Read 10000 spots for SRR519926
Written 10000 spots for SRR519926
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... 0.01 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index db/AF086833.fa
[main] Real time: 0.358 sec; CPU: 0.020 sec
10000 reads; of these:
  10000 (100.00%) were unpaired; of these:
    10000 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 10000 sequences (2510000 bp)...
[M::mem_process_seqs] Processed 10000 reads in 0.540 CPU sec, 0.540 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem db/AF086833.fa SRR519926_1.fastq
[main] Real time: 0.669 sec; CPU: 0.552 sec
10000 reads; of these:
  10000 (100.00%) were paired; of these:
    10000 (100.00%) aligned concordantly 0 times
    0 (0.00%) aligned concordantly exactly 1 time
    0 (0.00%) aligned concordantly >1 times
    ----
    10000 pairs aligned concordantly 0 times; of these:
      0 (0.00%) aligned discordantly 1 time
    ----
    10000 pairs aligned 0 times concordantly or discordantly; of these:
      20000 mates make up the pairs; of these:
        20000 (100.00%) aligned 0 times
        0 (0.00%) aligned exactly 1 time
        0 (0.00%) aligned >1 times
0.00% overall alignment rate
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 20000 sequences (5020000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 20000 reads in 1.084 CPU sec, 1.083 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem db/AF086833.fa SRR519926_1.fastq SRR519926_2.fastq
[main] Real time: 1.258 sec; CPU: 1.108 sec