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) GCC/12.2.0 => GCC/11.3.0 2) GCCcore/12.2.0 => GCCcore/11.3.0 3) binutils/2.39-GCCcore-12.2.0 => binutils/2.38-GCCcore-11.3.0 4) zlib/1.2.12-GCCcore-12.2.0 => zlib/1.2.12-GCCcore-11.3.0 The following have been reloaded with a version change: 1) FFTW/3.3.10-GCC-12.2.0 => FFTW/3.3.10-gompi-2021b 2) FlexiBLAS/3.2.1-GCC-12.2.0 => FlexiBLAS/3.0.4-GCC-11.2.0 3) GCC/11.3.0 => GCC/11.2.0 4) GCCcore/11.3.0 => GCCcore/11.2.0 5) GMP/6.2.1-GCCcore-12.2.0 => GMP/6.2.1-GCCcore-11.2.0 6) OpenBLAS/0.3.21-GCC-12.2.0 => OpenBLAS/0.3.18-GCC-11.2.0 7) OpenMPI/4.1.4-GCC-12.2.0 => OpenMPI/4.1.1-GCC-11.2.0 8) PMIx/4.2.2-GCCcore-12.2.0 => PMIx/4.1.0-GCCcore-11.2.0 9) Python/3.10.8-GCCcore-12.2.0 => Python/3.9.6-GCCcore-11.2.0 10) SQLite/3.39.4-GCCcore-12.2.0 => SQLite/3.36-GCCcore-11.2.0 11) ScaLAPACK/2.2.0-gompi-2022b-fb => ScaLAPACK/2.1.0-gompi-2021b-fb 12) SciPy-bundle/2023.02-gfbf-2022b => SciPy-bundle/2021.10-foss-2021b 13) Tcl/8.6.12-GCCcore-12.2.0 => Tcl/8.6.11-GCCcore-11.2.0 14) UCX/1.13.1-GCCcore-12.2.0 => UCX/1.11.2-GCCcore-11.2.0 15) XZ/5.2.7-GCCcore-12.2.0 => XZ/5.2.5-GCCcore-11.2.0 16) binutils/2.38-GCCcore-11.3.0 => binutils/2.37-GCCcore-11.2.0 17) bzip2/1.0.8-GCCcore-12.2.0 => bzip2/1.0.8-GCCcore-11.2.0 18) cURL/7.83.0-GCCcore-11.3.0 => cURL/7.78.0-GCCcore-11.2.0 19) foss/2022b => foss/2021b 20) gompi/2022b => gompi/2021b 21) hwloc/2.8.0-GCCcore-12.2.0 => hwloc/2.5.0-GCCcore-11.2.0 22) libevent/2.1.12-GCCcore-12.2.0 => libevent/2.1.12-GCCcore-11.2.0 23) libfabric/1.16.1-GCCcore-12.2.0 => libfabric/1.13.2-GCCcore-11.2.0 24) libffi/3.4.4-GCCcore-12.2.0 => libffi/3.4.2-GCCcore-11.2.0 25) libpciaccess/0.17-GCCcore-12.2.0 => libpciaccess/0.16-GCCcore-11.2.0 26) libreadline/8.2-GCCcore-12.2.0 => libreadline/8.1-GCCcore-11.2.0 27) libxml2/2.10.3-GCCcore-12.2.0 => libxml2/2.9.10-GCCcore-11.2.0 28) ncurses/6.3-GCCcore-12.2.0 => ncurses/6.2-GCCcore-11.2.0 29) numactl/2.0.16-GCCcore-12.2.0 => numactl/2.0.14-GCCcore-11.2.0 30) pybind11/2.10.3-GCCcore-12.2.0 => pybind11/2.7.1-GCCcore-11.2.0 31) zlib/1.2.12-GCCcore-11.3.0 => zlib/1.2.11-GCCcore-11.2.0 ========== featureCount: SS036_01 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_01.sorted.bam || || || || Output file : SS036_01.1.counts || || Summary : SS036_01.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_01.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 10631481 || || Successfully assigned alignments : 442515 (4.2%) || || Running time : 0.13 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_01.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_01.sorted.bam || || || || Output file : SS036_01.2.counts || || Summary : SS036_01.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_01.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 10631481 || || Successfully assigned alignments : 9313265 (87.6%) || || Running time : 0.13 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_01.2.counts.summary" || || || \\============================================================================// ========== featureCount: SS036_02 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_02.sorted.bam || || || || Output file : SS036_02.1.counts || || Summary : SS036_02.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_02.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 9078922 || || Successfully assigned alignments : 445695 (4.9%) || || Running time : 0.11 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_02.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_02.sorted.bam || || || || Output file : SS036_02.2.counts || || Summary : SS036_02.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_02.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 9078922 || || Successfully assigned alignments : 7921167 (87.2%) || || Running time : 0.11 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_02.2.counts.summary" || || || \\============================================================================// ========== featureCount: SS036_03 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_03.sorted.bam || || || || Output file : SS036_03.1.counts || || Summary : SS036_03.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_03.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 8151954 || || Successfully assigned alignments : 154576 (1.9%) || || Running time : 0.10 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_03.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_03.sorted.bam || || || || Output file : SS036_03.2.counts || || Summary : SS036_03.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_03.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 8151954 || || Successfully assigned alignments : 7312783 (89.7%) || || Running time : 0.10 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_03.2.counts.summary" || || || \\============================================================================// ========== featureCount: SS036_04 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_04.sorted.bam || || || || Output file : SS036_04.1.counts || || Summary : SS036_04.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_04.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 8379961 || || Successfully assigned alignments : 164932 (2.0%) || || Running time : 0.10 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_04.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_04.sorted.bam || || || || Output file : SS036_04.2.counts || || Summary : SS036_04.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_04.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 8379961 || || Successfully assigned alignments : 7562715 (90.2%) || || Running time : 0.10 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_04.2.counts.summary" || || || \\============================================================================// ========== featureCount: SS036_05 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_05.sorted.bam || || || || Output file : SS036_05.1.counts || || Summary : SS036_05.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_05.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 9530972 || || Successfully assigned alignments : 200580 (2.1%) || || Running time : 0.11 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_05.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_05.sorted.bam || || || || Output file : SS036_05.2.counts || || Summary : SS036_05.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_05.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 9530972 || || Successfully assigned alignments : 8605681 (90.3%) || || Running time : 0.11 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_05.2.counts.summary" || || || \\============================================================================// ========== featureCount: SS036_06 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_06.sorted.bam || || || || Output file : SS036_06.1.counts || || Summary : SS036_06.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_06.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 9004688 || || Successfully assigned alignments : 218925 (2.4%) || || Running time : 0.11 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_06.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_06.sorted.bam || || || || Output file : SS036_06.2.counts || || Summary : SS036_06.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_06.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 9004688 || || Successfully assigned alignments : 8088010 (89.8%) || || Running time : 0.11 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_06.2.counts.summary" || || || \\============================================================================// ========== featureCount: SS036_07 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_07.sorted.bam || || || || Output file : SS036_07.1.counts || || Summary : SS036_07.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_07.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 10108975 || || Successfully assigned alignments : 224335 (2.2%) || || Running time : 0.12 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_07.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_07.sorted.bam || || || || Output file : SS036_07.2.counts || || Summary : SS036_07.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_07.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 10108975 || || Successfully assigned alignments : 9206114 (91.1%) || || Running time : 0.12 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_07.2.counts.summary" || || || \\============================================================================// ========== featureCount: SS036_08 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_08.sorted.bam || || || || Output file : SS036_08.1.counts || || Summary : SS036_08.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_08.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 10156820 || || Successfully assigned alignments : 362083 (3.6%) || || Running time : 0.12 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_08.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SS036_08.sorted.bam || || || || Output file : SS036_08.2.counts || || Summary : SS036_08.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : Bifidobacterium_adolescentis_LMG.gff (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Sofia_2026_0 ... || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file Bifidobacterium_adolescentis_LMG.gff ... || || Features : 2294 || || Meta-features : 2294 || || Chromosomes/contigs : 1 || || || || Process BAM file SS036_08.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 10156820 || || Successfully assigned alignments : 8989522 (88.5%) || || Running time : 0.12 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "/scratch/p127804/PROJEC || || TS/Douwe/Sofia_2026_036/featureCounts/SS036_08.2.counts.summary" || || || \\============================================================================// SS036_01.1.counts SS036_02.1.counts SS036_03.1.counts SS036_04.1.counts SS036_05.1.counts SS036_06.1.counts SS036_07.1.counts SS036_08.1.counts SS036_01.2.counts SS036_02.2.counts SS036_03.2.counts SS036_04.2.counts SS036_05.2.counts SS036_06.2.counts SS036_07.2.counts SS036_08.2.counts SS036_01.1.rpkm SS036_02.1.rpkm SS036_03.1.rpkm SS036_04.1.rpkm SS036_05.1.rpkm SS036_06.1.rpkm SS036_07.1.rpkm SS036_08.1.rpkm SS036_01.2.rpkm SS036_02.2.rpkm SS036_03.2.rpkm SS036_04.2.rpkm SS036_05.2.rpkm SS036_06.2.rpkm SS036_07.2.rpkm SS036_08.2.rpkm /userapps/hb-molgen/AnneTools/Add_CV.py:30: RuntimeWarning: invalid value encountered in double_scalars cv = lambda x: np.std(x, ddof=1) / np.mean(x) * 100 RangeIndex: 2294 entries, 0 to 2293 Data columns (total 9 columns): # Column Non-Null Count Dtype --- ------ -------------- ----- 0 key 2294 non-null object 1 SS036_01.1.counts 2294 non-null int64 2 SS036_02.1.counts 2294 non-null int64 3 SS036_03.1.counts 2294 non-null int64 4 SS036_04.1.counts 2294 non-null int64 5 SS036_05.1.counts 2294 non-null int64 6 SS036_06.1.counts 2294 non-null int64 7 SS036_07.1.counts 2294 non-null int64 8 SS036_08.1.counts 2294 non-null int64 dtypes: int64(8), object(1) memory usage: 161.4+ KB /userapps/hb-molgen/AnneTools/Add_CV.py:30: RuntimeWarning: invalid value encountered in double_scalars cv = lambda x: np.std(x, ddof=1) / np.mean(x) * 100 RangeIndex: 2294 entries, 0 to 2293 Data columns (total 9 columns): # Column Non-Null Count Dtype --- ------ -------------- ----- 0 key 2294 non-null object 1 SS036_01.2.counts 2294 non-null int64 2 SS036_02.2.counts 2294 non-null int64 3 SS036_03.2.counts 2294 non-null int64 4 SS036_04.2.counts 2294 non-null int64 5 SS036_05.2.counts 2294 non-null int64 6 SS036_06.2.counts 2294 non-null int64 7 SS036_07.2.counts 2294 non-null int64 8 SS036_08.2.counts 2294 non-null int64 dtypes: int64(8), object(1) memory usage: 161.4+ KB /userapps/hb-molgen/AnneTools/Add_CV.py:30: RuntimeWarning: invalid value encountered in double_scalars cv = lambda x: np.std(x, ddof=1) / np.mean(x) * 100 RangeIndex: 2294 entries, 0 to 2293 Data columns (total 9 columns): # Column Non-Null Count Dtype --- ------ -------------- ----- 0 key 2294 non-null object 1 SS036_01.1.rpkm 2294 non-null float64 2 SS036_02.1.rpkm 2294 non-null float64 3 SS036_03.1.rpkm 2294 non-null float64 4 SS036_04.1.rpkm 2294 non-null float64 5 SS036_05.1.rpkm 2294 non-null float64 6 SS036_06.1.rpkm 2294 non-null float64 7 SS036_07.1.rpkm 2294 non-null float64 8 SS036_08.1.rpkm 2294 non-null float64 dtypes: float64(8), object(1) memory usage: 161.4+ KB /userapps/hb-molgen/AnneTools/Add_CV.py:30: RuntimeWarning: invalid value encountered in double_scalars cv = lambda x: np.std(x, ddof=1) / np.mean(x) * 100 RangeIndex: 2294 entries, 0 to 2293 Data columns (total 9 columns): # Column Non-Null Count Dtype --- ------ -------------- ----- 0 key 2294 non-null object 1 SS036_01.2.rpkm 2294 non-null float64 2 SS036_02.2.rpkm 2294 non-null float64 3 SS036_03.2.rpkm 2294 non-null float64 4 SS036_04.2.rpkm 2294 non-null float64 5 SS036_05.2.rpkm 2294 non-null float64 6 SS036_06.2.rpkm 2294 non-null float64 7 SS036_07.2.rpkm 2294 non-null float64 8 SS036_08.2.rpkm 2294 non-null float64 dtypes: float64(8), object(1) memory usage: 161.4+ KB ========== DeepTools: SS036_01 ====================================== normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_01.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: forward Offset: [1, -1] Due to filtering, 23.079257687928532% of the aforementioned alignments will be used 2453666.8960331613 normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_01.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: reverse Offset: [1, -1] Due to filtering, 76.92074231207147% of the aforementioned alignments will be used 8177814.103966839 ========== DeepTools: SS036_02 ====================================== normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_02.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: forward Offset: [1, -1] Due to filtering, 24.16047968138705% of the aforementioned alignments will be used 2193511.1050989786 normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_02.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: reverse Offset: [1, -1] Due to filtering, 75.83952031861295% of the aforementioned alignments will be used 6885410.894901021 ========== DeepTools: SS036_03 ====================================== normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_03.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: forward Offset: [1, -1] Due to filtering, 25.927493508236054% of the aforementioned alignments will be used 2113597.3441443895 normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_03.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: reverse Offset: [1, -1] Due to filtering, 74.07250649176395% of the aforementioned alignments will be used 6038356.655855611 ========== DeepTools: SS036_04 ====================================== normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_04.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: forward Offset: [1, -1] Due to filtering, 26.480049203437705% of the aforementioned alignments will be used 2219017.79602889 normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_04.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: reverse Offset: [1, -1] Due to filtering, 73.51995079656228% of the aforementioned alignments will be used 6160943.203971108 ========== DeepTools: SS036_05 ====================================== normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_05.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: forward Offset: [1, -1] Due to filtering, 24.64221511451451% of the aforementioned alignments will be used 2348642.622744146 normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_05.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: reverse Offset: [1, -1] Due to filtering, 75.35778488548549% of the aforementioned alignments will be used 7182329.377255854 ========== DeepTools: SS036_06 ====================================== normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_06.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: forward Offset: [1, -1] Due to filtering, 26.77067345433236% of the aforementioned alignments will be used 2410615.6200614516 normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_06.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: reverse Offset: [1, -1] Due to filtering, 73.22932654566765% of the aforementioned alignments will be used 6594072.379938549 ========== DeepTools: SS036_07 ====================================== normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_07.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: forward Offset: [1, -1] Due to filtering, 25.33149990456396% of the aforementioned alignments will be used 2560754.9924773946 normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_07.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: reverse Offset: [1, -1] Due to filtering, 74.66850009543604% of the aforementioned alignments will be used 7548220.007522605 ========== DeepTools: SS036_08 ====================================== normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_08.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: forward Offset: [1, -1] Due to filtering, 27.473457926784327% of the aforementioned alignments will be used 2790429.669399216 normalization: RPKM bamFilesList: ['/scratch/p127804/PROJECTS/Douwe/Sofia_2026_036/bam/SS036_08.sorted.bam'] binLength: 10 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 10 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: 30 save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: reverse Offset: [1, -1] Due to filtering, 72.52654207321567% of the aforementioned alignments will be used 7366390.330600784 ############################################################################### Hábrók Cluster Job 30963766 for user p127804 Finished at: Sun Aug 30 14:53:34 CEST 2026 Job details: ============ Job ID : 30963766 Name : featureCounts User : p127804 Partition : regularmedium Nodes : omni3 Number of Nodes : 1 Cores : 32 Number of Tasks : 1 State : COMPLETED Submit : 2026-08-30T13:24:38 Start : 2026-08-30T13:24:39 End : 2026-08-30T14:53:30 Reserved walltime : 1-00:00:00 Used walltime : 01:28:51 Used CPU time : 01:28:13 (Efficiency: 3.10%) % User (Computation) : 99.77% % System (I/O) : 0.23% Total memory reserved : 8G Maximum memory used : 1.97G Hints and tips : 1) The program efficiency is very low. Your program does not seem to run in parallel. Please check the program documentation to see how to make the program run in parallel. If you can't find information about this, the program will not run in parallel! Stop requesting multiple CPU cores if that is the case. *) For more information on these issues see: https://wiki.hpc.rug.nl/habrok/additional_information/job_hints Acknowledgements: ================= Please see this page for information about acknowledging Hábrók in your publications: https://wiki.hpc.rug.nl/habrok/introduction/scientific_output ################################################################################