ch4rr0
commented
1 year ago Hello,
I was not able to recreate this one. Below is the output that I get using the same command line.
Settings:
Output files: "out.*.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:
example/reference/lambda_virus.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: 12125
Using parameters --bmax 9094 and *no difference cover*
Constructing suffix-array element generator
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 12334
fchr[G]: 23696
fchr[T]: 36516
fchr[$]: 48502
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4210730 bytes to primary EBWT file: out.1.bt2.tmp
Wrote 12132 bytes to secondary EBWT file: out.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 48502
bwtLen: 48503
sz: 12126
bwtSz: 12126
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 3032
offsSz: 12128
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 253
numLines: 253
ebwtTotLen: 16192
ebwtTotSz: 16192
color: 0
reverse: 0
Total time for call to driver() for forward index: 00:00:00
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 12125
Using parameters --bmax 9094 and *no difference cover*
Constructing suffix-array element generator
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 12334
fchr[G]: 23696
fchr[T]: 36516
fchr[$]: 48502
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4210730 bytes to primary EBWT file: out.rev.1.bt2.tmp
Wrote 12132 bytes to secondary EBWT file: out.rev.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 48502
bwtLen: 48503
sz: 12126
bwtSz: 12126
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 3032
offsSz: 12128
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 253
numLines: 253
ebwtTotLen: 16192
ebwtTotSz: 16192
color: 0
reverse: 1
Total time for backward call to driver() for mirror index: 00:00:00
Renaming out.3.bt2.tmp to out.3.bt2
Renaming out.4.bt2.tmp to out.4.bt2
Renaming out.1.bt2.tmp to out.1.bt2
Renaming out.2.bt2.tmp to out.2.bt2
Renaming out.rev.1.bt2.tmp to out.rev.1.bt2
Renaming out.rev.2.bt2.tmp to out.rev.2.bt2
Hello,
I am familiarizing with the bowtie2-build, trying different options. However, --nodc option is not giving me output, stats are as follow:
Settings: Output files: "nodc..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: /Users/blabla/Downloads/bowtie2-2.4.5-macos-arm64/example/reference/lambda_virus.fa 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: 12125 Using parameters --bmax 9094 and no difference cover Doing ahead-of-time memory usage test
and the command line I've used is: bowtie2-build --nodc /Users/blabla/Downloads/bowtie2-2.4.5-macos-arm64/example/reference/lambda_virus.fa nodc
as an output I get: nodc.1.bt2.tmp nodc.2.bt2.tmp nodc.3.bt2.tmp nodc.4.bt2.tmp
What am I doing wrong? Thanks for the help in advance!