Read 10000 spots for SRR1972739 Written 10000 spots for SRR1972739 Settings: Output files: "db/AF086833.fa.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: db/AF086833.fa Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 4739 Using parameters --bmax 3555 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3555 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 18959 (target: 3554) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Sorting block of length 18959 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 18960 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6061 fchr[G]: 10096 fchr[T]: 13848 fchr[$]: 18959 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4200864 bytes to primary EBWT file: db/AF086833.fa.1.bt2 Wrote 4744 bytes to secondary EBWT file: db/AF086833.fa.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 18959 bwtLen: 18960 sz: 4740 bwtSz: 4740 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1185 offsSz: 4740 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 99 numLines: 99 ebwtTotLen: 6336 ebwtTotSz: 6336 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:00 Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 4739 Using parameters --bmax 3555 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3555 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 18959 (target: 3554) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Sorting block of length 18959 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 18960 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6061 fchr[G]: 10096 fchr[T]: 13848 fchr[$]: 18959 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4200864 bytes to primary EBWT file: db/AF086833.fa.rev.1.bt2 Wrote 4744 bytes to secondary EBWT file: db/AF086833.fa.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 18959 bwtLen: 18960 sz: 4740 bwtSz: 4740 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1185 offsSz: 4740 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 99 numLines: 99 ebwtTotLen: 6336 ebwtTotSz: 6336 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:00 [bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.01 seconds elapse. [bwa_index] Update BWT... 0.00 sec [bwa_index] Pack forward-only FASTA... 0.00 sec [bwa_index] Construct SA from BWT and Occ... 0.00 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index db/AF086833.fa [main] Real time: 0.369 sec; CPU: 0.012 sec 10000 reads; of these: 10000 (100.00%) were unpaired; of these: 3628 (36.28%) aligned 0 times 6372 (63.72%) aligned exactly 1 time 0 (0.00%) aligned >1 times 63.72% overall alignment rate [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 10000 sequences (1010000 bp)... [M::mem_process_seqs] Processed 10000 reads in 0.300 CPU sec, 0.301 real sec [main] Version: 0.7.17-r1188 [main] CMD: bwa mem db/AF086833.fa SRR1972739_1.fastq [main] Real time: 0.413 sec; CPU: 0.308 sec 10000 reads; of these: 10000 (100.00%) were paired; of these: 5086 (50.86%) aligned concordantly 0 times 4914 (49.14%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times ---- 5086 pairs aligned concordantly 0 times; of these: 827 (16.26%) aligned discordantly 1 time ---- 4259 pairs aligned 0 times concordantly or discordantly; of these: 8518 mates make up the pairs; of these: 7463 (87.61%) aligned 0 times 1055 (12.39%) aligned exactly 1 time 0 (0.00%) aligned >1 times 62.69% overall alignment rate [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 20000 sequences (2020000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (738, 5739, 6, 663) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (74, 114, 180) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 392) [M::mem_pestat] mean and std.dev: (131.35, 75.24) [M::mem_pestat] low and high boundaries for proper pairs: (1, 498) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (174, 220, 276) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 480) [M::mem_pestat] mean and std.dev: (227.70, 77.37) [M::mem_pestat] low and high boundaries for proper pairs: (1, 582) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (77, 122, 175) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 371) [M::mem_pestat] mean and std.dev: (131.18, 71.99) [M::mem_pestat] low and high boundaries for proper pairs: (1, 469) [M::mem_process_seqs] Processed 20000 reads in 0.972 CPU sec, 0.972 real sec [main] Version: 0.7.17-r1188 [main] CMD: bwa mem db/AF086833.fa SRR1972739_1.fastq SRR1972739_2.fastq [main] Real time: 1.093 sec; CPU: 0.984 sec