[Fri Oct 9 08:11:02 PDT 2026] Pum1 (Pum/Pumalin) Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools' Reference genome folder provided is data/13-wgbs-genome/ (absolute path is '/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 2 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil'): output/13-wgbs/trimmed/Pum1_R1.fq.gz output/13-wgbs/trimmed/Pum1_R2.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!) Output will be written into the directory: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/ Using temp directory: /tmp/13-wgbs-Pum1-3530457 Temporary files will be written into the directory: /tmp/13-wgbs-Pum1-3530457/ Summary of all aligner options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Running Bismark Parallel version. Number of parallel instances to be spawned: 8 Current working directory is: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil Now reading in and storing sequence information of the genome specified in: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ chr Chromosome_10A (41401248 bp) chr Chromosome_2A (98156180 bp) chr Chromosome_4A (93973257 bp) chr Chromosome_6A (76092957 bp) chr Chromosome_1B (231619483 bp) chr Chromosome_5B (125625032 bp) chr Chromosome_6B (129267145 bp) chr Chromosome_7B (183991082 bp) chr Chromosome_8B (108828118 bp) chr Chromosome_9B (91966420 bp) Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum1_R1.fq.gz and output/13-wgbs/trimmed/Pum1_R2.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum1_R1.fq.gz and output/13-wgbs/trimmed/Pum1_R2.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum1_R1.fq.gz and output/13-wgbs/trimmed/Pum1_R2.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum1_R1.fq.gz and output/13-wgbs/trimmed/Pum1_R2.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum1_R1.fq.gz and output/13-wgbs/trimmed/Pum1_R2.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum1_R1.fq.gz and output/13-wgbs/trimmed/Pum1_R2.fq.gz Paired-end alignments will be performed ======================================= Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum1_R1.fq.gz and output/13-wgbs/trimmed/Pum1_R2.fq.gz The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum1_R1.fq.gz and output/13-wgbs/trimmed/Pum1_R2.fq.gz Finished subdividing output/13-wgbs/trimmed/Pum1_R1.fq.gz for PID: 3531003 and offset 8 (sequences written out: 4797033) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.8< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum1_R1.fq.gz<) Finished subdividing output/13-wgbs/trimmed/Pum1_R1.fq.gz for PID: 0 and offset 5 (sequences written out: 4797033) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.5< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum1_R1.fq.gz<) Finished subdividing output/13-wgbs/trimmed/Pum1_R1.fq.gz for PID: 0 and offset 6 (sequences written out: 4797033) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.6< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum1_R1.fq.gz<) Finished subdividing output/13-wgbs/trimmed/Pum1_R1.fq.gz for PID: 0 and offset 7 (sequences written out: 4797033) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.7< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum1_R1.fq.gz<) Finished subdividing output/13-wgbs/trimmed/Pum1_R1.fq.gz for PID: 0 and offset 4 (sequences written out: 4797033) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.4< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum1_R1.fq.gz<) Finished subdividing output/13-wgbs/trimmed/Pum1_R1.fq.gz for PID: 0 and offset 2 (sequences written out: 4797033) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.2< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum1_R1.fq.gz<) Finished subdividing output/13-wgbs/trimmed/Pum1_R1.fq.gz for PID: 0 and offset 1 (sequences written out: 4797034) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.1< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum1_R1.fq.gz<) Finished subdividing output/13-wgbs/trimmed/Pum1_R1.fq.gz for PID: 0 and offset 3 (sequences written out: 4797033) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.3< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum1_R1.fq.gz<) Finished subdividing output/13-wgbs/trimmed/Pum1_R2.fq.gz for PID: 3531003 and offset 8 (sequences written out: 4797033) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.8< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum1_R2.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file Pum1_R1.fq.gz.temp.8 to /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.8_C_to_T.fastq Finished subdividing output/13-wgbs/trimmed/Pum1_R2.fq.gz for PID: 0 and offset 6 (sequences written out: 4797033) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.6< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum1_R2.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file Pum1_R1.fq.gz.temp.6 to /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.6_C_to_T.fastq Finished subdividing output/13-wgbs/trimmed/Pum1_R2.fq.gz for PID: 0 and offset 4 (sequences written out: 4797033) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.4< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum1_R2.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file Pum1_R1.fq.gz.temp.4 to /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.4_C_to_T.fastq Finished subdividing output/13-wgbs/trimmed/Pum1_R2.fq.gz for PID: 0 and offset 7 (sequences written out: 4797033) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.7< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum1_R2.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file Pum1_R1.fq.gz.temp.7 to /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.7_C_to_T.fastq Finished subdividing output/13-wgbs/trimmed/Pum1_R2.fq.gz for PID: 0 and offset 2 (sequences written out: 4797033) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.2< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum1_R2.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file Pum1_R1.fq.gz.temp.2 to /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.2_C_to_T.fastq Finished subdividing output/13-wgbs/trimmed/Pum1_R2.fq.gz for PID: 0 and offset 5 (sequences written out: 4797033) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.5< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum1_R2.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file Pum1_R1.fq.gz.temp.5 to /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.5_C_to_T.fastq Finished subdividing output/13-wgbs/trimmed/Pum1_R2.fq.gz for PID: 0 and offset 3 (sequences written out: 4797033) Finished subdividing output/13-wgbs/trimmed/Pum1_R2.fq.gz for PID: 0 and offset 1 (sequences written out: 4797034) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.3< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum1_R2.fq.gz<) Using the subset file >/tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.1< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum1_R2.fq.gz<) Input files are in FastQ format Input files are in FastQ format Writing a C -> T converted version of the input file Pum1_R1.fq.gz.temp.1 to /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.1_C_to_T.fastq Writing a C -> T converted version of the input file Pum1_R1.fq.gz.temp.3 to /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.3_C_to_T.fastq Created C -> T converted version of the FastQ file Pum1_R1.fq.gz.temp.8 (4797033 sequences in total) Writing a G -> A converted version of the input file Pum1_R2.fq.gz.temp.8 to /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.8_G_to_A.fastq Created C -> T converted version of the FastQ file Pum1_R1.fq.gz.temp.6 (4797033 sequences in total) Writing a G -> A converted version of the input file Pum1_R2.fq.gz.temp.6 to /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.6_G_to_A.fastq Created C -> T converted version of the FastQ file Pum1_R1.fq.gz.temp.4 (4797033 sequences in total) Writing a G -> A converted version of the input file Pum1_R2.fq.gz.temp.4 to /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.4_G_to_A.fastq Created C -> T converted version of the FastQ file Pum1_R1.fq.gz.temp.7 (4797033 sequences in total) Writing a G -> A converted version of the input file Pum1_R2.fq.gz.temp.7 to /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.7_G_to_A.fastq Created C -> T converted version of the FastQ file Pum1_R1.fq.gz.temp.5 (4797033 sequences in total) Writing a G -> A converted version of the input file Pum1_R2.fq.gz.temp.5 to /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.5_G_to_A.fastq Created C -> T converted version of the FastQ file Pum1_R1.fq.gz.temp.2 (4797033 sequences in total) Writing a G -> A converted version of the input file Pum1_R2.fq.gz.temp.2 to /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.2_G_to_A.fastq Created C -> T converted version of the FastQ file Pum1_R1.fq.gz.temp.1 (4797034 sequences in total) Writing a G -> A converted version of the input file Pum1_R2.fq.gz.temp.1 to /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.1_G_to_A.fastq Created C -> T converted version of the FastQ file Pum1_R1.fq.gz.temp.3 (4797033 sequences in total) Writing a G -> A converted version of the input file Pum1_R2.fq.gz.temp.3 to /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.3_G_to_A.fastq Created G -> A converted version of the FastQ file Pum1_R2.fq.gz.temp.8 (4797033 sequences in total) Input files are Pum1_R1.fq.gz.temp.8_C_to_T.fastq and Pum1_R2.fq.gz.temp.8_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.8_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.8_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created G -> A converted version of the FastQ file Pum1_R2.fq.gz.temp.6 (4797033 sequences in total) Input files are Pum1_R1.fq.gz.temp.6_C_to_T.fastq and Pum1_R2.fq.gz.temp.6_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.6_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.6_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created G -> A converted version of the FastQ file Pum1_R2.fq.gz.temp.4 (4797033 sequences in total) Input files are Pum1_R1.fq.gz.temp.4_C_to_T.fastq and Pum1_R2.fq.gz.temp.4_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.4_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.4_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created G -> A converted version of the FastQ file Pum1_R2.fq.gz.temp.5 (4797033 sequences in total) Input files are Pum1_R1.fq.gz.temp.5_C_to_T.fastq and Pum1_R2.fq.gz.temp.5_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.5_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.5_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created G -> A converted version of the FastQ file Pum1_R2.fq.gz.temp.7 (4797033 sequences in total) Input files are Pum1_R1.fq.gz.temp.7_C_to_T.fastq and Pum1_R2.fq.gz.temp.7_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.7_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.7_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created G -> A converted version of the FastQ file Pum1_R2.fq.gz.temp.2 (4797033 sequences in total) Input files are Pum1_R1.fq.gz.temp.2_C_to_T.fastq and Pum1_R2.fq.gz.temp.2_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.2_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.2_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created G -> A converted version of the FastQ file Pum1_R2.fq.gz.temp.1 (4797034 sequences in total) Input files are Pum1_R1.fq.gz.temp.1_C_to_T.fastq and Pum1_R2.fq.gz.temp.1_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.1_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.1_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created G -> A converted version of the FastQ file Pum1_R2.fq.gz.temp.3 (4797033 sequences in total) Input files are Pum1_R1.fq.gz.temp.3_C_to_T.fastq and Pum1_R2.fq.gz.temp.3_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.3_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.3_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00129:489:23JFWNLT4:8:1101:39516:1042_1:N:0:TGAGTACT+GACAATAA/1 99 Chromosome_1B_CT_converted 165086635 42 141M = 165086690 196 TATGTTTATTTATTTTGTAATGTTATTGAATTTAAAAAAAAATATTTATGAATAAATAAAAATTTTTGTATGGTATGAAAATAAATTTTAAATAGTATAAGTTTTGATGTGATAAAGTAGGGTTTATAGGGTTTGTAGATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:0 YT:Z:CP LH00129:489:23JFWNLT4:8:1101:39516:1042_2:N:0:TGAGTACT+GACAATAA/2 147 Chromosome_1B_CT_converted 165086690 42 141M = 165086635 -196 ATAAAAATTTTTGTATGGTATGAAAATAAATTTTAAATAGTATAAGTTTTGATGTGATAAAGTAGGGTTTATAGGGTTTGTAGATTTTATTTTTTATGTTAAAAAGTAGGTATTTTTTTTAATTTTTGTTTTAAAATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.3_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.3_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00129:489:23JFWNLT4:8:1101:13863:1056_1:N:0:TGAGTACT+GACAATAA/1 77 * 0 0 * * 0 0 TTGTTAAAATATTTTGTTTGAAGTATTATTTTATTATTGAAAAAGTGATATAAGTTTTTAAATTATAATTTATGTGAGGTGATTAAAGGAGTTATTAAATAAAATTTTAGTGTAATGAGTTATTTTAATATTTGTATGGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00129:489:23JFWNLT4:8:1101:13863:1056_2:N:0:TGAGTACT+GACAATAA/2 141 * 0 0 * * 0 0 AAAACTTCTTACACAACATATTAATTAATAAATTAAATATTTTTTCACAAAATTTATCTAAATTTTCTTCAAAATTAAAAACACCATACAAATATTAAAATAACTCATTACACTAAAATTTTATTTAATAACTCCTTTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.7_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.7_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00129:489:23JFWNLT4:8:1101:29938:1042_1:N:0:TGAGTACT+GNCAATAA/1 99 Chromosome_8B_CT_converted 1661251 6 141M = 1661285 175 TTTATTTGAGTTATTTTGGTTTATATTAGAAGAATTTATATATATTTGTATGTAAAATTATAGTTTTTATTATGGTTTTAATTTATTTTTGGAGGATATGGTTTTTGTAAATTTGAATTTATATTATGTTAGAAAGTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:-12 YT:Z:CP LH00129:489:23JFWNLT4:8:1101:29938:1042_2:N:0:TGAGTACT+GNCAATAA/2 147 Chromosome_8B_CT_converted 1661285 6 141M = 1661251 -175 TTTATATATATTTGTATGTAAAATTATAGTTTTTATTATGGTTTTAATTTATTTTTGGAGGATATGGTTTTTGTAAATTTGAATTTATATTATGTTAGAAAGTTTTTAAGTAAATGTGAATTTTTTTGGTTTAATGGTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:108T8T23 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.2_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.2_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00129:489:23JFWNLT4:8:1101:13993:1056_1:N:0:TGAGTACT+GACAATAA/1 99 Chromosome_6B_CT_converted 37777289 7 72M1D69M = 37777332 185 AATTGTAAAAGAATTAAATAATAGGATTTGTTTATGAAATTGATAGGGTAATAGATTATTTTTTATTAAATAGGATAGAATTTAGGTGATTTAAATAAGTGTTAAAAATGAAGATGATTTTAGGGAAGAAAATATATTAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XS:i:-22 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:72^T69 YS:i:-14 YT:Z:CP LH00129:489:23JFWNLT4:8:1101:13993:1056_2:N:0:TGAGTACT+GACAATAA/2 147 Chromosome_6B_CT_converted 37777332 7 29M1D112M = 37777289 -185 TAGGGTAATAGATTATTTTTTATTAAATAGGATAGAATTTAGGTGATTTAAATAAGTGTTAAAAATGAAGATGATTTTAGGGAAGAAAATATATTAGATTATTTAATTGATTTTTATATTAGATTTATAGAGAATTTAGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XS:i:-28 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:29^T110A1 YS:i:-8 YT:Z:CP Found first alignment: LH00129:489:23JFWNLT4:8:1101:46781:1042_1:N:0:TGAGTACT+GACAATAA/1 99 Chromosome_6B_CT_converted 9009 2 141M = 9084 216 TATTAATTTTTTGATTTTATAAATTAGATAGTTATAAATATTTTAGTATTATTTAATTAAAAAGAAGTGTATGTATATGTGTGTGTAAATTGGTAATTTTGATAATGTAAATTAGTTAAGGGTTTTAATATTTATTTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-30 XS:i:-34 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:12T0T10A49G64T1 YS:i:-30 YT:Z:CP LH00129:489:23JFWNLT4:8:1101:46781:1042_2:N:0:TGAGTACT+GACAATAA/2 147 Chromosome_6B_CT_converted 9084 2 141M = 9009 -216 TATGTGTGTGTAAATTGGTAATTTTGATAATGTAAATTAGTTAAGGGTTTTAATATTTATTTATGATATGAATATTAAGTTATTTTAATGAATAATAAAAAAGTTAGGTTGATTTTAAAGTTTGTGAATAAATGTTGTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-30 XS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:64T42A14A7T2T7 YS:i:-30 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.8_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.8_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.4_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.4_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00129:489:23JFWNLT4:8:1101:12326:1056_1:N:0:TGAGTACT+GACAATAA/1 99 Chromosome_2A_CT_converted 92910652 42 141M = 92910759 248 AATTTAATAAATAAAGATAAAAGTTTGAGATATTTGTTAATAAGTGTTAATGATGATTATTTTTTAATGGTTTGGTTGTGATTATTTTTGGTATAAGGAATGGTATTGATTTTTTTTAAAAAAAAAGAAATTGTTTTGTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:26A114 YS:i:0 YT:Z:CP LH00129:489:23JFWNLT4:8:1101:12326:1056_2:N:0:TGAGTACT+GACAATAA/2 147 Chromosome_2A_CT_converted 92910759 42 141M = 92910652 -248 GATTTTTTTTAAAAAAAAAGAAATTGTTTTGTTATTTAAAAAGAAAAAGTAAGATTATAAGTTTAATTAAAATAAGTTGATATAGTGGTGATAAATTTGATAATAAATTTTTTAGTAAGTTATATTTTGAATTTAATAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.6_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.6_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00129:489:23JFWNLT4:8:1101:10142:1056_1:N:0:TGAGTACT+GACAATAA/1 77 * 0 0 * * 0 0 ATTGGGAAATTTTTTTATTGGTGTAAGTGGGATTTGAATTTGTGTTGATAGAGTTGAGAGGTTGTGTGATTTTGAGTGTAATGTTTTAATTATTTGGTTATGGAGGTTTTATATGAGAAGATATTAGTAGTATTGTTATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00129:489:23JFWNLT4:8:1101:10142:1056_2:N:0:TGAGTACT+GACAATAA/2 141 * 0 0 * * 0 0 AAAAACATCAAATTTTTTTTAACTCTCTAACCCTCATTATAACCCCATCCCTACCAAACAAAATCATAACTTAACCAATTTTAAATCCATACAATATAAAAATACATTTATAACAATACTACAAATATCTTCTCATATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.5_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.5_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00129:489:23JFWNLT4:8:1101:24954:1042_1:N:0:TGAGTACT+GNCAATAA/1 77 * 0 0 * * 0 0 TTTATTTAGAGAAAAATTTAATTTTTAAATTTAAAATATGTATAGTTTATTTAGTGAATAAAAATTGTATTAGAGTTTTGTGGGGATTAAAATATTAAATAATGTGTGAAGTGTTTAAAGTTAAAATTTTGTTTTAGTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00129:489:23JFWNLT4:8:1101:24954:1042_2:N:0:TGAGTACT+GNCAATAA/2 141 * 0 0 * * 0 0 TTATCAACAAAAAATCAAATTATAACTACTTTAATAAAACTAAAACAAAATTTTAACTTTAAACACTTCACACATTATTTAATATTTTAATCCCCACAAAACTCTAATACAATTTTTATTCACTAAATAAACTATACATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.1_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.1_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00129:489:23JFWNLT4:8:1101:46781:1042_1:N:0:TGAGTACT+GACAATAA/1 83 Chromosome_8B_GA_converted 94145035 32 141M = 94144960 -216 TCATAAATAAATATTAAAACCCTTAACTAATTTACATTATCAAAATTACCAATTTACACACACATATACATACACTTCTTTTTAATTAAATAATACTAAAATATTTATAACTATCTAATTTATAAAATCAAAAAATTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-36 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:0 YT:Z:CP LH00129:489:23JFWNLT4:8:1101:46781:1042_2:N:0:TGAGTACT+GACAATAA/2 163 Chromosome_8B_GA_converted 94144960 32 141M = 94145035 216 ATTACAACATTTATTCACAAACTTTAAAATCAACCTAACTTTTTTATTATTCATTAAAATAACTTAATATTCATATCATAAATAAATATTAAAACCCTTAACTAATTTACATTATCAAAATTACCAATTTACACACACATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-30 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to Pum1_R1.fq.gz.temp.4_bismark_bt2_pe.bam <<< Found first alignment: LH00129:489:23JFWNLT4:8:1101:29938:1042_1:N:0:TGAGTACT+GNCAATAA/1 83 Chromosome_1B_GA_converted 110242932 6 104M2D37M = 110242898 -177 AAAAACTTTCTAACATAATATAAATTCAAATTTACAAAAACCATATCCTCCAAAAATAAATTAAAACCATAATAAAAACTATAATTTTACATACAAATATATATAAATTCTTCTAATATAAACCAAAATAACTCAAATAAA IIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-29 XS:i:-26 XN:i:0 XM:i:3 XO:i:1 XG:i:2 NM:i:5 MD:Z:45A35C22^AA3A33 YS:i:-18 YT:Z:CP LH00129:489:23JFWNLT4:8:1101:29938:1042_2:N:0:TGAGTACT+GNCAATAA/2 163 Chromosome_1B_GA_converted 110242898 6 141M = 110242932 177 AAAACCATTAAACCAAAAAAATTCACATTTACTTAAAAACTTTCTAACATAATATAAATTCAAATTTACAAAAACCATATCCTCCAAAAATAAATTAAAACCATAATAAAAACTATAATTTTACATACAAATATATATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-20 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:32A46A35C25 YS:i:-29 YT:Z:CP Found first alignment: LH00129:489:23JFWNLT4:8:1101:39516:1042_1:N:0:TGAGTACT+GACAATAA/1 83 Chromosome_1B_GA_converted 90944069 42 141M = 90944014 -196 AATCTACAAACCCTATAAACCCTACTTTATCACATCAAAACTTATACTATTTAAAATTTATTTTCATACCATACAAAAATTTTTATTTATTCATAAATATTTTTTTTTAAATTCAATAACATTACAAAATAAATAAACATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21T119 YS:i:-6 YT:Z:CP LH00129:489:23JFWNLT4:8:1101:39516:1042_2:N:0:TGAGTACT+GACAATAA/2 163 Chromosome_1B_GA_converted 90944014 42 141M = 90944069 196 AAAAATTTTAAAACAAAAATTAAAAAAAATACCTACTTTTTAACATAAAAAATAAAATCTACAAACCCTATAAACCCTACTTTATCACATCAAAACTTATACTATTTAAAATTTATTTTCATACCATACAAAAATTTTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:76T64 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to Pum1_R1.fq.gz.temp.2_bismark_bt2_pe.bam <<< Found first alignment: LH00129:489:23JFWNLT4:8:1101:13993:1056_1:N:0:TGAGTACT+GACAATAA/1 83 Chromosome_7B_GA_converted 153244284 1 141M = 153244241 -184 TCTAATATATTTTCTTCCCTAAAATCATCTTCATTTTTAACACTTATTTAAATCACCTAAATTCTATCCTATTTAATAAAAAATAATCTATTACCCTATCAATTTCATAAACAAATCCTATTATTTAATTCTTTTACAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:-6 YT:Z:CP LH00129:489:23JFWNLT4:8:1101:13993:1056_2:N:0:TGAGTACT+GACAATAA/2 163 Chromosome_7B_GA_converted 153244241 1 141M = 153244284 184 AACTAAATTCTCTATAAATCTAATATAAAAATCAATTAAATAATCTAATATATTTTCTTCCCTAAAATCATCTTCATTTTTAACACTTATTTAAATCACCTAAATTCTATCCTATTTAATAAAAAATAATCTATTACCCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:1T139 YS:i:0 YT:Z:CP Found first alignment: LH00129:489:23JFWNLT4:8:1101:13863:1056_1:N:0:TGAGTACT+GACAATAA/1 83 Chromosome_4A_GA_converted 6500079 42 141M = 6499998 -222 CACCATACAAATATTAAAATAACTCATTACACTAAAATTTTATTTAATAACTCCTTTAATCACCTCACATAAATTATAATTTAAAAACTTATATCACTTTTTCAATAATAAAATAATACTTCAAACAAAATATTTTAACAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:0 YT:Z:CP LH00129:489:23JFWNLT4:8:1101:13863:1056_2:N:0:TGAGTACT+GACAATAA/2 163 Chromosome_4A_GA_converted 6499998 42 141M = 6500079 222 AAAACTTCTTACACAACATATTAATTAATAAATTAAATATTTTTTCACAAAATTTATCTAAATTTTCTTCAAAATTAAAAACACCATACAAATATTAAAATAACTCATTACACTAAAATTTTATTTAATAACTCCTTTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:0 YT:Z:CP Found first alignment: LH00129:489:23JFWNLT4:8:1101:24954:1042_1:N:0:TGAGTACT+GNCAATAA/1 83 Chromosome_7B_GA_converted 38773985 0 126M2D15M = 38773950 -178 AAAACTAAAACAAAATTTTAACTTTAAACACTTCACACATTATTTAATATTTTAATCCCCACAAAACTCTAATACAATTTTTATTCACTAAATAAACTATACATATTTTAAATTTAAAAATTAAATTTTTCTCTAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-71 XS:i:-71 XN:i:0 XM:i:10 XO:i:1 XG:i:2 NM:i:12 MD:Z:25C5A1T16A5T1T24C20T17T3^TA4A10 YS:i:-60 YT:Z:CP LH00129:489:23JFWNLT4:8:1101:24954:1042_2:N:0:TGAGTACT+GNCAATAA/2 163 Chromosome_7B_GA_converted 38773950 0 141M = 38773985 178 TTATCAACAAAAAATCAAATTATAACTACTTTAATAAAACTAAAACAAAATTTTAACTTTAAACACTTCACACATTATTTAATATTTTAATCCCCACAAAACTCTAATACAATTTTTATTCACTAAATAAACTATACATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII AS:i:-60 XS:i:-60 XN:i:0 XM:i:10 XO:i:0 XG:i:0 NM:i:10 MD:Z:21C8C29C5A1T16A5T1T24C20T1 YS:i:-71 YT:Z:CP >>> Writing bisulfite mapping results to Pum1_R1.fq.gz.temp.7_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to Pum1_R1.fq.gz.temp.3_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to Pum1_R1.fq.gz.temp.8_bismark_bt2_pe.bam <<< Found first alignment: LH00129:489:23JFWNLT4:8:1101:10142:1056_1:N:0:TGAGTACT+GACAATAA/1 77 * 0 0 * * 0 0 ATTGGGAAATTTTTTTATTGGTGTAAGTGGGATTTGAATTTGTGTTGATAGAGTTGAGAGGTTGTGTGATTTTGAGTGTAATGTTTTAATTATTTGGTTATGGAGGTTTTATATGAGAAGATATTAGTAGTATTGTTATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00129:489:23JFWNLT4:8:1101:10142:1056_2:N:0:TGAGTACT+GACAATAA/2 141 * 0 0 * * 0 0 AAAAACATCAAATTTTTTTTAACTCTCTAACCCTCATTATAACCCCATCCCTACCAAACAAAATCATAACTTAACCAATTTTAAATCCATACAATATAAAAATACATTTATAACAATACTACAAATATCTTCTCATATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to Pum1_R1.fq.gz.temp.1_bismark_bt2_pe.bam <<< Found first alignment: LH00129:489:23JFWNLT4:8:1101:12326:1056_1:N:0:TGAGTACT+GACAATAA/1 77 * 0 0 * * 0 0 AATTTAATAAATAAAGATAAAAGTTTGAGATATTTGTTAATAAGTGTTAATGATGATTATTTTTTAATGGTTTGGTTGTGATTATTTTTGGTATAAGGAATGGTATTGATTTTTTTTAAAAAAAAAGAAATTGTTTTGTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00129:489:23JFWNLT4:8:1101:12326:1056_2:N:0:TGAGTACT+GACAATAA/2 141 * 0 0 * * 0 0 AATTATTAAATTCAAAATATAACTTACTAAAAAATTTATTATCAAATTTATCACCACTATATCAACTTATTTTAATTAAACTTATAATCTTACTTTTTCTTTTTAAATAACAAAACAATTTCTTTTTTTTTAAAAAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to Pum1_R1.fq.gz.temp.5_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to Pum1_R1.fq.gz.temp.6_bismark_bt2_pe.bam <<< Reading in the sequence files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.4 and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.4 Reading in the sequence files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.7 and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.7 Reading in the sequence files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.2 and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.2 Reading in the sequence files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.8 and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.8 Reading in the sequence files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.1 and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.1 Reading in the sequence files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.3 and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.3 Reading in the sequence files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.5 and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.5 Reading in the sequence files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.6 and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.6 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00129:489:23JFWNLT4:8:2252:8119:10388_1:N:0:TGAGTACT+GACAATAA Chromosome_9B 91966292 Chromosomal sequence could not be extracted for LH00129:489:23JFWNLT4:8:2358:38165:8931_1:N:0:TGAGTACT+GACAATAA Chromosome_9B 91966292 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far 4797033 reads; of these: 4797033 (100.00%) were paired; of these: 1692475 (35.28%) aligned concordantly 0 times 1100649 (22.94%) aligned concordantly exactly 1 time 2003909 (41.77%) aligned concordantly >1 times 64.72% overall alignment rate 4797033 reads; of these: 4797033 (100.00%) were paired; of these: 1691344 (35.26%) aligned concordantly 0 times 1101823 (22.97%) aligned concordantly exactly 1 time 2003866 (41.77%) aligned concordantly >1 times 64.74% overall alignment rate Processed 4797033 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.6_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.6_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4797033 Number of paired-end alignments with a unique best hit: 2684626 Mapping efficiency: 56.0% Sequence pairs with no alignments under any condition: 615179 Sequence pairs did not map uniquely: 1497228 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: 1344034 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1340592 ((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: 118581142 Total methylated C's in CpG context: 2806430 Total methylated C's in CHG context: 120889 Total methylated C's in CHH context: 538894 Total methylated C's in Unknown context: 14477 Total unmethylated C's in CpG context: 11632470 Total unmethylated C's in CHG context: 20126115 Total unmethylated C's in CHH context: 83356344 Total unmethylated C's in Unknown context: 129004 C methylated in CpG context: 19.4% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 10.1% 4797033 reads; of these: 4797033 (100.00%) were paired; of these: 1690718 (35.25%) aligned concordantly 0 times 1101305 (22.96%) aligned concordantly exactly 1 time 2005010 (41.80%) aligned concordantly >1 times 64.75% overall alignment rate 4797033 reads; of these: 4797033 (100.00%) were paired; of these: 1692093 (35.27%) aligned concordantly 0 times 1099681 (22.92%) aligned concordantly exactly 1 time 2005259 (41.80%) aligned concordantly >1 times 64.73% overall alignment rate Processed 4797033 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.2_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.2_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4797033 Number of paired-end alignments with a unique best hit: 2682236 Mapping efficiency: 55.9% Sequence pairs with no alignments under any condition: 614720 Sequence pairs did not map uniquely: 1500077 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1343045 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1339190 ((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: 118509312 Total methylated C's in CpG context: 2807516 Total methylated C's in CHG context: 121186 Total methylated C's in CHH context: 536825 Total methylated C's in Unknown context: 14007 Total unmethylated C's in CpG context: 11617323 Total unmethylated C's in CHG context: 20112288 Total unmethylated C's in CHH context: 83314174 Total unmethylated C's in Unknown context: 128005 C methylated in CpG context: 19.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 9.9% 4797033 reads; of these: 4797033 (100.00%) were paired; of these: 1688967 (35.21%) aligned concordantly 0 times 1101581 (22.96%) aligned concordantly exactly 1 time 2006485 (41.83%) aligned concordantly >1 times 64.79% overall alignment rate 4797033 reads; of these: 4797033 (100.00%) were paired; of these: 1693080 (35.29%) aligned concordantly 0 times 1099508 (22.92%) aligned concordantly exactly 1 time 2004445 (41.79%) aligned concordantly >1 times 64.71% overall alignment rate Processed 4797033 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.5_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.5_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4797033 Number of paired-end alignments with a unique best hit: 2686291 Mapping efficiency: 56.0% Sequence pairs with no alignments under any condition: 613868 Sequence pairs did not map uniquely: 1496874 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: 1346363 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1339928 ((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: 118679983 Total methylated C's in CpG context: 2815952 Total methylated C's in CHG context: 121867 Total methylated C's in CHH context: 537740 Total methylated C's in Unknown context: 14368 Total unmethylated C's in CpG context: 11634532 Total unmethylated C's in CHG context: 20134592 Total unmethylated C's in CHH context: 83435300 Total unmethylated C's in Unknown context: 128617 C methylated in CpG context: 19.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 10.0% 4797033 reads; of these: 4797033 (100.00%) were paired; of these: 1688602 (35.20%) aligned concordantly 0 times 1100638 (22.94%) aligned concordantly exactly 1 time 2007793 (41.85%) aligned concordantly >1 times 64.80% overall alignment rate 4797033 reads; of these: 4797033 (100.00%) were paired; of these: 1690897 (35.25%) aligned concordantly 0 times 1099593 (22.92%) aligned concordantly exactly 1 time 2006543 (41.83%) aligned concordantly >1 times 64.75% overall alignment rate 4797033 reads; of these: 4797033 (100.00%) were paired; of these: 1688998 (35.21%) aligned concordantly 0 times 1100301 (22.94%) aligned concordantly exactly 1 time 2007734 (41.85%) aligned concordantly >1 times 64.79% overall alignment rate Processed 4797033 sequences in total 4797033 reads; of these: 4797033 (100.00%) were paired; of these: 1692882 (35.29%) aligned concordantly 0 times 1099455 (22.92%) aligned concordantly exactly 1 time 2004696 (41.79%) aligned concordantly >1 times 64.71% overall alignment rate Successfully deleted the temporary files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.8_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.8_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4797033 Number of paired-end alignments with a unique best hit: 2685689 Mapping efficiency: 56.0% Sequence pairs with no alignments under any condition: 612957 Sequence pairs did not map uniquely: 1498387 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: 1344449 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1341240 ((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: 118617550 Total methylated C's in CpG context: 2806238 Total methylated C's in CHG context: 121734 Total methylated C's in CHH context: 537209 Total methylated C's in Unknown context: 14160 Total unmethylated C's in CpG context: 11626986 Total unmethylated C's in CHG context: 20128871 Total unmethylated C's in CHH context: 83396512 Total unmethylated C's in Unknown context: 128242 C methylated in CpG context: 19.4% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 9.9% Now waiting for all child processes to complete Processed 4797033 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.3_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.3_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4797033 Number of paired-end alignments with a unique best hit: 2684607 Mapping efficiency: 56.0% Sequence pairs with no alignments under any condition: 614109 Sequence pairs did not map uniquely: 1498317 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1343644 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1340962 ((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: 118615327 Total methylated C's in CpG context: 2810925 Total methylated C's in CHG context: 121040 Total methylated C's in CHH context: 539144 Total methylated C's in Unknown context: 14265 Total unmethylated C's in CpG context: 11615430 Total unmethylated C's in CHG context: 20129609 Total unmethylated C's in CHH context: 83399179 Total unmethylated C's in Unknown context: 128200 C methylated in CpG context: 19.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 10.0% 4797034 reads; of these: 4797034 (100.00%) were paired; of these: 1689774 (35.23%) aligned concordantly 0 times 1100443 (22.94%) aligned concordantly exactly 1 time 2006817 (41.83%) aligned concordantly >1 times 64.77% overall alignment rate 4797034 reads; of these: 4797034 (100.00%) were paired; of these: 1691497 (35.26%) aligned concordantly 0 times 1101171 (22.96%) aligned concordantly exactly 1 time 2004366 (41.78%) aligned concordantly >1 times 64.74% overall alignment rate Processed 4797034 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.1_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.1_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4797034 Number of paired-end alignments with a unique best hit: 2686264 Mapping efficiency: 56.0% Sequence pairs with no alignments under any condition: 613637 Sequence pairs did not map uniquely: 1497133 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: 1345205 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1341059 ((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: 118674816 Total methylated C's in CpG context: 2815892 Total methylated C's in CHG context: 121394 Total methylated C's in CHH context: 538780 Total methylated C's in Unknown context: 14162 Total unmethylated C's in CpG context: 11624275 Total unmethylated C's in CHG context: 20140201 Total unmethylated C's in CHH context: 83434274 Total unmethylated C's in Unknown context: 128648 C methylated in CpG context: 19.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 9.9% 4797033 reads; of these: 4797033 (100.00%) were paired; of these: 1689617 (35.22%) aligned concordantly 0 times 1098709 (22.90%) aligned concordantly exactly 1 time 2008707 (41.87%) aligned concordantly >1 times 64.78% overall alignment rate 4797033 reads; of these: 4797033 (100.00%) were paired; of these: 1689700 (35.22%) aligned concordantly 0 times 1099368 (22.92%) aligned concordantly exactly 1 time 2007965 (41.86%) aligned concordantly >1 times 64.78% overall alignment rate Processed 4797033 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.7_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.7_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4797033 Number of paired-end alignments with a unique best hit: 2686523 Mapping efficiency: 56.0% Sequence pairs with no alignments under any condition: 613656 Sequence pairs did not map uniquely: 1496854 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: 1344522 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1342001 ((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: 118681013 Total methylated C's in CpG context: 2816828 Total methylated C's in CHG context: 121707 Total methylated C's in CHH context: 538854 Total methylated C's in Unknown context: 14094 Total unmethylated C's in CpG context: 11616925 Total unmethylated C's in CHG context: 20140596 Total unmethylated C's in CHH context: 83446103 Total unmethylated C's in Unknown context: 127655 C methylated in CpG context: 19.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 9.9% 4797033 reads; of these: 4797033 (100.00%) were paired; of these: 1691291 (35.26%) aligned concordantly 0 times 1100143 (22.93%) aligned concordantly exactly 1 time 2005599 (41.81%) aligned concordantly >1 times 64.74% overall alignment rate 4797033 reads; of these: 4797033 (100.00%) were paired; of these: 1693544 (35.30%) aligned concordantly 0 times 1099002 (22.91%) aligned concordantly exactly 1 time 2004487 (41.79%) aligned concordantly >1 times 64.70% overall alignment rate Processed 4797033 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.4_C_to_T.fastq and /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.4_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4797033 Number of paired-end alignments with a unique best hit: 2681755 Mapping efficiency: 55.9% Sequence pairs with no alignments under any condition: 616837 Sequence pairs did not map uniquely: 1498441 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: 1341635 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1340120 ((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: 118459839 Total methylated C's in CpG context: 2804641 Total methylated C's in CHG context: 121519 Total methylated C's in CHH context: 537600 Total methylated C's in Unknown context: 14307 Total unmethylated C's in CpG context: 11596423 Total unmethylated C's in CHG context: 20109308 Total unmethylated C's in CHH context: 83290348 Total unmethylated C's in Unknown context: 127904 C methylated in CpG context: 19.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 10.1% All child processes successfully finished. at /mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/bismark line 599, line 19188132. Right, cleaning up now... Deleting temporary sequence files... /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.1 /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.1 /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.2 /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.2 /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.3 /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.3 /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.4 /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.4 /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.5 /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.5 /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.6 /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.6 /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.7 /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.7 /tmp/13-wgbs-Pum1-3530457/Pum1_R1.fq.gz.temp.8 /tmp/13-wgbs-Pum1-3530457/Pum1_R2.fq.gz.temp.8 Now merging BAM files Pum1_R1.fq.gz.temp.1_bismark_bt2_pe.bam Pum1_R1.fq.gz.temp.2_bismark_bt2_pe.bam Pum1_R1.fq.gz.temp.3_bismark_bt2_pe.bam Pum1_R1.fq.gz.temp.4_bismark_bt2_pe.bam Pum1_R1.fq.gz.temp.5_bismark_bt2_pe.bam Pum1_R1.fq.gz.temp.6_bismark_bt2_pe.bam Pum1_R1.fq.gz.temp.7_bismark_bt2_pe.bam Pum1_R1.fq.gz.temp.8_bismark_bt2_pe.bam into >>> Pum1_R1_bismark_bt2_pe.bam <<< (using --threads 4) Merging from file >> Pum1_R1.fq.gz.temp.1_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.1_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.1_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> Pum1_R1.fq.gz.temp.2_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.2_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.2_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> Pum1_R1.fq.gz.temp.3_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.3_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.3_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> Pum1_R1.fq.gz.temp.4_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.4_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.4_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> Pum1_R1.fq.gz.temp.5_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.5_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.5_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> Pum1_R1.fq.gz.temp.6_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.6_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.6_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> Pum1_R1.fq.gz.temp.7_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.7_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.7_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> Pum1_R1.fq.gz.temp.8_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.8_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.8_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Failed to close output filehandle Deleting temporary BAM files... /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.1_bismark_bt2_pe.bam Failed to delete temporary BAM file /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.1_bismark_bt2_pe.bam: No such file or directory /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.2_bismark_bt2_pe.bam Failed to delete temporary BAM file /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.2_bismark_bt2_pe.bam: No such file or directory /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.3_bismark_bt2_pe.bam Failed to delete temporary BAM file /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.3_bismark_bt2_pe.bam: No such file or directory /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.4_bismark_bt2_pe.bam Failed to delete temporary BAM file /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.4_bismark_bt2_pe.bam: No such file or directory /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.5_bismark_bt2_pe.bam Failed to delete temporary BAM file /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.5_bismark_bt2_pe.bam: No such file or directory /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.6_bismark_bt2_pe.bam Failed to delete temporary BAM file /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.6_bismark_bt2_pe.bam: No such file or directory /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.7_bismark_bt2_pe.bam Failed to delete temporary BAM file /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.7_bismark_bt2_pe.bam: No such file or directory /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.8_bismark_bt2_pe.bam Failed to delete temporary BAM file /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.8_bismark_bt2_pe.bam: No such file or directory Writing report to /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1_bismark_bt2_PE_report.txt Now merging temporary reports Pum1_R1.fq.gz.temp.1_bismark_bt2_PE_report.txt Pum1_R1.fq.gz.temp.2_bismark_bt2_PE_report.txt Pum1_R1.fq.gz.temp.3_bismark_bt2_PE_report.txt Pum1_R1.fq.gz.temp.4_bismark_bt2_PE_report.txt Pum1_R1.fq.gz.temp.5_bismark_bt2_PE_report.txt Pum1_R1.fq.gz.temp.6_bismark_bt2_PE_report.txt Pum1_R1.fq.gz.temp.7_bismark_bt2_PE_report.txt Pum1_R1.fq.gz.temp.8_bismark_bt2_PE_report.txt into >>> /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1_bismark_bt2_PE_report.txt <<< Merging from file >> Pum1_R1.fq.gz.temp.1_bismark_bt2_PE_report.txt << Failed to read from temporary mapping report '/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum1_R1.fq.gz.temp.1_bismark_bt2_PE_report.txt'