b'[MAIN] NextGenMap 0.5.5\n'b'[MAIN] Startup : x64 (build Mar  2 2019 21:24:17)\n'b'[MAIN] Starting time: 2020-09-14.03:51:59\n'b'[CONFIG] Parameter:  --affine 0 --argos_min_score 0 --bam 1 --bin_size 2 --block_multiplier 2 --broken_pairs 0 --bs_cutoff 6 --bs_mapping 0 --cpu_threads 60 --dualstrand 1 --fast 0 --fast_pairing 0 --force_rlength_check 0 --format 2 --gap_extend_penalty 5 --gap_read_penalty 20 --gap_ref_penalty 20 --hard_clip 0 --keep_tags 0 --kmer 13 --kmer_min 0 --kmer_skip 2 --local 1 --match_bonus 10 --match_bonus_tc 2 --match_bonus_tt 10 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --max_polya 4 --max_read_length 0 --min_identity 0.650000 --min_insert_size 0 --min_mq 0 --min_residues 0.500000 --min_score 0.000000 --mismatch_penalty 15 --mode 0 --no_progress 1 --no_unal 0 --ocl_threads 1 --output slamdunk-L565-Input.symbB.v1.0.genome.500bp.step_100bp/map/L565-Input.trimmed.end1+end2.fastq_slamdunk_mapped.bam --overwrite 1 --pair_score_cutoff 0.900000 --paired 0 --parse_all 1 --pe_delimiter / --qry L565-Input.trimmed.end1+end2.fastq.gz --qry_count -1 --qry_start 0 --ref /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa --ref_mode -1 --rg_id 0 --rg_sm L565-Input.trimmed.end1+end2.fastq:pulse:0 --sensitive 0 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --slam_seq 2 --step_count 4 --strata 1 --topn 100 --trim5 9 --update_check 0 --very_fast 0 --very_sensitive 0\n'b'[NGM] Opening for output (BAM): slamdunk-L565-Input.symbB.v1.0.genome.500bp.step_100bp/map/L565-Input.trimmed.end1+end2.fastq_slamdunk_mapped.bam\n'b'[SEQPROV] Encoding reference sequence.\n'b'[SEQPROV] Size of reference genome 631 Mbp (max. 17179 Mbp)\n'b'[SEQPROV] Allocating 315704692 (622040107) bytes for the reference.\n'b'[SEQPROV] BinRef length: 315693694ll (elapsed 11.019588)\n'b'[SEQPROV] 0 reference sequences were skipped (length < 10).\n'b'[SEQPROV] Writing encoded reference to /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa-enc.2.ngm\n'b'[SEQPROV] Writing to disk took 4.63s\n'b'[PREPROCESS] Building reference table\n'b'[PREPROCESS] Allocated 1 hashtable units (tableLocMax=2^32.000000, genomeSize=2^29.233950)\n'b'[PREPROCESS] Building RefTable #0 (kmer length: 13, reference skip: 2)\n'b'[PREPROCESS] \tNumber of k-mers: 67108865\n'b'[PREPROCESS] \tCounting kmers took 68.05s\n'b'[PREPROCESS] \tAverage number of positions per prefix: 4.029088\n'b'[PREPROCESS] \tIndex size: 335544325 byte (67108865 x 5)\n'b'[PREPROCESS] \tGenerating index took 14.49s\n'b'[PREPROCESS] \tAllocating and initializing prefix Table took 1.23s\n'b'[PREPROCESS] \tNumber of prefix positions is 200922950 (4)\n'b'[PREPROCESS] \tSize of RefTable is 803691800\n'b'[PREPROCESS] \tNumber of repetitive k-mers ignored: 132342\n'b'[PREPROCESS] \tOverall time for creating RefTable: 310.79s\n'b'[PREPROCESS] Writing RefTable to /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa-ht-13-2.3.ngm\n'b'[PREPROCESS] Writing to disk took 21.10s\n'b'[PREPROCESS] Max. k-mer frequency set so 107!\n'b'[INPUT] Input is single end data.\n'b'[INPUT] Opening file L565-Input.trimmed.end1+end2.fastq.gz for reading\n'b'[INPUT] Input is Fastq\n'b'[INPUT] Estimating parameter from data\n'b"[INPUT] Input reads don't have the same length!\n"b'[INPUT] Maximum read length found in the first 10000000 reads is 24. For longer reads only the first 26 bp will be mapped.\n'b"[INPUT] The maximum read length can be overwritten with the '--max-read-length' parameter. With '--force-rlength-check', NextGenMap will run through all reads to find the max. read length. This might take some time.\n"b'[INPUT] Average read length: 23 (min: 11, max: 28)\n'b'[INPUT] Corridor width: 8\n'b'[INPUT] Average kmer hits pro read: 2.174569\n'b'[INPUT] Max possible kmer hit: 3\n'b'[INPUT] Estimated sensitivity: 0.724856\n'b'[INPUT] Estimating parameter took 35.134s\n'b'[INPUT] Input is Fastq\n'b'[OPENCL] Available platforms: 2\n'b'[OPENCL] AMD Accelerated Parallel Processing\n'b'[OPENCL] Selecting OpenCl platform: AMD Accelerated Parallel Processing\n'b'[OPENCL] Platform: OpenCL 1.2 AMD-APP (1214.3)\n'b'[OPENCL] 1 CPU device found.\n'b'[OPENCL] Device 0: Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz (Driver: 1214.3 (sse2,avx))\n'b'[OPENCL] 56 CPU cores available.\n'b'[MAIN] Alignments computed: 39532889\n'b'[MAIN] Done (18489224 reads mapped (99.27%), 135736 reads not mapped, 39667956 lines written)(elapsed: 845.883362s)\n'b'[UPDATE_CHECK] Your version of NGM is more than 6 months old - a newer version may be available. (For performing an automatic check use --update-check)\n'