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/ (absolute path is '/gscratch/srlab/sam/data/C_virginica/genomes/)' Processing sequences up to read no. 10000000 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/20190222_cvirginica_se_bismark/subset_10000000'): /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.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: /gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_10000000 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sam/data/C_virginica/genomes/ Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 10000000 from /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz Writing a C -> T converted version of the input file cvir_bsseq_all_R1.fastq.gz to cvir_bsseq_all_R1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file cvir_bsseq_all_R1.fastq.gz (10000001 sequences in total) Input file is cvir_bsseq_all_R1.fastq.gz_C_to_T.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/data/C_virginica/genomes/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from cvir_bsseq_all_R1.fastq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sam/data/C_virginica/genomes/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: M03631:341:000000000-BLY9V:1:1101:13318:1785_1:N:0:32 0 NC_035780.1_CT_converted 13737422 0 76M * 0 0 TTTAGTTTTAGTTTGTATATTTTTTTTTAGTTGTATTTTTTTTTATAATTTTATATTAAGATGTGTGTGTAAGAAT CCCCCGGGGGGGGGGGFFCFGGGGGGGG8,CE,C,CEEFFEFEG,,,,>> Writing bisulfite mapping results to cvir_bsseq_all_R1_bismark_bt2.bam <<< Reading in the sequence file /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Chromosomal sequence could not be extracted for M03631:341:000000000-BLY9V:1:1107:8847:18815_1:N:0:10 NC_007175.2 1 Processed 6000000 sequences so far Chromosomal sequence could not be extracted for M03631:341:000000000-BLY9V:1:2103:24948:17877_1:N:0:10 NC_007175.2 17169 Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far 10000000 reads; of these: 10000000 (100.00%) were unpaired; of these: 8210494 (82.10%) aligned 0 times 714600 (7.15%) aligned exactly 1 time 1074906 (10.75%) aligned >1 times 17.90% overall alignment rate 10000000 reads; of these: 10000000 (100.00%) were unpaired; of these: 8214634 (82.15%) aligned 0 times 712279 (7.12%) aligned exactly 1 time 1073087 (10.73%) aligned >1 times 17.85% overall alignment rate Processed 10000000 sequences so far Successfully deleted the temporary file cvir_bsseq_all_R1.fastq.gz_C_to_T.fastq Final Alignment report ====================== Sequences analysed in total: 10000000 Number of alignments with a unique best hit from the different alignments: 1613096 Mapping efficiency: 16.1% Final Cytosine Methylation Report ================================= Total number of C's analysed: 27169536 Total methylated C's in CpG context: 3071718 Total methylated C's in CHG context: 1494709 Total methylated C's in CHH context: 6210808 Total methylated C's in Unknown context: 35867 Total unmethylated C's in CpG context: 1003105 Total unmethylated C's in CHG context: 4024305 Total unmethylated C's in CHH context: 11364891 Total unmethylated C's in Unknown context: 53763 C methylated in CpG context: 75.4% C methylated in CHG context: 27.1% C methylated in CHH context: 35.3% C methylated in Unknown context (CN or CHN): 40.0% Bismark completed in 0d 0h 23m 2s ==================== Bismark run complete ====================