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: ZH018_01 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_01.sorted.bam || || || || Output file : ZH018_01.1.counts || || Summary : ZH018_01.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_01.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 7139132 || || Successfully assigned alignments : 153140 (2.1%) || || Running time : 0.08 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/Zhe/results_Zhe/ZH018_01.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_01.sorted.bam || || || || Output file : ZH018_01.2.counts || || Summary : ZH018_01.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_01.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 7139132 || || Successfully assigned alignments : 6704707 (93.9%) || || Running time : 0.08 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/Zhe/results_Zhe/ZH018_01.2.counts.summary" || || || \\============================================================================// sed: can't read /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_01.counts: No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory ========== featureCount: ZH018_02 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_02.sorted.bam || || || || Output file : ZH018_02.1.counts || || Summary : ZH018_02.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_02.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 8183300 || || Successfully assigned alignments : 178136 (2.2%) || || Running time : 0.09 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/Zhe/results_Zhe/ZH018_02.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_02.sorted.bam || || || || Output file : ZH018_02.2.counts || || Summary : ZH018_02.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_02.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 8183300 || || Successfully assigned alignments : 7733821 (94.5%) || || Running time : 0.09 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/Zhe/results_Zhe/ZH018_02.2.counts.summary" || || || \\============================================================================// sed: can't read /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_02.counts: No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory ========== featureCount: ZH018_03 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_03.sorted.bam || || || || Output file : ZH018_03.1.counts || || Summary : ZH018_03.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_03.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 7935946 || || Successfully assigned alignments : 791200 (10.0%) || || Running time : 0.09 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/Zhe/results_Zhe/ZH018_03.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_03.sorted.bam || || || || Output file : ZH018_03.2.counts || || Summary : ZH018_03.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_03.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 7935946 || || Successfully assigned alignments : 6381109 (80.4%) || || Running time : 0.09 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/Zhe/results_Zhe/ZH018_03.2.counts.summary" || || || \\============================================================================// sed: can't read /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_03.counts: No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory ========== featureCount: ZH018_04 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_04.sorted.bam || || || || Output file : ZH018_04.1.counts || || Summary : ZH018_04.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_04.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 7678937 || || Successfully assigned alignments : 699444 (9.1%) || || Running time : 0.09 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/Zhe/results_Zhe/ZH018_04.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_04.sorted.bam || || || || Output file : ZH018_04.2.counts || || Summary : ZH018_04.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_04.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 7678937 || || Successfully assigned alignments : 6376269 (83.0%) || || Running time : 0.09 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/Zhe/results_Zhe/ZH018_04.2.counts.summary" || || || \\============================================================================// sed: can't read /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_04.counts: No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory ========== featureCount: ZH018_05 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_05.sorted.bam || || || || Output file : ZH018_05.1.counts || || Summary : ZH018_05.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_05.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 9822934 || || Successfully assigned alignments : 270016 (2.7%) || || 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/Zhe/results_Zhe/ZH018_05.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_05.sorted.bam || || || || Output file : ZH018_05.2.counts || || Summary : ZH018_05.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_05.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 9822934 || || Successfully assigned alignments : 9280011 (94.5%) || || 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/Zhe/results_Zhe/ZH018_05.2.counts.summary" || || || \\============================================================================// sed: can't read /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_05.counts: No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory ========== featureCount: ZH018_06 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_06.sorted.bam || || || || Output file : ZH018_06.1.counts || || Summary : ZH018_06.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_06.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 7519389 || || Successfully assigned alignments : 181829 (2.4%) || || Running time : 0.08 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/Zhe/results_Zhe/ZH018_06.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_06.sorted.bam || || || || Output file : ZH018_06.2.counts || || Summary : ZH018_06.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_06.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 7519389 || || Successfully assigned alignments : 7139873 (95.0%) || || Running time : 0.08 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/Zhe/results_Zhe/ZH018_06.2.counts.summary" || || || \\============================================================================// sed: can't read /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_06.counts: No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory ========== featureCount: ZH018_07 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_07.sorted.bam || || || || Output file : ZH018_07.1.counts || || Summary : ZH018_07.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_07.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 7599759 || || Successfully assigned alignments : 408658 (5.4%) || || Running time : 0.09 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/Zhe/results_Zhe/ZH018_07.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_07.sorted.bam || || || || Output file : ZH018_07.2.counts || || Summary : ZH018_07.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_07.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 7599759 || || Successfully assigned alignments : 6843217 (90.0%) || || Running time : 0.09 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/Zhe/results_Zhe/ZH018_07.2.counts.summary" || || || \\============================================================================// sed: can't read /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_07.counts: No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory ========== featureCount: ZH018_08 ====================================== ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_08.sorted.bam || || || || Output file : ZH018_08.1.counts || || Summary : ZH018_08.1.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_08.sorted.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 7396048 || || Successfully assigned alignments : 342222 (4.6%) || || Running time : 0.09 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/Zhe/results_Zhe/ZH018_08.1.counts.summary" || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.4 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || ZH018_08.sorted.bam || || || || Output file : ZH018_08.2.counts || || Summary : ZH018_08.2.counts.summary || || Paired-end : no || || Count read pairs : no || || Annotation : co-culture.gff3 (GTF) || || Dir for temp files : /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file co-culture.gff3 ... || || Features : 3959 || || Meta-features : 3959 || || Chromosomes/contigs : 2 || || || || Process BAM file ZH018_08.sorted.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 7396048 || || Successfully assigned alignments : 6723119 (90.9%) || || Running time : 0.08 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/Zhe/results_Zhe/ZH018_08.2.counts.summary" || || || \\============================================================================// sed: can't read /scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_08.counts: No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory python3: can't open file '/userapps/hb-molgen/AnneTools/rnaseq/Counts_Convert.py': [Errno 2] No such file or directory ZH018_01.1.counts ZH018_02.1.counts ZH018_03.1.counts ZH018_04.1.counts ZH018_05.1.counts ZH018_06.1.counts ZH018_07.1.counts ZH018_08.1.counts ZH018_01.2.counts ZH018_02.2.counts ZH018_03.2.counts ZH018_04.2.counts ZH018_05.2.counts ZH018_06.2.counts ZH018_07.2.counts ZH018_08.2.counts /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: 3959 entries, 0 to 3958 Data columns (total 9 columns): # Column Non-Null Count Dtype --- ------ -------------- ----- 0 key 3959 non-null object 1 ZH018_01.1.counts 3959 non-null int64 2 ZH018_02.1.counts 3959 non-null int64 3 ZH018_03.1.counts 3959 non-null int64 4 ZH018_04.1.counts 3959 non-null int64 5 ZH018_05.1.counts 3959 non-null int64 6 ZH018_06.1.counts 3959 non-null int64 7 ZH018_07.1.counts 3959 non-null int64 8 ZH018_08.1.counts 3959 non-null int64 dtypes: int64(8), object(1) memory usage: 278.5+ 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: 3959 entries, 0 to 3958 Data columns (total 9 columns): # Column Non-Null Count Dtype --- ------ -------------- ----- 0 key 3959 non-null object 1 ZH018_01.2.counts 3959 non-null int64 2 ZH018_02.2.counts 3959 non-null int64 3 ZH018_03.2.counts 3959 non-null int64 4 ZH018_04.2.counts 3959 non-null int64 5 ZH018_05.2.counts 3959 non-null int64 6 ZH018_06.2.counts 3959 non-null int64 7 ZH018_07.2.counts 3959 non-null int64 8 ZH018_08.2.counts 3959 non-null int64 dtypes: int64(8), object(1) memory usage: 278.5+ KB Traceback (most recent call last): File "/userapps/hb-molgen/AnneTools/Add_CV.py", line 33, in table = pd.read_csv(args.sessiondir + '/' + args.query, comment='#', sep='\t') File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv return _read(filepath_or_buffer, kwds) File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 482, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 811, in __init__ self._engine = self._make_engine(self.engine) File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1040, in _make_engine return mapping[engine](self.f, **self.options) # type: ignore[call-arg] File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 69, in __init__ self._reader = parsers.TextReader(self.handles.handle, **kwds) File "pandas/_libs/parsers.pyx", line 549, in pandas._libs.parsers.TextReader.__cinit__ pandas.errors.EmptyDataError: No columns to parse from file Traceback (most recent call last): File "/userapps/hb-molgen/AnneTools/Add_CV.py", line 33, in table = pd.read_csv(args.sessiondir + '/' + args.query, comment='#', sep='\t') File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv return _read(filepath_or_buffer, kwds) File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 482, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 811, in __init__ self._engine = self._make_engine(self.engine) File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1040, in _make_engine return mapping[engine](self.f, **self.options) # type: ignore[call-arg] File "/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 69, in __init__ self._reader = parsers.TextReader(self.handles.handle, **kwds) File "pandas/_libs/parsers.pyx", line 549, in pandas._libs.parsers.TextReader.__cinit__ pandas.errors.EmptyDataError: No columns to parse from file ========== DeepTools: ZH018_01DS018_01_M1 ====================================== [E::hts_open_format] Failed to open file "/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_01DS018_01_M1.sorted.bam" : No such file or directory The file '/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_01DS018_01_M1.sorted.bam' does not exist ========== DeepTools: ZH018_02DS018_02_D1 ====================================== [E::hts_open_format] Failed to open file "/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_02DS018_02_D1.sorted.bam" : No such file or directory The file '/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_02DS018_02_D1.sorted.bam' does not exist ========== DeepTools: ZH018_03DS018_03_B1 ====================================== [E::hts_open_format] Failed to open file "/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_03DS018_03_B1.sorted.bam" : No such file or directory The file '/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_03DS018_03_B1.sorted.bam' does not exist ========== DeepTools: ZH018_04DS018_05_M3 ====================================== [E::hts_open_format] Failed to open file "/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_04DS018_05_M3.sorted.bam" : No such file or directory The file '/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_04DS018_05_M3.sorted.bam' does not exist ========== DeepTools: ZH018_05DS018_06_D3 ====================================== [E::hts_open_format] Failed to open file "/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_05DS018_06_D3.sorted.bam" : No such file or directory The file '/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_05DS018_06_D3.sorted.bam' does not exist ========== DeepTools: ZH018_06DS018_07_B3 ====================================== [E::hts_open_format] Failed to open file "/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_06DS018_07_B3.sorted.bam" : No such file or directory The file '/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_06DS018_07_B3.sorted.bam' does not exist ========== DeepTools: ZH018_07DS018_08_P3 ====================================== [E::hts_open_format] Failed to open file "/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_07DS018_08_P3.sorted.bam" : No such file or directory The file '/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_07DS018_08_P3.sorted.bam' does not exist ========== DeepTools: ZH018_08DS018_09_M4 ====================================== [E::hts_open_format] Failed to open file "/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_08DS018_09_M4.sorted.bam" : No such file or directory The file '/scratch/p127804/PROJECTS/Douwe/Zhe/results_Zhe/ZH018_08DS018_09_M4.sorted.bam' does not exist ############################################################################### Hábrók Cluster Job 12421173 for user p127804 Finished at: Mon Aug 12 10:31:01 CEST 2024 Job details: ============ Job ID : 12421173 Name : featureCounts User : p127804 Partition : regularmedium Nodes : node2 Number of Nodes : 1 Cores : 2 Number of Tasks : 1 State : RUNNING,FAILED Submit : 2024-08-12T10:29:13 Start : 2024-08-12T10:29:14 End : -- Reserved walltime : 1-00:00:00 Used walltime : 00:01:47 Used CPU time : 00:01:38 (Efficiency: 45.85%) % User (Computation) : 94.86% % System (I/O) : 5.14% Total memory reserved : 8G Maximum memory used : 19.36M Acknowledgements: ================= Please see this page for information about acknowledging Hábrók in your publications: https://wiki.hpc.rug.nl/habrok/introduction/scientific_output ################################################################################