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/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/ (absolute path is '/gscratch/srlab/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/)' Processing sequences up to read no. 100000 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/20190224_olurida_se_bismark/subset_100000'): /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/olur_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/20190224_olurida_se_bismark/subset_100000 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/ 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. 100000 from /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/olur_bsseq_all_R1.fastq.gz Writing a C -> T converted version of the input file olur_bsseq_all_R1.fastq.gz to olur_bsseq_all_R1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file olur_bsseq_all_R1.fastq.gz (100001 sequences in total) Input file is olur_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/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/ 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 olur_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/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-D00743:54:C8MOMACXX:1:1101:1413:2213_1:N:0:GGCTAC 0 Contig68945_CT_converted 3260 40 51M * 0 0 AGATGGATTTTTTTTGGAATAAATTTGATTGTTATTGTTTTTGATATTTTA CCCFFFFFHHHHHJJHJIIJIIIJJJJIJJJJJGIJIIIIJJIGIGIJJJI AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15A35 YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from olur_bsseq_all_R1.fastq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-D00743:54:C8MOMACXX:1:1101:1413:2213_1:N:0:GGCTAC 4 * 0 0 * * 0 0 AGATGGATTTTTTTTGGAATAAATTTGATTGTTATTGTTTTTGATATTTTA CCCFFFFFHHHHHJJHJIIJIIIJJJJIJJJJJGIJIIIIJJIGIGIJJJI YT:Z:UU >>> Writing bisulfite mapping results to olur_bsseq_all_R1_bismark_bt2.bam <<< Reading in the sequence file /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/olur_bsseq_all_R1.fastq.gz Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4347:2281_1:N:0:GGCTAC Contig150331 1132 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:5376:3134_1:N:0:GGCTAC Contig91563 4015 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:17166:4061_1:N:0:GGCTAC Contig137622 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:5908:8127_1:N:0:GGCTAC Contig62700 12542 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:15584:10948_1:N:0:GGCTAC Contig136606 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:20895:11557_1:N:0:GGCTAC Contig61059 13263 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:16834:12905_1:N:0:GGCTAC Contig103061 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:13764:15530_1:N:0:GGCTAC Contig58471 12756 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:5252:17437_1:N:0:GGCTAC Contig64696 1930 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4688:18123_1:N:0:GGCTAC Contig58295 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:9031:21273_1:N:0:GGCTAC Contig81887 7685 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:11541:23175_1:N:0:GGCTAC Contig31194 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4494:28672_1:N:0:GGCTAC Contig86549 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:1455:32979_1:N:0:GGCTAC Contig89321 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:13971:35149_1:N:0:GGCTAC Contig8342 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:20218:35803_1:N:0:GGCTAC Contig4243 4822 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:8283:36165_1:N:0:GGCTAC Contig91786 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:19453:43618_1:N:0:GGCTAC Contig73061 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:3706:48640_1:N:0:GGCTAC Contig61175 21107 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:11593:48655_1:N:0:GGCTAC Contig7889 4048 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:2939:50408_1:N:0:GGCTAC Contig85771 3766 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:6515:51728_1:N:0:GGCTAC Contig170236 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:18033:53654_1:N:0:GGCTAC Contig155853 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4646:54966_1:N:0:GGCTAC Contig95638 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4910:55470_1:N:0:GGCTAC Contig273050 2048 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:18569:55548_1:N:0:GGCTAC Contig151615 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:1532:60430_1:N:0:GGCTAC Contig198517 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:3845:61407_1:N:0:GGCTAC Contig140986 5961 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:18023:64092_1:N:0:GGCTAC Contig136884 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:17964:68817_1:N:0:GGCTAC Contig147984 3646 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:7470:74674_1:N:0:GGCTAC Contig73164 4170 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:13391:83918_1:N:0:GGCTAC Contig50092 14727 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:12498:85448_1:N:0:GGCTAC Contig77238 1311 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:8953:94533_1:N:0:GGCTAC Contig68181 2475 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 36968 (36.97%) aligned 0 times 20455 (20.45%) aligned exactly 1 time 42577 (42.58%) aligned >1 times 63.03% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 37069 (37.07%) aligned 0 times 20507 (20.51%) aligned exactly 1 time 42424 (42.42%) aligned >1 times 62.93% overall alignment rate Successfully deleted the temporary file olur_bsseq_all_R1.fastq.gz_C_to_T.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 54214 Mapping efficiency: 54.2% Final Cytosine Methylation Report ================================= Total number of C's analysed: 477096 Total methylated C's in CpG context: 23778 Total methylated C's in CHG context: 2838 Total methylated C's in CHH context: 5458 Total methylated C's in Unknown context: 132 Total unmethylated C's in CpG context: 55237 Total unmethylated C's in CHG context: 97131 Total unmethylated C's in CHH context: 292654 Total unmethylated C's in Unknown context: 1676 C methylated in CpG context: 30.1% C methylated in CHG context: 2.8% C methylated in CHH context: 1.8% C methylated in Unknown context (CN or CHN): 7.3% Bismark completed in 0d 0h 0m 58s ==================== Bismark run complete ====================