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/Co-culture_NRBB57_CNCM_I-4319/co-culture.*.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/Co-culture_NRBB57_CNCM_I-4319/co-culture.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: 1176025
Using parameters --bmax 882019 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 882019 --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 6; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 588012 (target: 882018)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (882019) 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 100071 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 100072 for bucket 1
Getting block 2 of 8
  Reserving size (882019) 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 832357 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 832358 for bucket 2
Getting block 3 of 8
  Reserving size (882019) 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 813318 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 813319 for bucket 3
Getting block 4 of 8
  Reserving size (882019) 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 778162 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 778163 for bucket 4
Getting block 5 of 8
  Reserving size (882019) 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 352036 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 352037 for bucket 5
Getting block 6 of 8
  Reserving size (882019) 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 817929 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 817930 for bucket 6
Getting block 7 of 8
  Reserving size (882019) 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 205986 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 205987 for bucket 7
Getting block 8 of 8
  Reserving size (882019) for bucket 8
  Calculating Z arrays for bucket 8
  Entering block accumulator loop for bucket 8:
  bucket 8: 10%
  bucket 8: 20%
  bucket 8: 30%
  bucket 8: 40%
  bucket 8: 50%
  bucket 8: 60%
  bucket 8: 70%
  bucket 8: 80%
  bucket 8: 90%
  bucket 8: 100%
  Sorting block of length 804235 for bucket 8
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 804236 for bucket 8
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 918559
fchr[G]: 2354189
fchr[T]: 3785380
fchr[$]: 4704101
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 5762708 bytes to primary EBWT file: /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.1.bt2.tmp
Wrote 1176032 bytes to secondary EBWT file: /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 4704101
    bwtLen: 4704102
    sz: 1176026
    bwtSz: 1176026
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 294007
    offsSz: 1176028
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 24501
    numLines: 24501
    ebwtTotLen: 1568064
    ebwtTotSz: 1568064
    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: 1176025
Using parameters --bmax 882019 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 882019 --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 6; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 588012 (target: 882018)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (882019) 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 661972 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 661973 for bucket 1
Getting block 2 of 8
  Reserving size (882019) 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 337867 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 337868 for bucket 2
Getting block 3 of 8
  Reserving size (882019) 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 778464 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 778465 for bucket 3
Getting block 4 of 8
  Reserving size (882019) 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 337404 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 337405 for bucket 4
Getting block 5 of 8
  Reserving size (882019) 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 653256 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 653257 for bucket 5
Getting block 6 of 8
  Reserving size (882019) 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 685413 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 685414 for bucket 6
Getting block 7 of 8
  Reserving size (882019) 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 610329 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 610330 for bucket 7
Getting block 8 of 8
  Reserving size (882019) for bucket 8
  Calculating Z arrays for bucket 8
  Entering block accumulator loop for bucket 8:
  bucket 8: 10%
  bucket 8: 20%
  bucket 8: 30%
  bucket 8: 40%
  bucket 8: 50%
  bucket 8: 60%
  bucket 8: 70%
  bucket 8: 80%
  bucket 8: 90%
  bucket 8: 100%
  Sorting block of length 639389 for bucket 8
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 639390 for bucket 8
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 918559
fchr[G]: 2354189
fchr[T]: 3785380
fchr[$]: 4704101
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 5762708 bytes to primary EBWT file: /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.rev.1.bt2.tmp
Wrote 1176032 bytes to secondary EBWT file: /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.rev.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 4704101
    bwtLen: 4704102
    sz: 1176026
    bwtSz: 1176026
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 294007
    offsSz: 1176028
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 24501
    numLines: 24501
    ebwtTotLen: 1568064
    ebwtTotSz: 1568064
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:02
Renaming /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.3.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.3.bt2
Renaming /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.4.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.4.bt2
Renaming /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.1.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.1.bt2
Renaming /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.2.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.2.bt2
Renaming /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.rev.1.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.rev.1.bt2
Renaming /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.rev.2.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/Co-culture_NRBB57_CNCM_I-4319/co-culture.rev.2.bt2

========== Convert ZH018_01 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert ZH018_02 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert ZH018_03 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert ZH018_04 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert ZH018_05 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert ZH018_06 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert ZH018_07 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

========== Convert ZH018_08 ======================================
[bam_sort_core] merging from 0 files and 32 in-memory blocks...

###############################################################################
Hábrók Cluster
Job 12420623 for user p127804
Finished at: Mon Aug 12 10:22:44 CEST 2024

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

Job ID                         : 12420623
Name                           : 01.bowtie2.sh
User                           : p127804
Partition                      : regularmedium
Nodes                          : node23
Number of Nodes                : 1
Cores                          : 32
Number of Tasks                : 1
State                          : RUNNING  
Submit                         : 2024-08-12T10:06:58
Start                          : 2024-08-12T10:06:59
End                            : --
Reserved walltime              : 1-00:00:00
Used walltime                  :   00:15:45
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

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