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_gigas/genomes/ (absolute path is '/gscratch/srlab/sam/data/C_gigas/genomes/)' Processing sequences up to read no. 2000000 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_cgigas_se_bismark/subset_2000000'): /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_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_cgigas_se_bismark/subset_2000000 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sam/data/C_gigas/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. 2000000 from /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_all_R1.fastq.gz Writing a C -> T converted version of the input file cgig_bsseq_all_R1.fastq.gz to cgig_bsseq_all_R1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file cgig_bsseq_all_R1.fastq.gz (2000001 sequences in total) Input file is cgig_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_gigas/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 cgig_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_gigas/genomes/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-D00743:54:C8MOMACXX:1:1101:1599:2153_1:N:0:TAGCTT 4 * 0 0 * * 0 0 TNGGGGTAGGTTGAATTTGTATTTTTTATGTAGTTTTTTGAGAAAGATTGA C#1AD;2@;D>> Writing bisulfite mapping results to cgig_bsseq_all_R1_bismark_bt2.bam <<< Reading in the sequence file /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_all_R1.fastq.gz Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:1773:34563_1:N:0:TAGCTT scaffold33742 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:3577:18659_1:N:0:TAGCTT C23010 2001 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:12835:3587_1:N:0:TAGCTT C23010 2002 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:10421:24530_1:N:0:TAGCTT scaffold38030 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:18665:62350_1:N:0:TAGCTT C34600 19430 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:2988:100874_1:N:0:TAGCTT scaffold811 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:13327:43238_1:N:0:TAGCTT C28016 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:12755:63320_1:N:0:TAGCTT C32222 11023 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:20213:64837_1:N:0:TAGCTT scaffold845 3217 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:12588:36512_1:N:0:TAGCTT scaffold838 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:15893:2479_1:N:0:TAGCTT C35992 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:10332:16567_1:N:0:TAGCTT C15208 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:19128:57495_1:N:0:TAGCTT C14656 214 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1110:6194:34264_1:N:0:TAGCTT scaffold38856 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1110:1976:74862_1:N:0:TAGCTT C15654 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1110:17016:83695_1:N:0:TAGCTT C15162 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1110:8021:96188_1:N:0:TAGCTT scaffold1895 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1111:7845:68788_1:N:0:TAGCTT C32222 11023 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1111:20543:93295_1:N:0:TAGCTT scaffold38030 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1111:5799:96032_1:N:0:TAGCTT scaffold26586 3991 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1112:5325:37641_1:N:0:TAGCTT C32222 11023 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1112:3805:88811_1:N:0:TAGCTT C33332 13914 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1112:7692:91397_1:N:0:TAGCTT scaffold33742 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1114:18516:50545_1:N:0:TAGCTT C23010 2002 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1114:21097:60128_1:N:0:TAGCTT scaffold39464 72101 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1114:21061:89547_1:N:0:TAGCTT scaffold42790 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1115:9662:19845_1:N:0:TAGCTT C14724 214 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1115:14174:28027_1:N:0:TAGCTT scaffold681 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1115:9463:37538_1:N:0:TAGCTT scaffold25910 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1115:10253:44431_1:N:0:TAGCTT scaffold33902 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1115:8202:63048_1:N:0:TAGCTT scaffold33742 2 2000000 reads; of these: 2000000 (100.00%) were unpaired; of these: 902826 (45.14%) aligned 0 times 507716 (25.39%) aligned exactly 1 time 589458 (29.47%) aligned >1 times 54.86% overall alignment rate 2000000 reads; of these: 2000000 (100.00%) were unpaired; of these: 901471 (45.07%) aligned 0 times 508748 (25.44%) aligned exactly 1 time 589781 (29.49%) aligned >1 times 54.93% overall alignment rate Processed 2000000 sequences so far Successfully deleted the temporary file cgig_bsseq_all_R1.fastq.gz_C_to_T.fastq Final Alignment report ====================== Sequences analysed in total: 2000000 Number of alignments with a unique best hit from the different alignments: 1100869 Mapping efficiency: 55.0% Final Cytosine Methylation Report ================================= Total number of C's analysed: 9308926 Total methylated C's in CpG context: 370442 Total methylated C's in CHG context: 58337 Total methylated C's in CHH context: 109852 Total methylated C's in Unknown context: 1797 Total unmethylated C's in CpG context: 1054425 Total unmethylated C's in CHG context: 1918510 Total unmethylated C's in CHH context: 5797360 Total unmethylated C's in Unknown context: 15233 C methylated in CpG context: 26.0% C methylated in CHG context: 3.0% C methylated in CHH context: 1.9% C methylated in Unknown context (CN or CHN): 10.6% Bismark completed in 0d 0h 10m 16s ==================== Bismark run complete ====================