Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.9/samtools' Reference genome folder provided is /gscratch/srlab/sam/data/C_virginica/genomes/GCF_002022765.2_C_virginica-3.0/ (absolute path is '/gscratch/srlab/sam/data/C_virginica/genomes/GCF_002022765.2_C_virginica-3.0/)' Processing sequences up to read no. 137957136 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 '/gscratch/scrubbed/samwhite/outputs/20190312_cvir_gonad_bismark/half_total_reads_bismark'): /gscratch/scrubbed/samwhite/outputs/20190312_cvir_gonad_bismark/cvir_bsseq_all_pe_R1.fastq.gz /gscratch/scrubbed/samwhite/outputs/20190312_cvir_gonad_bismark/cvir_bsseq_all_pe_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: /gscratch/scrubbed/samwhite/outputs/20190312_cvir_gonad_bismark/half_total_reads_bismark Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sam/data/C_virginica/genomes/GCF_002022765.2_C_virginica-3.0/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/samwhite/outputs/20190312_cvir_gonad_bismark/cvir_bsseq_all_pe_R1.fastq.gz and /gscratch/scrubbed/samwhite/outputs/20190312_cvir_gonad_bismark/cvir_bsseq_all_pe_R2.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 137957136 from /gscratch/scrubbed/samwhite/outputs/20190312_cvir_gonad_bismark/cvir_bsseq_all_pe_R1.fastq.gz Writing a C -> T converted version of the input file cvir_bsseq_all_pe_R1.fastq.gz to cvir_bsseq_all_pe_R1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file cvir_bsseq_all_pe_R1.fastq.gz to cvir_bsseq_all_pe_R1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file cvir_bsseq_all_pe_R1.fastq.gz (137957137 sequences in total) Processing reads up to sequence no. 137957136 from /gscratch/scrubbed/samwhite/outputs/20190312_cvir_gonad_bismark/cvir_bsseq_all_pe_R2.fastq.gz Writing a C -> T converted version of the input file cvir_bsseq_all_pe_R2.fastq.gz to cvir_bsseq_all_pe_R2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file cvir_bsseq_all_pe_R2.fastq.gz to cvir_bsseq_all_pe_R2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file cvir_bsseq_all_pe_R2.fastq.gz (137957137 sequences in total) Input files are cvir_bsseq_all_pe_R1.fastq.gz_C_to_T.fastq and cvir_bsseq_all_pe_R1.fastq.gz_G_to_A.fastq and cvir_bsseq_all_pe_R2.fastq.gz_C_to_T.fastq and cvir_bsseq_all_pe_R2.fastq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/data/C_virginica/genomes/GCF_002022765.2_C_virginica-3.0/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from cvir_bsseq_all_pe_R1.fastq.gz_C_to_T.fastq and cvir_bsseq_all_pe_R2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:2:1101:1232:2155_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 ATTGTATTAATTATAAAAAATATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATTTATTATTAAAAATATTAAATA FFFFFFFFFBFFFFFFFFFFFFF#################################<>> Writing bisulfite mapping results to cvir_bsseq_all_pe_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/samwhite/outputs/20190312_cvir_gonad_bismark/cvir_bsseq_all_pe_R1.fastq.gz and /gscratch/scrubbed/samwhite/outputs/20190312_cvir_gonad_bismark/cvir_bsseq_all_pe_R2.fastq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1210:4310:17386_1:N:0:TGACCA NC_035780.1 1 Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1316:4047:74652_1:N:0:TGACCA NC_007175.2 17170 Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 102000000 sequence pairs so far Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 105000000 sequence pairs so far Processed 106000000 sequence pairs so far Processed 107000000 sequence pairs so far Processed 108000000 sequence pairs so far Processed 109000000 sequence pairs so far Processed 110000000 sequence pairs so far Processed 111000000 sequence pairs so far Processed 112000000 sequence pairs so far Processed 113000000 sequence pairs so far Processed 114000000 sequence pairs so far Processed 115000000 sequence pairs so far Processed 116000000 sequence pairs so far Processed 117000000 sequence pairs so far Processed 118000000 sequence pairs so far Processed 119000000 sequence pairs so far Processed 120000000 sequence pairs so far Processed 121000000 sequence pairs so far Processed 122000000 sequence pairs so far Processed 123000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2206:10235:74664_1:N:0:GCCAAT NC_007175.2 17189 Processed 124000000 sequence pairs so far Processed 125000000 sequence pairs so far Processed 126000000 sequence pairs so far Processed 127000000 sequence pairs so far Processed 128000000 sequence pairs so far Processed 129000000 sequence pairs so far Processed 130000000 sequence pairs so far Processed 131000000 sequence pairs so far Processed 132000000 sequence pairs so far Processed 133000000 sequence pairs so far Processed 134000000 sequence pairs so far Processed 135000000 sequence pairs so far Processed 136000000 sequence pairs so far Processed 137000000 sequence pairs so far 137957136 reads; of these: 137957136 (100.00%) were paired; of these: 113250461 (82.09%) aligned concordantly 0 times 10979647 (7.96%) aligned concordantly exactly 1 time137957136 reads; of these: 13727028 (1379571369.95 (%) aligned concordantly >1 times 17.91% overall alignment rate 100.00%) were paired; of these: 113281155 (82.11%) aligned concordantly 0 times 10923544 (7.92%) aligned concordantly exactly 1 time 13752437 (9.97%) aligned concordantly >1 times 17.89% overall alignment rate 137957136 reads; of these: 137957136 (100.00%) were paired; of these: 113742492 (82.45%) aligned concordantly 0 times 10782875 (7.82%) aligned concordantly exactly 1 time 13431769 (9.74%) aligned concordantly >1 times 17.55% overall alignment rate 137957136 reads; of these: 137957136 (100.00%) were paired; of these: 113771938 (82.47%) aligned concordantly 0 times 10734548 (7.78%) aligned concordantly exactly 1 time 13450650 (9.75%) aligned concordantly >1 times 17.53% overall alignment rate Processed 137957136 sequences in total Successfully deleted the temporary files cvir_bsseq_all_pe_R1.fastq.gz_C_to_T.fastq, cvir_bsseq_all_pe_R1.fastq.gz_G_to_A.fastq, cvir_bsseq_all_pe_R2.fastq.gz_C_to_T.fastq and cvir_bsseq_all_pe_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 137957136 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1164865379 Total methylated C's in CpG context: 122873598 Total methylated C's in CHG context: 5054655 Total methylated C's in CHH context: 18234442 Total methylated C's in Unknown context: 674287 Total unmethylated C's in CpG context: 40470898 Total unmethylated C's in CHG context: 261834434 Total unmethylated C's in CHH context: 716397352 Total unmethylated C's in Unknown context: 3802925 C methylated in CpG context: 75.2% C methylated in CHG context: 1.9% C methylated in CHH context: 2.5% C methylated in unknown context (CN or CHN): 15.1% Bismark completed in 1d 9h 0m 47s ==================== Bismark run complete ====================