Settings:
Output files: "Olurida_v081.*.ht2"
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
Local offset rate: 3 (one in 8)
Local fTable chars: 6
Local sequence length: 57344
Local sequence overlap between two consecutive indexes: 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:
/gscratch/srlab/sam/data/O_lurida/oly_genome_assemblies/Olurida_v081.fa
Reading reference sizes
Time reading reference sizes: 00:00:08
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:07
Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 201985331 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 201985331 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:10
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:05
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:09
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
Split 2, merged 6; iterating...
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 1.53894e+08 (target: 201985330)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Getting block 1 of 7
Reserving size (201985331) for bucket 1
Getting block 3 of 7
Getting block 5 of 7
Getting block 2 of 7
Reserving size (201985331) for bucket 5
Reserving size (201985331) for bucket 3
Getting block 4 of 7
Getting block 6 of 7
Calculating Z arrays for bucket 1
Reserving size (201985331) for bucket 6
Reserving size (201985331) for bucket 2
Calculating Z arrays for bucket 5
Entering block accumulator loop for bucket 1:
Reserving size (201985331) for bucket 4
Getting block 7 of 7
Calculating Z arrays for bucket 6
Entering block accumulator loop for bucket 5:
Reserving size (201985331) for bucket 7
Calculating Z arrays for bucket 3
Calculating Z arrays for bucket 2
Calculating Z arrays for bucket 4
Entering block accumulator loop for bucket 6:
Entering block accumulator loop for bucket 4:
Entering block accumulator loop for bucket 2:
Calculating Z arrays for bucket 7
Entering block accumulator loop for bucket 7:
Entering block accumulator loop for bucket 3:
bucket 7: 10%
bucket 4: 10%
bucket 1: 10%
bucket 6: 10%
bucket 7: 20%
bucket 2: 10%
bucket 4: 20%
bucket 3: 10%
bucket 7: 30%
bucket 5: 10%
bucket 1: 20%
bucket 4: 30%
bucket 6: 20%
bucket 7: 40%
bucket 7: 50%
bucket 3: 20%
bucket 4: 40%
bucket 2: 20%
bucket 1: 30%
bucket 7: 60%
bucket 6: 30%
bucket 5: 20%
bucket 4: 50%
bucket 7: 70%
bucket 1: 40%
bucket 6: 40%
bucket 3: 30%
bucket 7: 80%
bucket 4: 60%
bucket 2: 30%
bucket 1: 50%
bucket 7: 90%
bucket 5: 30%
bucket 4: 70%
bucket 6: 50%
bucket 3: 40%
bucket 2: 40%
bucket 1: 60%
bucket 7: 100%
Sorting block of length 196557760 for bucket 7
(Using difference cover)
bucket 4: 80%
bucket 6: 60%
bucket 1: 70%
bucket 2: 50%
bucket 5: 40%
bucket 3: 50%
bucket 4: 90%
bucket 1: 80%
bucket 6: 70%
bucket 4: 100%
Sorting block of length 37852883 for bucket 4
(Using difference cover)
bucket 2: 60%
bucket 6: 80%
bucket 1: 90%
bucket 3: 60%
bucket 5: 50%
bucket 6: 90%
bucket 1: 100%
Sorting block of length 94844445 for bucket 1
(Using difference cover)
bucket 2: 70%
bucket 3: 70%
bucket 6: 100%
Sorting block of length 160307639 for bucket 6
(Using difference cover)
bucket 5: 60%
bucket 2: 80%
bucket 3: 80%
bucket 5: 70%
bucket 2: 90%
bucket 3: 90%
bucket 5: 80%
bucket 2: 100%
Sorting block of length 196120598 for bucket 2
(Using difference cover)
Sorting block time: 00:00:10
Returning block of 37852884 for bucket 4
bucket 3: 100%
Sorting block of length 192178709 for bucket 3
(Using difference cover)
bucket 5: 90%
bucket 5: 100%
Sorting block of length 199393059 for bucket 5
(Using difference cover)
Sorting block time: 00:00:28
Returning block of 94844446 for bucket 1
Sorting block time: 00:00:47
Returning block of 160307640 for bucket 6
Sorting block time: 00:00:59
Returning block of 196557761 for bucket 7
Sorting block time: 00:00:58
Returning block of 192178710 for bucket 3
Sorting block time: 00:01:01
Returning block of 196120599 for bucket 2
Sorting block time: 00:01:01
Returning block of 199393060 for bucket 5
Exited GFM loop
fchr[A]: 0
fchr[C]: 341519526
fchr[G]: 538577822
fchr[T]: 735626959
fchr[$]: 1077255099
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 371985018 bytes to primary GFM file: Olurida_v081.1.ht2
Wrote 269313780 bytes to secondary GFM file: Olurida_v081.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 1637469477 bytes to primary GFM file: Olurida_v081.5.ht2
Wrote 269635742 bytes to secondary GFM file: Olurida_v081.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HierEbwt constructor
Headers:
len: 1077255099
gbwtLen: 1077255100
nodes: 1077255100
sz: 269313775
gbwtSz: 269313776
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 0
eftabSz: 0
ftabLen: 1048577
ftabSz: 4194308
offsLen: 67328444
offsSz: 269313776
lineSz: 64
sideSz: 64
sideGbwtSz: 48
sideGbwtLen: 192
numSides: 5610704
numLines: 5610704
gbwtTotLen: 359085056
gbwtTotSz: 359085056
reverse: 0
linearFM: Yes
Total time for call to driver() for forward index: 00:12:17
690074520 reads; of these:
690074520 (100.00%) were paired; of these:
358162653 (51.90%) aligned concordantly 0 times
323838161 (46.93%) aligned concordantly exactly 1 time
8073706 (1.17%) aligned concordantly >1 times
----
358162653 pairs aligned concordantly 0 times; of these:
8826059 (2.46%) aligned discordantly 1 time
----
349336594 pairs aligned 0 times concordantly or discordantly; of these:
698673188 mates make up the pairs; of these:
581334817 (83.21%) aligned 0 times
110970559 (15.88%) aligned exactly 1 time
6367812 (0.91%) aligned >1 times
57.88% overall alignment rate
[E::hts_open_format] Failed to open file 20180919_Olurida_v081.bam
samtools sort: can't open "20180919_Olurida_v081.bam": No such file or directory
[E::hts_open_format] Failed to open file 20180925_Olurida_v081.sorted.bam
samtools index: failed to open "20180925_Olurida_v081.sorted.bam": No such file or directory