 29 different position(s) Total count of deduplicated leftover sequences: 486 (91.35% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam: 608 Total number duplicated alignments removed: 69 (11.35%) Duplicated alignments were found at: 43 different position(s) Total count of deduplicated leftover sequences: 539 (88.65% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam: 488 Total number duplicated alignments removed: 69 (14.14%) Duplicated alignments were found at: 42 different position(s) Total count of deduplicated leftover sequences: 419 (85.86% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam: 472 Total number duplicated alignments removed: 42 (8.90%) Duplicated alignments were found at: 34 different position(s) Total count of deduplicated leftover sequences: 430 (91.10% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam: 505 Total number duplicated alignments removed: 38 (7.52%) Duplicated alignments were found at: 29 different position(s) Total count of deduplicated leftover sequences: 467 (92.48% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam: 513 Total number duplicated alignments removed: 40 (7.80%) Duplicated alignments were found at: 29 different position(s) Total count of deduplicated leftover sequences: 473 (92.20% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam: 1086 Total number duplicated alignments removed: 137 (12.62%) Duplicated alignments were found at: 80 different position(s) Total count of deduplicated leftover sequences: 949 (87.38% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam: 640 Total number duplicated alignments removed: 50 (7.81%) Duplicated alignments were found at: 43 different position(s) Total count of deduplicated leftover sequences: 590 (92.19% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam: 624 Total number duplicated alignments removed: 63 (10.10%) Duplicated alignments were found at: 38 different position(s) Total count of deduplicated leftover sequences: 561 (89.90% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam: 689 Total number duplicated alignments removed: 85 (12.34%) Duplicated alignments were found at: 52 different position(s) Total count of deduplicated leftover sequences: 604 (87.66% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam: 409 Total number duplicated alignments removed: 29 (7.09%) Duplicated alignments were found at: 19 different position(s) Total count of deduplicated leftover sequences: 380 (92.91% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam: 469 Total number duplicated alignments removed: 38 (8.10%) Duplicated alignments were found at: 26 different position(s) Total count of deduplicated leftover sequences: 431 (91.90% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam: 321 Total number duplicated alignments removed: 23 (7.17%) Duplicated alignments were found at: 16 different position(s) Total count of deduplicated leftover sequences: 298 (92.83% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam: 393 Total number duplicated alignments removed: 25 (6.36%) Duplicated alignments were found at: 22 different position(s) Total count of deduplicated leftover sequences: 368 (93.64% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam: 706 Total number duplicated alignments removed: 78 (11.05%) Duplicated alignments were found at: 54 different position(s) Total count of deduplicated leftover sequences: 628 (88.95% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam: 710 Total number duplicated alignments removed: 71 (10.00%) Duplicated alignments were found at: 53 different position(s) Total count of deduplicated leftover sequences: 639 (90.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam: 617 Total number duplicated alignments removed: 78 (12.64%) Duplicated alignments were found at: 43 different position(s) Total count of deduplicated leftover sequences: 539 (87.36% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam: 521 Total number duplicated alignments removed: 50 (9.60%) Duplicated alignments were found at: 34 different position(s) Total count of deduplicated leftover sequences: 471 (90.40% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam: 841 Total number duplicated alignments removed: 114 (13.56%) Duplicated alignments were found at: 62 different position(s) Total count of deduplicated leftover sequences: 727 (86.44% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam: 662 Total number duplicated alignments removed: 114 (17.22%) Duplicated alignments were found at: 66 different position(s) Total count of deduplicated leftover sequences: 548 (82.78% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz" *** Bismark methylation extractor version v0.21.0 *** Trying to determine the type of mapping from the SAM header line of file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Treating file(s) as paired-end data (as extracted from @PG line) Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 14 Output will be written to the current directory ('/gscratch/scrubbed/sr320/1104b') Summarising bedGraph parameters: =============================================================== Generating additional output in bedGraph and coverage format bedGraph format: coverage format: Using a cutoff of 1 read(s) to report cytosine positions Reporting and sorting cytosine methylation information in CpG context only (default) The bedGraph UNIX sort command will use the following memory setting: '75%'. Temporary directory used for sorting is the output directory Checking file >>EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 611 lines in total Total number of methylation call strings processed: 1222 Final Cytosine Methylation Report ================================= Total number of C's analysed: 18654 Total methylated C's in CpG context: 49 Total methylated C's in CHG context: 153 Total methylated C's in CHH context: 58 Total C to T conversions in CpG context: 5272 Total C to T conversions in CHG context: 5187 Total C to T conversions in CHH context: 7935 C methylated in CpG context: 0.9% C methylated in CHG context: 2.9% C methylated in CHH context: 0.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 497 lines in total Total number of methylation call strings processed: 994 Final Cytosine Methylation Report ================================= Total number of C's analysed: 14389 Total methylated C's in CpG context: 50 Total methylated C's in CHG context: 129 Total methylated C's in CHH context: 54 Total C to T conversions in CpG context: 4077 Total C to T conversions in CHG context: 3941 Total C to T conversions in CHH context: 6138 C methylated in CpG context: 1.2% C methylated in CHG context: 3.2% C methylated in CHH context: 0.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 324 lines in total Total number of methylation call strings processed: 648 Final Cytosine Methylation Report ================================= Total number of C's analysed: 8929 Total methylated C's in CpG context: 25 Total methylated C's in CHG context: 77 Total methylated C's in CHH context: 24 Total C to T conversions in CpG context: 2521 Total C to T conversions in CHG context: 2422 Total C to T conversions in CHH context: 3860 C methylated in CpG context: 1.0% C methylated in CHG context: 3.1% C methylated in CHH context: 0.6% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz" Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 693 lines in total Total number of methylation call strings processed: 1386 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19356 Total methylated C's in CpG context: 50 Total methylated C's in CHG context: 169 Total methylated C's in CHH context: 71 Total C to T conversions in CpG context: 5494 Total C to T conversions in CHG context: 5243 Total C to T conversions in CHH context: 8329 C methylated in CpG context: 0.9% C methylated in CHG context: 3.1% C methylated in CHH context: 0.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 1741 lines in total Total number of methylation call strings processed: 3482 Final Cytosine Methylation Report ================================= Total number of C's analysed: 53002 Total methylated C's in CpG context: 144 Total methylated C's in CHG context: 442 Total methylated C's in CHH context: 176 Total C to T conversions in CpG context: 15363 Total C to T conversions in CHG context: 14896 Total C to T conversions in CHH context: 21981 C methylated in CpG context: 0.9% C methylated in CHG context: 2.9% C methylated in CHH context: 0.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 485 lines in total Total number of methylation call strings processed: 970 Final Cytosine Methylation Report ================================= Total number of C's analysed: 13549 Total methylated C's in CpG context: 42 Total methylated C's in CHG context: 117 Total methylated C's in CHH context: 51 Total C to T conversions in CpG context: 3848 Total C to T conversions in CHG context: 3831 Total C to T conversions in CHH context: 5660 C methylated in CpG context: 1.1% C methylated in CHG context: 3.0% C methylated in CHH context: 0.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 454 lines in total Total number of methylation call strings processed: 908 Final Cytosine Methylation Report ================================= Total number of C's analysed: 13318 Total methylated C's in CpG context: 35 Total methylated C's in CHG context: 121 Total methylated C's in CHH context: 37 Total C to T conversions in CpG context: 3839 Total C to T conversions in CHG context: 3702 Total C to T conversions in CHH context: 5584 C methylated in CpG context: 0.9% C methylated in CHG context: 3.2% C methylated in CHH context: 0.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 302 lines in total Total number of methylation call strings processed: 604 Final Cytosine Methylation Report ================================= Total number of C's analysed: 8566 Total methylated C's in CpG context: 34 Total methylated C's in CHG context: 88 Total methylated C's in CHH context: 25 Total C to T conversions in CpG context: 2453 Total C to T conversions in CHG context: 2319 Total C to T conversions in CHH context: 3647 C methylated in CpG context: 1.4% C methylated in CHG context: 3.7% C methylated in CHH context: 0.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 382 lines in total Total number of methylation call strings processed: 764 Final Cytosine Methylation Report ================================= Total number of C's analysed: 9552 Total methylated C's in CpG context: 33 Total methylated C's in CHG context: 113 Total methylated C's in CHH context: 23 Total C to T conversions in CpG context: 2762 Total C to T conversions in CHG context: 2680 Total C to T conversions in CHH context: 3941 C methylated in CpG context: 1.2% C methylated in CHG context: 4.0% C methylated in CHH context: 0.6% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz" Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 551 lines in total Total number of methylation call strings processed: 1102 Final Cytosine Methylation Report ================================= Total number of C's analysed: 14291 Total methylated C's in CpG context: 42 Total methylated C's in CHG context: 145 Total methylated C's in CHH context: 45 Total C to T conversions in CpG context: 3913 Total C to T conversions in CHG context: 3786 Total C to T conversions in CHH context: 6360 C methylated in CpG context: 1.1% C methylated in CHG context: 3.7% C methylated in CHH context: 0.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 695 lines in total Total number of methylation call strings processed: 1390 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19494 Total methylated C's in CpG context: 52 Total methylated C's in CHG context: 168 Total methylated C's in CHH context: 55 Total C to T conversions in CpG context: 5481 Total C to T conversions in CHG context: 5356 Total C to T conversions in CHH context: 8382 C methylated in CpG context: 0.9% C methylated in CHG context: 3.0% C methylated in CHH context: 0.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 438 lines in total Total number of methylation call strings processed: 876 Final Cytosine Methylation Report ================================= Total number of C's analysed: 12533 Total methylated C's in CpG context: 38 Total methylated C's in CHG context: 131 Total methylated C's in CHH context: 48 Total C to T conversions in CpG context: 3610 Total C to T conversions in CHG context: 3351 Total C to T conversions in CHH context: 5355 C methylated in CpG context: 1.0% C methylated in CHG context: 3.8% C methylated in CHH context: 0.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 554 lines in total Total number of methylation call strings processed: 1108 Final Cytosine Methylation Report ================================= Total number of C's analysed: 14731 Total methylated C's in CpG context: 52 Total methylated C's in CHG context: 173 Total methylated C's in CHH context: 63 Total C to T conversions in CpG context: 4112 Total C to T conversions in CHG context: 4085 Total C to T conversions in CHH context: 6246 C methylated in CpG context: 1.2% C methylated in CHG context: 4.1% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 429 lines in total Total number of methylation call strings processed: 858 Final Cytosine Methylation Report ================================= Total number of C's analysed: 11618 Total methylated C's in CpG context: 33 Total methylated C's in CHG context: 119 Total methylated C's in CHH context: 55 Total C to T conversions in CpG context: 3293 Total C to T conversions in CHG context: 3160 Total C to T conversions in CHH context: 4958 C methylated in CpG context: 1.0% C methylated in CHG context: 3.6% C methylated in CHH context: 1.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz" Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 609 lines in total Total number of methylation call strings processed: 1218 Final Cytosine Methylation Report ================================= Total number of C's analysed: 16860 Total methylated C's in CpG context: 63 Total methylated C's in CHG context: 182 Total methylated C's in CHH context: 108 Total C to T conversions in CpG context: 4751 Total C to T conversions in CHG context: 4561 Total C to T conversions in CHH context: 7195 C methylated in CpG context: 1.3% C methylated in CHG context: 3.8% C methylated in CHH context: 1.5% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 734 lines in total Total number of methylation call strings processed: 1468 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19966 Total methylated C's in CpG context: 72 Total methylated C's in CHG context: 222 Total methylated C's in CHH context: 91 Total C to T conversions in CpG context: 5701 Total C to T conversions in CHG context: 5462 Total C to T conversions in CHH context: 8418 C methylated in CpG context: 1.2% C methylated in CHG context: 3.9% C methylated in CHH context: 1.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 452 lines in total Total number of methylation call strings processed: 904 Final Cytosine Methylation Report ================================= Total number of C's analysed: 12096 Total methylated C's in CpG context: 42 Total methylated C's in CHG context: 122 Total methylated C's in CHH context: 55 Total C to T conversions in CpG context: 3449 Total C to T conversions in CHG context: 3269 Total C to T conversions in CHH context: 5159 C methylated in CpG context: 1.2% C methylated in CHG context: 3.6% C methylated in CHH context: 1.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 1540 lines in total Total number of methylation call strings processed: 3080 Final Cytosine Methylation Report ================================= Total number of C's analysed: 37041 Total methylated C's in CpG context: 119 Total methylated C's in CHG context: 404 Total methylated C's in CHH context: 194 Total C to T conversions in CpG context: 10386 Total C to T conversions in CHG context: 9934 Total C to T conversions in CHH context: 16004 C methylated in CpG context: 1.1% C methylated in CHG context: 3.9% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 533 lines in total Total number of methylation call strings processed: 1066 Final Cytosine Methylation Report ================================= Total number of C's analysed: 13454 Total methylated C's in CpG context: 56 Total methylated C's in CHG context: 130 Total methylated C's in CHH context: 61 Total C to T conversions in CpG context: 3815 Total C to T conversions in CHG context: 3620 Total C to T conversions in CHH context: 5772 C methylated in CpG context: 1.4% C methylated in CHG context: 3.5% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 577 lines in total Total number of methylation call strings processed: 1154 Final Cytosine Methylation Report ================================= Total number of C's analysed: 13600 Total methylated C's in CpG context: 46 Total methylated C's in CHG context: 163 Total methylated C's in CHH context: 77 Total C to T conversions in CpG context: 3867 Total C to T conversions in CHG context: 3658 Total C to T conversions in CHH context: 5789 C methylated in CpG context: 1.2% C methylated in CHG context: 4.3% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz" Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 778 lines in total Total number of methylation call strings processed: 1556 Final Cytosine Methylation Report ================================= Total number of C's analysed: 25908 Total methylated C's in CpG context: 141 Total methylated C's in CHG context: 274 Total methylated C's in CHH context: 229 Total C to T conversions in CpG context: 7575 Total C to T conversions in CHG context: 7400 Total C to T conversions in CHH context: 10289 C methylated in CpG context: 1.8% C methylated in CHG context: 3.6% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 545 lines in total Total number of methylation call strings processed: 1090 Final Cytosine Methylation Report ================================= Total number of C's analysed: 15205 Total methylated C's in CpG context: 50 Total methylated C's in CHG context: 157 Total methylated C's in CHH context: 81 Total C to T conversions in CpG context: 4307 Total C to T conversions in CHG context: 4240 Total C to T conversions in CHH context: 6370 C methylated in CpG context: 1.1% C methylated in CHG context: 3.6% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 306 lines in total Total number of methylation call strings processed: 612 Final Cytosine Methylation Report ================================= Total number of C's analysed: 7462 Total methylated C's in CpG context: 35 Total methylated C's in CHG context: 97 Total methylated C's in CHH context: 37 Total C to T conversions in CpG context: 2155 Total C to T conversions in CHG context: 1968 Total C to T conversions in CHH context: 3170 C methylated in CpG context: 1.6% C methylated in CHG context: 4.7% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 446 lines in total Total number of methylation call strings processed: 892 Final Cytosine Methylation Report ================================= Total number of C's analysed: 10292 Total methylated C's in CpG context: 33 Total methylated C's in CHG context: 134 Total methylated C's in CHH context: 51 Total C to T conversions in CpG context: 2966 Total C to T conversions in CHG context: 2731 Total C to T conversions in CHH context: 4377 C methylated in CpG context: 1.1% C methylated in CHG context: 4.7% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz" Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 701 lines in total Total number of methylation call strings processed: 1402 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19358 Total methylated C's in CpG context: 55 Total methylated C's in CHG context: 197 Total methylated C's in CHH context: 79 Total C to T conversions in CpG context: 5529 Total C to T conversions in CHG context: 5183 Total C to T conversions in CHH context: 8315 C methylated in CpG context: 1.0% C methylated in CHG context: 3.7% C methylated in CHH context: 0.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 1024 lines in total Total number of methylation call strings processed: 2048 Final Cytosine Methylation Report ================================= Total number of C's analysed: 28773 Total methylated C's in CpG context: 89 Total methylated C's in CHG context: 313 Total methylated C's in CHH context: 116 Total C to T conversions in CpG context: 8039 Total C to T conversions in CHG context: 7716 Total C to T conversions in CHH context: 12500 C methylated in CpG context: 1.1% C methylated in CHG context: 3.9% C methylated in CHH context: 0.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 404 lines in total Total number of methylation call strings processed: 808 Final Cytosine Methylation Report ================================= Total number of C's analysed: 11808 Total methylated C's in CpG context: 38 Total methylated C's in CHG context: 100 Total methylated C's in CHH context: 51 Total C to T conversions in CpG context: 3223 Total C to T conversions in CHG context: 3187 Total C to T conversions in CHH context: 5209 C methylated in CpG context: 1.2% C methylated in CHG context: 3.0% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 439 lines in total Total number of methylation call strings processed: 878 Final Cytosine Methylation Report ================================= Total number of C's analysed: 12269 Total methylated C's in CpG context: 36 Total methylated C's in CHG context: 114 Total methylated C's in CHH context: 50 Total C to T conversions in CpG context: 3461 Total C to T conversions in CHG context: 3259 Total C to T conversions in CHH context: 5349 C methylated in CpG context: 1.0% C methylated in CHG context: 3.4% C methylated in CHH context: 0.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 430 lines in total Total number of methylation call strings processed: 860 Final Cytosine Methylation Report ================================= Total number of C's analysed: 11172 Total methylated C's in CpG context: 37 Total methylated C's in CHG context: 114 Total methylated C's in CHH context: 57 Total C to T conversions in CpG context: 3105 Total C to T conversions in CHG context: 3016 Total C to T conversions in CHH context: 4843 C methylated in CpG context: 1.2% C methylated in CHG context: 3.6% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 464 lines in total Total number of methylation call strings processed: 928 Final Cytosine Methylation Report ================================= Total number of C's analysed: 11528 Total methylated C's in CpG context: 53 Total methylated C's in CHG context: 122 Total methylated C's in CHH context: 44 Total C to T conversions in CpG context: 3227 Total C to T conversions in CHG context: 2992 Total C to T conversions in CHH context: 5090 C methylated in CpG context: 1.6% C methylated in CHG context: 3.9% C methylated in CHH context: 0.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 369 lines in total Total number of methylation call strings processed: 738 Final Cytosine Methylation Report ================================= Total number of C's analysed: 9684 Total methylated C's in CpG context: 41 Total methylated C's in CHG context: 99 Total methylated C's in CHH context: 45 Total C to T conversions in CpG context: 2765 Total C to T conversions in CHG context: 2683 Total C to T conversions in CHH context: 4051 C methylated in CpG context: 1.5% C methylated in CHG context: 3.6% C methylated in CHH context: 1.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 530 lines in total Total number of methylation call strings processed: 1060 Final Cytosine Methylation Report ================================= Total number of C's analysed: 11593 Total methylated C's in CpG context: 47 Total methylated C's in CHG context: 132 Total methylated C's in CHH context: 56 Total C to T conversions in CpG context: 3255 Total C to T conversions in CHG context: 3131 Total C to T conversions in CHH context: 4972 C methylated in CpG context: 1.4% C methylated in CHG context: 4.0% C methylated in CHH context: 1.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 486 lines in total Total number of methylation call strings processed: 972 Final Cytosine Methylation Report ================================= Total number of C's analysed: 11192 Total methylated C's in CpG context: 48 Total methylated C's in CHG context: 130 Total methylated C's in CHH context: 47 Total C to T conversions in CpG context: 3142 Total C to T conversions in CHG context: 3089 Total C to T conversions in CHH context: 4736 C methylated in CpG context: 1.5% C methylated in CHG context: 4.0% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 539 lines in total Total number of methylation call strings processed: 1078 Final Cytosine Methylation Report ================================= Total number of C's analysed: 14288 Total methylated C's in CpG context: 46 Total methylated C's in CHG context: 162 Total methylated C's in CHH context: 73 Total C to T conversions in CpG context: 4116 Total C to T conversions in CHG context: 3776 Total C to T conversions in CHH context: 6115 C methylated in CpG context: 1.1% C methylated in CHG context: 4.1% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 419 lines in total Total number of methylation call strings processed: 838 Final Cytosine Methylation Report ================================= Total number of C's analysed: 9683 Total methylated C's in CpG context: 35 Total methylated C's in CHG context: 106 Total methylated C's in CHH context: 44 Total C to T conversions in CpG context: 2658 Total C to T conversions in CHG context: 2560 Total C to T conversions in CHH context: 4280 C methylated in CpG context: 1.3% C methylated in CHG context: 4.0% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 430 lines in total Total number of methylation call strings processed: 860 Final Cytosine Methylation Report ================================= Total number of C's analysed: 9743 Total methylated C's in CpG context: 31 Total methylated C's in CHG context: 129 Total methylated C's in CHH context: 52 Total C to T conversions in CpG context: 2716 Total C to T conversions in CHG context: 2646 Total C to T conversions in CHH context: 4169 C methylated in CpG context: 1.1% C methylated in CHG context: 4.6% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 467 lines in total Total number of methylation call strings processed: 934 Final Cytosine Methylation Report ================================= Total number of C's analysed: 10791 Total methylated C's in CpG context: 46 Total methylated C's in CHG context: 119 Total methylated C's in CHH context: 49 Total C to T conversions in CpG context: 3064 Total C to T conversions in CHG context: 2993 Total C to T conversions in CHH context: 4520 C methylated in CpG context: 1.5% C methylated in CHG context: 3.8% C methylated in CHH context: 1.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz" Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 473 lines in total Total number of methylation call strings processed: 946 Final Cytosine Methylation Report ================================= Total number of C's analysed: 10280 Total methylated C's in CpG context: 37 Total methylated C's in CHG context: 112 Total methylated C's in CHH context: 54 Total C to T conversions in CpG context: 2932 Total C to T conversions in CHG context: 2805 Total C to T conversions in CHH context: 4340 C methylated in CpG context: 1.2% C methylated in CHG context: 3.8% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 949 lines in total Total number of methylation call strings processed: 1898 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19603 Total methylated C's in CpG context: 90 Total methylated C's in CHG context: 260 Total methylated C's in CHH context: 107 Total C to T conversions in CpG context: 5645 Total C to T conversions in CHG context: 5406 Total C to T conversions in CHH context: 8095 C methylated in CpG context: 1.6% C methylated in CHG context: 4.6% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 590 lines in total Total number of methylation call strings processed: 1180 Final Cytosine Methylation Report ================================= Total number of C's analysed: 14628 Total methylated C's in CpG context: 55 Total methylated C's in CHG context: 175 Total methylated C's in CHH context: 46 Total C to T conversions in CpG context: 4196 Total C to T conversions in CHG context: 4002 Total C to T conversions in CHH context: 6154 C methylated in CpG context: 1.3% C methylated in CHG context: 4.2% C methylated in CHH context: 0.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 561 lines in total Total number of methylation call strings processed: 1122 Final Cytosine Methylation Report ================================= Total number of C's analysed: 14784 Total methylated C's in CpG context: 49 Total methylated C's in CHG context: 143 Total methylated C's in CHH context: 62 Total C to T conversions in CpG context: 4185 Total C to T conversions in CHG context: 3998 Total C to T conversions in CHH context: 6347 C methylated in CpG context: 1.2% C methylated in CHG context: 3.5% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 604 lines in total Total number of methylation call strings processed: 1208 Final Cytosine Methylation Report ================================= Total number of C's analysed: 13319 Total methylated C's in CpG context: 48 Total methylated C's in CHG context: 175 Total methylated C's in CHH context: 54 Total C to T conversions in CpG context: 3846 Total C to T conversions in CHG context: 3720 Total C to T conversions in CHH context: 5476 C methylated in CpG context: 1.2% C methylated in CHG context: 4.5% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 380 lines in total Total number of methylation call strings processed: 760 Final Cytosine Methylation Report ================================= Total number of C's analysed: 9032 Total methylated C's in CpG context: 31 Total methylated C's in CHG context: 84 Total methylated C's in CHH context: 49 Total C to T conversions in CpG context: 2523 Total C to T conversions in CHG context: 2458 Total C to T conversions in CHH context: 3887 C methylated in CpG context: 1.2% C methylated in CHG context: 3.3% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 431 lines in total Total number of methylation call strings processed: 862 Final Cytosine Methylation Report ================================= Total number of C's analysed: 9867 Total methylated C's in CpG context: 36 Total methylated C's in CHG context: 119 Total methylated C's in CHH context: 49 Total C to T conversions in CpG context: 2818 Total C to T conversions in CHG context: 2742 Total C to T conversions in CHH context: 4103 C methylated in CpG context: 1.3% C methylated in CHG context: 4.2% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 298 lines in total Total number of methylation call strings processed: 596 Final Cytosine Methylation Report ================================= Total number of C's analysed: 7486 Total methylated C's in CpG context: 16 Total methylated C's in CHG context: 85 Total methylated C's in CHH context: 41 Total C to T conversions in CpG context: 2160 Total C to T conversions in CHG context: 2046 Total C to T conversions in CHH context: 3138 C methylated in CpG context: 0.7% C methylated in CHG context: 4.0% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz" Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 368 lines in total Total number of methylation call strings processed: 736 Final Cytosine Methylation Report ================================= Total number of C's analysed: 8619 Total methylated C's in CpG context: 34 Total methylated C's in CHG context: 118 Total methylated C's in CHH context: 36 Total C to T conversions in CpG context: 2515 Total C to T conversions in CHG context: 2277 Total C to T conversions in CHH context: 3639 C methylated in CpG context: 1.3% C methylated in CHG context: 4.9% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 628 lines in total Total number of methylation call strings processed: 1256 Final Cytosine Methylation Report ================================= Total number of C's analysed: 14593 Total methylated C's in CpG context: 36 Total methylated C's in CHG context: 199 Total methylated C's in CHH context: 61 Total C to T conversions in CpG context: 4152 Total C to T conversions in CHG context: 3985 Total C to T conversions in CHH context: 6160 C methylated in CpG context: 0.9% C methylated in CHG context: 4.8% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz" Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 639 lines in total Total number of methylation call strings processed: 1278 Final Cytosine Methylation Report ================================= Total number of C's analysed: 16104 Total methylated C's in CpG context: 50 Total methylated C's in CHG context: 179 Total methylated C's in CHH context: 49 Total C to T conversions in CpG context: 4617 Total C to T conversions in CHG context: 4304 Total C to T conversions in CHH context: 6905 C methylated in CpG context: 1.1% C methylated in CHG context: 4.0% C methylated in CHH context: 0.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 539 lines in total Total number of methylation call strings processed: 1078 Final Cytosine Methylation Report ================================= Total number of C's analysed: 12164 Total methylated C's in CpG context: 37 Total methylated C's in CHG context: 136 Total methylated C's in CHH context: 60 Total C to T conversions in CpG context: 3620 Total C to T conversions in CHG context: 3380 Total C to T conversions in CHH context: 4931 C methylated in CpG context: 1.0% C methylated in CHG context: 3.9% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 471 lines in total Total number of methylation call strings processed: 942 Final Cytosine Methylation Report ================================= Total number of C's analysed: 10284 Total methylated C's in CpG context: 29 Total methylated C's in CHG context: 127 Total methylated C's in CHH context: 48 Total C to T conversions in CpG context: 3058 Total C to T conversions in CHG context: 2873 Total C to T conversions in CHH context: 4149 C methylated in CpG context: 0.9% C methylated in CHG context: 4.2% C methylated in CHH context: 1.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 727 lines in total Total number of methylation call strings processed: 1454 Final Cytosine Methylation Report ================================= Total number of C's analysed: 16624 Total methylated C's in CpG context: 52 Total methylated C's in CHG context: 205 Total methylated C's in CHH context: 58 Total C to T conversions in CpG context: 4807 Total C to T conversions in CHG context: 4570 Total C to T conversions in CHH context: 6932 C methylated in CpG context: 1.1% C methylated in CHG context: 4.3% C methylated in CHH context: 0.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 548 lines in total Total number of methylation call strings processed: 1096 Final Cytosine Methylation Report ================================= Total number of C's analysed: 11969 Total methylated C's in CpG context: 30 Total methylated C's in CHG context: 140 Total methylated C's in CHH context: 51 Total C to T conversions in CpG context: 3484 Total C to T conversions in CHG context: 3241 Total C to T conversions in CHH context: 5023 C methylated in CpG context: 0.9% C methylated in CHG context: 4.1% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104b/CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104b/CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found 52 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> EPI-103_S27_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-103_S27_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-103_S27_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-104_S28_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-104_S28_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-104_S28_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-111_S29_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-111_S29_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-111_S29_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-113_S30_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-113_S30_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-113_S30_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-119_S31_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-119_S31_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-119_S31_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-120_S32_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-120_S32_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-120_S32_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-127_S33_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-127_S33_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-127_S33_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-128_S34_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-128_S34_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-128_S34_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-135_S35_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-135_S35_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-135_S35_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-136_S36_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-136_S36_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-136_S36_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-143_S37_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-143_S37_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-143_S37_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-145_S38_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-145_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-145_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-151_S2_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-151_S2_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-151_S2_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-152_S3_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-152_S3_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-152_S3_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-153_S4_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-153_S4_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-153_S4_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-154_S5_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-154_S5_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-154_S5_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-159_S6_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-159_S6_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-159_S6_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-160_S7_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-160_S7_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-160_S7_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-161_S8_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-161_S8_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-161_S8_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-162_S9_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-162_S9_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-162_S9_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-168_S11_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-168_S11_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-168_S11_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-169_S12_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-169_S12_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-169_S12_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-170_S13_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-170_S13_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-170_S13_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-175_S14_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-175_S14_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-175_S14_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-176_S15_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-176_S15_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-176_S15_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-181_S16_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-181_S16_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-181_S16_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-182_S17_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-182_S17_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-182_S17_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-184_S18_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-184_S18_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-184_S18_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-185_S19_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-185_S19_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-185_S19_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-187_S20_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-187_S20_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-187_S20_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-188_S21_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-188_S21_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-188_S21_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-193_S22_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-193_S22_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-193_S22_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-194_S23_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-194_S23_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-194_S23_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-199_S24_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-199_S24_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-199_S24_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-200_S25_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-200_S25_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-200_S25_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-208_S28_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-208_S28_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-208_S28_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-209_S29_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-209_S29_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-209_S29_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-229_S36_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-229_S36_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-229_S36_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-230_S37_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-230_S37_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-230_S37_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-41_S38_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-41_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-41_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-42_S39_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-42_S39_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-42_S39_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-43_S40_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-43_S40_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-43_S40_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-44_S41_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-44_S41_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-44_S41_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== No Bismark/Bowtie2 single-end BAM files detected Found Bismark/Bowtie2 paired-end files No Bismark/HISAT2 single-end BAM files detected No Bismark/HISAT2 paired-end BAM files detected Generating Bismark summary report from 52 Bismark BAM file(s)... >> Reading from Bismark report: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_PE_report.txt Wrote Bismark project summary to >> bismark_summary_report.html << [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks...