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/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Processing sequences up to read no. 10000 from the input file Input files to be analysed (in current folder '/Volumes/Serine/wd/18-04-12/tmp2'): /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R1.fastq.gz /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R2.fastq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-04-12/tmp2 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R1.fastq.gz and /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R2.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000 from /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R1.fastq.gz Writing a C -> T converted version of the input file zr2096_6_s1_R1.fastq.gz to zr2096_6_s1_R1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_6_s1_R1.fastq.gz to zr2096_6_s1_R1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_6_s1_R1.fastq.gz (10001 sequences in total) gunzip: error writing to output: Broken pipe gunzip: /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R1.fastq.gz: uncompress failed Processing reads up to sequence no. 10000 from /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R2.fastq.gz Writing a C -> T converted version of the input file zr2096_6_s1_R2.fastq.gz to zr2096_6_s1_R2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_6_s1_R2.fastq.gz to zr2096_6_s1_R2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_6_s1_R2.fastq.gz (10001 sequences in total) Input files are zr2096_6_s1_R1.fastq.gz_C_to_T.fastq and zr2096_6_s1_R1.fastq.gz_G_to_A.fastq and zr2096_6_s1_R2.fastq.gz_C_to_T.fastq and zr2096_6_s1_R2.fastq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_6_s1_R1.fastq.gz_C_to_T.fastq and zr2096_6_s1_R2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1093:2134_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 NTTATTAAATTTAATTTTATTATTAAATAAAAANNNNNNNNNNNNNNNNNNNNNNANNTANANAAATATTAATTAAATATTTTTAAAATAATAAATTTAA #<>> Writing bisulfite mapping results to zr2096_6_s1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R1.fastq.gz and /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R2.fastq.gz 10000 reads; of these: 10000 (100.00%) were paired; of these: 6713 (67.13%) aligned concordant1ly 0 times 1382 (13.82%) aligned concordantly exactly 1 time 1905 (19.05%) aligned concordantly >1 times 32.87% overall alignm0000 reads; of these: ent rate 10000 (100.00%) were paired; of these: 7034 (70.34%) aligned concordantly 0 times 1254 (12.54%) aligned concordantly exactly 1 time 1712 (17.12%) aligned concordantly >1 times 29.66% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 6692 (66.92%) aligned concordantly 0 times 1327 (13.27%) aligned concordantly exactly 1 time 1981 (19.81%) aligned concordantly >1 times 33.08% overall alignment rate 10000 reads; of these: 10000 (100.00%) were paired; of these: 7041 (70.41%) aligned concordantly 0 times 1251 (12.51%) aligned concordantly exactly 1 time 1708 (17.08%) aligned concordantly >1 times 29.59% overall alignment rate Processed 10000 sequences in total Successfully deleted the temporary files zr2096_6_s1_R1.fastq.gz_C_to_T.fastq, zr2096_6_s1_R1.fastq.gz_G_to_A.fastq, zr2096_6_s1_R2.fastq.gz_C_to_T.fastq and zr2096_6_s1_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 180677 Total methylated C's in CpG context: 17859 Total methylated C's in CHG context: 1203 Total methylated C's in CHH context: 4603 Total methylated C's in Unknown context: 643 Total unmethylated C's in CpG context: 6629 Total unmethylated C's in CHG context: 39618 Total unmethylated C's in CHH context: 110765 Total unmethylated C's in Unknown context: 2946 C methylated in CpG context: 72.9% C methylated in CHG context: 2.9% C methylated in CHH context: 4.0% C methylated in unknown context (CN or CHN): 17.9% Bismark completed in 0d 0h 0m 31s ==================== Bismark run complete ==================== gunzip: error writing to output: Broken pipe gunzip: /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R1.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R2.fastq.gz: uncompress failed gunzip: error writing to output: Broken pipe gunzip: /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R2.fastq.gz: uncompress failed