Processing paired-end Bismark output file(s) (SAM format): zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam zr2096_9_s1_R1_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 >>zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam: 9282636 Total number duplicated alignments removed: 323003 (3.48%) Duplicated alignments were found at: 273923 different position(s) Total count of deduplicated leftover sequences: 8959633 (96.52% of total) Checking file >>zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_10_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_10_s1_R2_val_2.fq.gz" Now testing Bismark result file zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam: 8273828 Total number duplicated alignments removed: 995382 (12.03%) Duplicated alignments were found at: 326089 different position(s) Total count of deduplicated leftover sequences: 7278446 (87.97% of total) Checking file >>zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_1_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_1_s1_R2_val_2.fq.gz" Now testing Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam: 15247790 Total number duplicated alignments removed: 1127798 (7.40%) Duplicated alignments were found at: 674697 different position(s) Total count of deduplicated leftover sequences: 14119992 (92.60% of total) Checking file >>zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_2_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_2_s1_R2_val_2.fq.gz" Now testing Bismark result file zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam: 15542347 Total number duplicated alignments removed: 734845 (4.73%) Duplicated alignments were found at: 572664 different position(s) Total count of deduplicated leftover sequences: 14807502 (95.27% of total) Checking file >>zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_3_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_3_s1_R2_val_2.fq.gz" Now testing Bismark result file zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam: 12995899 Total number duplicated alignments removed: 332717 (2.56%) Duplicated alignments were found at: 284466 different position(s) Total count of deduplicated leftover sequences: 12663182 (97.44% of total) Checking file >>zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_4_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_4_s1_R2_val_2.fq.gz" Now testing Bismark result file zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam: 16377055 Total number duplicated alignments removed: 841786 (5.14%) Duplicated alignments were found at: 694983 different position(s) Total count of deduplicated leftover sequences: 15535269 (94.86% of total) Checking file >>zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_5_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_5_s1_R2_val_2.fq.gz" Now testing Bismark result file zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam: 13016029 Total number duplicated alignments removed: 367348 (2.82%) Duplicated alignments were found at: 309619 different position(s) Total count of deduplicated leftover sequences: 12648681 (97.18% of total) Checking file >>zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_6_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_6_s1_R2_val_2.fq.gz" Now testing Bismark result file zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam: 15123226 Total number duplicated alignments removed: 505812 (3.34%) Duplicated alignments were found at: 440344 different position(s) Total count of deduplicated leftover sequences: 14617414 (96.66% of total) Checking file >>zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_7_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_7_s1_R2_val_2.fq.gz" Now testing Bismark result file zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam: 14200405 Total number duplicated alignments removed: 747564 (5.26%) Duplicated alignments were found at: 527675 different position(s) Total count of deduplicated leftover sequences: 13452841 (94.74% of total) Checking file >>zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_8_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_8_s1_R2_val_2.fq.gz" Now testing Bismark result file zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam: 16108083 Total number duplicated alignments removed: 2024669 (12.57%) Duplicated alignments were found at: 1660011 different position(s) Total count of deduplicated leftover sequences: 14083414 (87.43% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_9_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_9_s1_R2_val_2.fq.gz" [bam_sort_core] merging from 8 files and 1 in-memory blocks... [bam_sort_core] merging from 6 files and 1 in-memory blocks... [bam_sort_core] merging from 12 files and 1 in-memory blocks... [bam_sort_core] merging from 13 files and 1 in-memory blocks... [bam_sort_core] merging from 11 files and 1 in-memory blocks... [bam_sort_core] merging from 14 files and 1 in-memory blocks... [bam_sort_core] merging from 11 files and 1 in-memory blocks... [bam_sort_core] merging from 13 files and 1 in-memory blocks... [bam_sort_core] merging from 12 files and 1 in-memory blocks... [bam_sort_core] merging from 12 files and 1 in-memory blocks... *** Bismark methylation extractor version v0.19.0 *** No SAMtools installation found. Please add SAMtools to the PATH or specify its location with --samtools_path [path] Found 10 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete No splitting report file specified, skipping this step No M-bias report file specified, skipping this step 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/Bowtie single-end BAM files detected No Bismark/Bowtie paired-end BAM files detected Generating Bismark summary report from 10 Bismark BAM file(s)... >> Reading from Bismark report: zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.txt No methylation extractor report present, skipping... >> Reading from Bismark report: zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.txt No methylation extractor report present, skipping... >> Reading from Bismark report: zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.txt No methylation extractor report present, skipping... >> Reading from Bismark report: zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.txt No methylation extractor report present, skipping... >> Reading from Bismark report: zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.txt No methylation extractor report present, skipping... >> Reading from Bismark report: zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.txt No methylation extractor report present, skipping... >> Reading from Bismark report: zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.txt No methylation extractor report present, skipping... >> Reading from Bismark report: zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.txt No methylation extractor report present, skipping... >> Reading from Bismark report: zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.txt No methylation extractor report present, skipping... >> Reading from Bismark report: zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.txt No methylation extractor report present, skipping... Wrote Bismark project summary to >> bismark_summary_report.html <<