The following have been reloaded with a version change:
  1) GCC/11.3.0 => GCC/12.2.0
  2) GCCcore/11.3.0 => GCCcore/12.2.0
  3) XZ/5.2.5-GCCcore-11.3.0 => XZ/5.2.7-GCCcore-12.2.0
  4) binutils/2.38-GCCcore-11.3.0 => binutils/2.39-GCCcore-12.2.0
  5) bzip2/1.0.8-GCCcore-11.3.0 => bzip2/1.0.8-GCCcore-12.2.0
  6) ncurses/6.3-GCCcore-11.3.0 => ncurses/6.3-GCCcore-12.2.0
  7) zlib/1.2.12-GCCcore-11.3.0 => zlib/1.2.12-GCCcore-12.2.0


The following have been reloaded with a version change:
  1) GMP/6.2.1-GCCcore-11.3.0 => GMP/6.2.1-GCCcore-12.2.0
  2) Python/3.10.4-GCCcore-11.3.0 => Python/3.10.8-GCCcore-12.2.0
  3) SQLite/3.38.3-GCCcore-11.3.0 => SQLite/3.39.4-GCCcore-12.2.0
  4) Tcl/8.6.12-GCCcore-11.3.0 => Tcl/8.6.12-GCCcore-12.2.0
  5) libffi/3.4.2-GCCcore-11.3.0 => libffi/3.4.4-GCCcore-12.2.0
  6) libreadline/8.1.2-GCCcore-11.3.0 => libreadline/8.2-GCCcore-12.2.0

Settings:
  Output files: "/scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.*.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:
  /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.fna
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: 627595
Using parameters --bmax 470697 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 470697 --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
Split 1, merged 7; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 358625 (target: 470696)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (470697) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 404911 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 404912 for bucket 1
Getting block 2 of 7
  Reserving size (470697) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 432284 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 432285 for bucket 2
Getting block 3 of 7
  Reserving size (470697) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 418811 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 418812 for bucket 3
Getting block 4 of 7
  Reserving size (470697) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 385632 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 385633 for bucket 4
Getting block 5 of 7
  Reserving size (470697) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 181948 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 181949 for bucket 5
Getting block 6 of 7
  Reserving size (470697) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 415854 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 415855 for bucket 6
Getting block 7 of 7
  Reserving size (470697) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 270935 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 270936 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 511257
fchr[G]: 1258701
fchr[T]: 2001816
fchr[$]: 2510381
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 5031270 bytes to primary EBWT file: /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.1.bt2.tmp
Wrote 627600 bytes to secondary EBWT file: /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 2510381
    bwtLen: 2510382
    sz: 627596
    bwtSz: 627596
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 156899
    offsSz: 627596
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 13075
    numLines: 13075
    ebwtTotLen: 836800
    ebwtTotSz: 836800
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:01
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: 627595
Using parameters --bmax 470697 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 470697 --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
Split 1, merged 7; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 358625 (target: 470696)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (470697) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 426426 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 426427 for bucket 1
Getting block 2 of 7
  Reserving size (470697) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 382384 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 382385 for bucket 2
Getting block 3 of 7
  Reserving size (470697) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 411140 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 411141 for bucket 3
Getting block 4 of 7
  Reserving size (470697) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 319383 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 319384 for bucket 4
Getting block 5 of 7
  Reserving size (470697) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 360146 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 360147 for bucket 5
Getting block 6 of 7
  Reserving size (470697) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 447211 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 447212 for bucket 6
Getting block 7 of 7
  Reserving size (470697) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 163685 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 163686 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 511257
fchr[G]: 1258701
fchr[T]: 2001816
fchr[$]: 2510381
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 5031270 bytes to primary EBWT file: /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.rev.1.bt2.tmp
Wrote 627600 bytes to secondary EBWT file: /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.rev.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 2510381
    bwtLen: 2510382
    sz: 627596
    bwtSz: 627596
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 156899
    offsSz: 627596
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 13075
    numLines: 13075
    ebwtTotLen: 836800
    ebwtTotSz: 836800
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:01
Renaming /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.3.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.3.bt2
Renaming /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.4.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.4.bt2
Renaming /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.1.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.1.bt2
Renaming /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.2.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.2.bt2
Renaming /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.rev.1.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.rev.1.bt2
Renaming /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.rev.2.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/EB75/Bifidobacterium_EB75.rev.2.bt2

========== Convert DS018_01_M1 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_02_D1 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_03_B1 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_05_M3 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_06_D3 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_07_B3 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_08_P3 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_09_M4 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_10_D4 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_11_B4 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_12_P4 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_13_M5 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_14_D5 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_15_B5 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_16_P5 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_17_M6 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_18_D6 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_19_B6 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_20_P6 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_21_M7 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_22_D7 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_23_B7 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert DS018_24_P7 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

###############################################################################
Hábrók Cluster
Job 12420838 for user p127804
Finished at: Mon Aug 12 11:11:12 CEST 2024

Job details:
============

Job ID                         : 12420838
Name                           : 01.bowtie2_EB75.sh
User                           : p127804
Partition                      : regularmedium
Nodes                          : node23
Number of Nodes                : 1
Cores                          : 32
Number of Tasks                : 1
State                          : RUNNING  
Submit                         : 2024-08-12T10:15:18
Start                          : 2024-08-12T10:15:19
End                            : --
Reserved walltime              : 1-00:00:00
Used walltime                  :   00:55:54
Used CPU time                  : -- 
% User (Computation)           : --
% System (I/O)                 : --
Total memory reserved          : 32G
Maximum memory used            : --

Acknowledgements:
=================

Please see this page for information about acknowledging Hábrók in your publications:

https://wiki.hpc.rug.nl/habrok/introduction/scientific_output

################################################################################