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/MM0160/MM0160.*.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/MM0160/MM0160.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: 578423 Using parameters --bmax 433818 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 433818 --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: 330527 (target: 433817) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (433818) 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 348203 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 348204 for bucket 1 Getting block 2 of 7 Reserving size (433818) 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 374526 for bucket 2 (Using difference cover) Sorting block time: 00:00:00 Returning block of 374527 for bucket 2 Getting block 3 of 7 Reserving size (433818) 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 401344 for bucket 3 (Using difference cover) Sorting block time: 00:00:00 Returning block of 401345 for bucket 3 Getting block 4 of 7 Reserving size (433818) 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 323188 for bucket 4 (Using difference cover) Sorting block time: 00:00:00 Returning block of 323189 for bucket 4 Getting block 5 of 7 Reserving size (433818) 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 383902 for bucket 5 (Using difference cover) Sorting block time: 00:00:00 Returning block of 383903 for bucket 5 Getting block 6 of 7 Reserving size (433818) 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 419178 for bucket 6 (Using difference cover) Sorting block time: 00:00:00 Returning block of 419179 for bucket 6 Getting block 7 of 7 Reserving size (433818) 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 63346 for bucket 7 (Using difference cover) Sorting block time: 00:00:00 Returning block of 63347 for bucket 7 Exited Ebwt loop fchr[A]: 0 fchr[C]: 460672 fchr[G]: 1155902 fchr[T]: 1852377 fchr[$]: 2313693 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4966105 bytes to primary EBWT file: /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.1.bt2.tmp Wrote 578428 bytes to secondary EBWT file: /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.2.bt2.tmp Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2313693 bwtLen: 2313694 sz: 578424 bwtSz: 578424 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 144606 offsSz: 578424 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 12051 numLines: 12051 ebwtTotLen: 771264 ebwtTotSz: 771264 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: 00:00:01 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 578423 Using parameters --bmax 433818 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 433818 --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 1; 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 Avg bucket size: 289211 (target: 433817) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (433818) 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 297343 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 297344 for bucket 1 Getting block 2 of 8 Reserving size (433818) 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 292139 for bucket 2 (Using difference cover) Sorting block time: 00:00:00 Returning block of 292140 for bucket 2 Getting block 3 of 8 Reserving size (433818) 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 152300 for bucket 3 (Using difference cover) Sorting block time: 00:00:00 Returning block of 152301 for bucket 3 Getting block 4 of 8 Reserving size (433818) 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 287374 for bucket 4 (Using difference cover) Sorting block time: 00:00:00 Returning block of 287375 for bucket 4 Getting block 5 of 8 Reserving size (433818) 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 418652 for bucket 5 (Using difference cover) Sorting block time: 00:00:00 Returning block of 418653 for bucket 5 Getting block 6 of 8 Reserving size (433818) 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 392604 for bucket 6 (Using difference cover) Sorting block time: 00:00:00 Returning block of 392605 for bucket 6 Getting block 7 of 8 Reserving size (433818) 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 293301 for bucket 7 (Using difference cover) Sorting block time: 00:00:00 Returning block of 293302 for bucket 7 Getting block 8 of 8 Reserving size (433818) 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 179973 for bucket 8 (Using difference cover) Sorting block time: 00:00:00 Returning block of 179974 for bucket 8 Exited Ebwt loop fchr[A]: 0 fchr[C]: 460672 fchr[G]: 1155902 fchr[T]: 1852377 fchr[$]: 2313693 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4966105 bytes to primary EBWT file: /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.rev.1.bt2.tmp Wrote 578428 bytes to secondary EBWT file: /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.rev.2.bt2.tmp Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2313693 bwtLen: 2313694 sz: 578424 bwtSz: 578424 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 144606 offsSz: 578424 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 12051 numLines: 12051 ebwtTotLen: 771264 ebwtTotSz: 771264 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:01 Renaming /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.3.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.3.bt2 Renaming /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.4.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.4.bt2 Renaming /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.1.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.1.bt2 Renaming /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.2.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.2.bt2 Renaming /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.rev.1.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.rev.1.bt2 Renaming /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.rev.2.bt2.tmp to /scratch/p127804/PROJECTS/Douwe/genomes/MM0160/MM0160.rev.2.bt2 ========== Convert DS019_01 ====================================== [bam_sort_core] merging from 0 files and 32 in-memory blocks... ========== Convert DS019_02 ====================================== [bam_sort_core] merging from 0 files and 32 in-memory blocks... ========== Convert DS019_03 ====================================== [bam_sort_core] merging from 0 files and 32 in-memory blocks... ========== Convert DS019_04 ====================================== [bam_sort_core] merging from 0 files and 32 in-memory blocks... ========== Convert DS019_05 ====================================== [bam_sort_core] merging from 0 files and 32 in-memory blocks... ========== Convert DS019_06 ====================================== [bam_sort_core] merging from 0 files and 32 in-memory blocks... ========== Convert DS019_07 ====================================== [bam_sort_core] merging from 0 files and 32 in-memory blocks... ========== Convert DS019_08 ====================================== [bam_sort_core] merging from 0 files and 32 in-memory blocks... ========== Convert DS019_09 ====================================== [bam_sort_core] merging from 0 files and 32 in-memory blocks... ========== Convert DS019_10 ====================================== [bam_sort_core] merging from 0 files and 32 in-memory blocks... ========== Convert DS019_11 ====================================== [bam_sort_core] merging from 0 files and 32 in-memory blocks... ========== Convert DS019_12 ====================================== [bam_sort_core] merging from 0 files and 32 in-memory blocks... ############################################################################### Hábrók Cluster Job 13075693 for user p127804 Finished at: Thu Oct 3 09:50:18 CEST 2024 Job details: ============ Job ID : 13075693 Name : 01.bowtie2_Douwe_202409_19.sh User : p127804 Partition : regularmedium Nodes : node35 Number of Nodes : 1 Cores : 32 Number of Tasks : 1 State : RUNNING Submit : 2024-10-03T09:40:20 Start : 2024-10-03T09:40:21 End : -- Reserved walltime : 1-00:00:00 Used walltime : 00:09:57 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 ################################################################################