Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-103_S27_L005_R1_001.fastq.gz EPI-103_S27_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-103_S27_L005_R1_001.fastq.gz and EPI-103_S27_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-103_S27_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-103_S27_L005_R1_001.fastq.gz to EPI-103_S27_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-103_S27_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-103_S27_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-103_S27_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-103_S27_L005_R2_001.fastq.gz to EPI-103_S27_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-103_S27_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-103_S27_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-103_S27_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-103_S27_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-103_S27_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-103_S27_L005_R1_001.fastq.gz and EPI-103_S27_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-103_S27_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 56s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-103_S27_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-103_S27_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-103_S27_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-104_S28_L005_R1_001.fastq.gz EPI-104_S28_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-104_S28_L005_R1_001.fastq.gz and EPI-104_S28_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-104_S28_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-104_S28_L005_R1_001.fastq.gz to EPI-104_S28_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-104_S28_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-104_S28_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-104_S28_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-104_S28_L005_R2_001.fastq.gz to EPI-104_S28_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-104_S28_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-104_S28_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-104_S28_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-104_S28_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-104_S28_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-104_S28_L005_R1_001.fastq.gz and EPI-104_S28_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-104_S28_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 28s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-104_S28_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-104_S28_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-104_S28_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-111_S29_L005_R1_001.fastq.gz EPI-111_S29_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-111_S29_L005_R1_001.fastq.gz and EPI-111_S29_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-111_S29_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-111_S29_L005_R1_001.fastq.gz to EPI-111_S29_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-111_S29_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-111_S29_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-111_S29_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-111_S29_L005_R2_001.fastq.gz to EPI-111_S29_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-111_S29_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-111_S29_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-111_S29_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-111_S29_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-111_S29_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-111_S29_L005_R1_001.fastq.gz and EPI-111_S29_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-111_S29_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-111_S29_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-111_S29_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-111_S29_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-113_S30_L005_R1_001.fastq.gz EPI-113_S30_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-113_S30_L005_R1_001.fastq.gz and EPI-113_S30_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-113_S30_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-113_S30_L005_R1_001.fastq.gz to EPI-113_S30_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-113_S30_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-113_S30_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-113_S30_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-113_S30_L005_R2_001.fastq.gz to EPI-113_S30_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-113_S30_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-113_S30_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-113_S30_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-113_S30_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-113_S30_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-113_S30_L005_R1_001.fastq.gz and EPI-113_S30_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-113_S30_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 28s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-113_S30_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-113_S30_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-113_S30_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-119_S31_L005_R1_001.fastq.gz EPI-119_S31_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-119_S31_L005_R1_001.fastq.gz and EPI-119_S31_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-119_S31_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-119_S31_L005_R1_001.fastq.gz to EPI-119_S31_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-119_S31_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-119_S31_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-119_S31_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-119_S31_L005_R2_001.fastq.gz to EPI-119_S31_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-119_S31_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-119_S31_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-119_S31_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-119_S31_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-119_S31_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-119_S31_L005_R1_001.fastq.gz and EPI-119_S31_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-119_S31_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-119_S31_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-119_S31_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-119_S31_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-120_S32_L005_R1_001.fastq.gz EPI-120_S32_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-120_S32_L005_R1_001.fastq.gz and EPI-120_S32_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-120_S32_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-120_S32_L005_R1_001.fastq.gz to EPI-120_S32_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-120_S32_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-120_S32_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-120_S32_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-120_S32_L005_R2_001.fastq.gz to EPI-120_S32_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-120_S32_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-120_S32_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-120_S32_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-120_S32_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-120_S32_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-120_S32_L005_R1_001.fastq.gz and EPI-120_S32_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-120_S32_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-120_S32_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-120_S32_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-120_S32_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-127_S33_L005_R1_001.fastq.gz EPI-127_S33_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-127_S33_L005_R1_001.fastq.gz and EPI-127_S33_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-127_S33_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-127_S33_L005_R1_001.fastq.gz to EPI-127_S33_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-127_S33_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-127_S33_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-127_S33_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-127_S33_L005_R2_001.fastq.gz to EPI-127_S33_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-127_S33_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-127_S33_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-127_S33_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-127_S33_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-127_S33_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-127_S33_L005_R1_001.fastq.gz and EPI-127_S33_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-127_S33_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-127_S33_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-127_S33_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-127_S33_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-128_S34_L005_R1_001.fastq.gz EPI-128_S34_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-128_S34_L005_R1_001.fastq.gz and EPI-128_S34_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-128_S34_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-128_S34_L005_R1_001.fastq.gz to EPI-128_S34_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-128_S34_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-128_S34_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-128_S34_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-128_S34_L005_R2_001.fastq.gz to EPI-128_S34_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-128_S34_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-128_S34_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-128_S34_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-128_S34_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-128_S34_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-128_S34_L005_R1_001.fastq.gz and EPI-128_S34_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-128_S34_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-128_S34_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-128_S34_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-128_S34_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-135WG_S42_L005_R1_001.fastq.gz EPI-135WG_S42_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-135WG_S42_L005_R1_001.fastq.gz and EPI-135WG_S42_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-135WG_S42_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-135WG_S42_L005_R1_001.fastq.gz to EPI-135WG_S42_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-135WG_S42_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-135WG_S42_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-135WG_S42_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-135WG_S42_L005_R2_001.fastq.gz to EPI-135WG_S42_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-135WG_S42_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-135WG_S42_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-135WG_S42_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-135WG_S42_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-135WG_S42_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-135WG_S42_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-135WG_S42_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-135WG_S42_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-135WG_S42_L005_R1_001.fastq.gz and EPI-135WG_S42_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-135WG_S42_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-135WG_S42_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-135WG_S42_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-135WG_S42_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-135WG_S42_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-135_S35_L005_R1_001.fastq.gz EPI-135_S35_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-135_S35_L005_R1_001.fastq.gz and EPI-135_S35_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-135_S35_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-135_S35_L005_R1_001.fastq.gz to EPI-135_S35_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-135_S35_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-135_S35_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-135_S35_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-135_S35_L005_R2_001.fastq.gz to EPI-135_S35_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-135_S35_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-135_S35_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-135_S35_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-135_S35_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-135_S35_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-135_S35_L005_R1_001.fastq.gz and EPI-135_S35_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-135_S35_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-135_S35_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-135_S35_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-135_S35_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-136_S36_L005_R1_001.fastq.gz EPI-136_S36_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-136_S36_L005_R1_001.fastq.gz and EPI-136_S36_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-136_S36_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-136_S36_L005_R1_001.fastq.gz to EPI-136_S36_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-136_S36_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-136_S36_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-136_S36_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-136_S36_L005_R2_001.fastq.gz to EPI-136_S36_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-136_S36_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-136_S36_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-136_S36_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-136_S36_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-136_S36_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-136_S36_L005_R1_001.fastq.gz and EPI-136_S36_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-136_S36_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-136_S36_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-136_S36_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-136_S36_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-143_S37_L005_R1_001.fastq.gz EPI-143_S37_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-143_S37_L005_R1_001.fastq.gz and EPI-143_S37_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-143_S37_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-143_S37_L005_R1_001.fastq.gz to EPI-143_S37_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-143_S37_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-143_S37_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-143_S37_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-143_S37_L005_R2_001.fastq.gz to EPI-143_S37_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-143_S37_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-143_S37_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-143_S37_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-143_S37_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-143_S37_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-143_S37_L005_R1_001.fastq.gz and EPI-143_S37_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-143_S37_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-143_S37_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-143_S37_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-143_S37_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-145_S38_L005_R1_001.fastq.gz EPI-145_S38_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-145_S38_L005_R1_001.fastq.gz and EPI-145_S38_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-145_S38_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-145_S38_L005_R1_001.fastq.gz to EPI-145_S38_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-145_S38_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-145_S38_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-145_S38_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-145_S38_L005_R2_001.fastq.gz to EPI-145_S38_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-145_S38_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-145_S38_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-145_S38_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-145_S38_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-145_S38_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-145_S38_L005_R1_001.fastq.gz and EPI-145_S38_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-145_S38_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-145_S38_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-145_S38_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-145_S38_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-151_S2_L002_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-152_S3_L002_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-153_S4_L002_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-154_S5_L002_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-159_S6_L002_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-160_S7_L002_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-161_S8_L002_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-162_S9_L002_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-167_S10_L002_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-168_S11_L002_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-169_S12_L002_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-170_S13_L002_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-175_S14_L003_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-176_S15_L003_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-181_S16_L003_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-182_S17_L003_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-184_S18_L003_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-185_S19_L003_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-187_S20_L003_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-188_S21_L003_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-193_S22_L003_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-194_S23_L003_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-199_S24_L003_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-200_S25_L003_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-205_S26_L004_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-206_S27_L004_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-208_S28_L004_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-209_S29_L004_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-214_S30_L004_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-215_S31_L004_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-220_S32_L004_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-221_S33_L004_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-226_S34_L004_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-227_S35_L004_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-229_S36_L004_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): Supplied filename 'EPI-230_S37_L004_R1_001.fastq.gz_L005_R1_001.fastq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-41_S38_L005_R1_001.fastq.gz EPI-41_S38_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-41_S38_L005_R1_001.fastq.gz and EPI-41_S38_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-41_S38_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-41_S38_L005_R1_001.fastq.gz to EPI-41_S38_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-41_S38_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-41_S38_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-41_S38_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-41_S38_L005_R2_001.fastq.gz to EPI-41_S38_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-41_S38_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-41_S38_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-41_S38_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-41_S38_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-41_S38_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-41_S38_L005_R1_001.fastq.gz and EPI-41_S38_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-41_S38_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-41_S38_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-41_S38_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-41_S38_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-42_S39_L005_R1_001.fastq.gz EPI-42_S39_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-42_S39_L005_R1_001.fastq.gz and EPI-42_S39_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-42_S39_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-42_S39_L005_R1_001.fastq.gz to EPI-42_S39_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-42_S39_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-42_S39_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-42_S39_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-42_S39_L005_R2_001.fastq.gz to EPI-42_S39_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-42_S39_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-42_S39_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-42_S39_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-42_S39_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-42_S39_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-42_S39_L005_R1_001.fastq.gz and EPI-42_S39_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-42_S39_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-42_S39_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-42_S39_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-42_S39_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-43_S40_L005_R1_001.fastq.gz EPI-43_S40_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-43_S40_L005_R1_001.fastq.gz and EPI-43_S40_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-43_S40_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-43_S40_L005_R1_001.fastq.gz to EPI-43_S40_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-43_S40_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-43_S40_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-43_S40_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-43_S40_L005_R2_001.fastq.gz to EPI-43_S40_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-43_S40_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-43_S40_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-43_S40_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-43_S40_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-43_S40_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-43_S40_L005_R1_001.fastq.gz and EPI-43_S40_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-43_S40_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-43_S40_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-43_S40_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-43_S40_L005_R2_001.fastq.gz: uncompress failed Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ (absolute path is '/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/)' Processing sequences up to read no. 10000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-03'): EPI-44_S41_L005_R1_001.fastq.gz EPI-44_S41_L005_R2_001.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-03 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are EPI-44_S41_L005_R1_001.fastq.gz and EPI-44_S41_L005_R2_001.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from EPI-44_S41_L005_R1_001.fastq.gz Writing a C -> T converted version of the input file EPI-44_S41_L005_R1_001.fastq.gz to EPI-44_S41_L005_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-44_S41_L005_R1_001.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: EPI-44_S41_L005_R1_001.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from EPI-44_S41_L005_R2_001.fastq.gz Writing a G -> A converted version of the input file EPI-44_S41_L005_R2_001.fastq.gz to EPI-44_S41_L005_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-44_S41_L005_R2_001.fastq.gz (10001 sequences in total) Input files are EPI-44_S41_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/ with the specified options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-44_S41_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-44_S41_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) (ERR): "/Volumes/Serine/wd/18-05-03/20180421_geoduck_hi-c/Results/geoduck_roberts" does not exist or is not a Bowtie 2 index Exiting now ... Found no alignment, assigning undef to last_seq_id and last_lines >>> Writing bisulfite mapping results to EPI-44_S41_L005_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files EPI-44_S41_L005_R1_001.fastq.gz and EPI-44_S41_L005_R2_001.fastq.gz Processed 10000 sequences in total Successfully deleted the temporary files EPI-44_S41_L005_R1_001.fastq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 0 Total methylated C's in CpG context: 0 Total methylated C's in CHG context: 0 Total methylated C's in CHH context: 0 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 0 Total unmethylated C's in CHG context: 0 Total unmethylated C's in CHH context: 0 Total unmethylated C's in Unknown context: 0 Can't determine percentage of methylated Cs in CpG context if value was 0 Can't determine percentage of methylated Cs in CHG context if value was 0 Can't determine percentage of methylated Cs in CHH context if value was 0 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 27s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: EPI-44_S41_L005_R1_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-44_S41_L005_R2_001.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: EPI-44_S41_L005_R2_001.fastq.gz: uncompress failed