==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
	  v2.0.5

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 79 BAM files                                     ||
||                                                                            ||
||                           100.sorted.bam                                   ||
||                           107.sorted.bam                                   ||
||                           108.sorted.bam                                   ||
||                           109.sorted.bam                                   ||
||                           10.sorted.bam                                    ||
||                           110.sorted.bam                                   ||
||                           117.sorted.bam                                   ||
||                           118.sorted.bam                                   ||
||                           119.sorted.bam                                   ||
||                           11.sorted.bam                                    ||
||                           120.sorted.bam                                   ||
||                           121.sorted.bam                                   ||
||                           127.sorted.bam                                   ||
||                           128.sorted.bam                                   ||
||                           129.sorted.bam                                   ||
||                           12.sorted.bam                                    ||
||                           131.sorted.bam                                   ||
||                           137.sorted.bam                                   ||
||                           138.sorted.bam                                   ||
||                           139.sorted.bam                                   ||
||                           13.sorted.bam                                    ||
||                           140.sorted.bam                                   ||
||                           147.sorted.bam                                   ||
||                           148.sorted.bam                                   ||
||                           149.sorted.bam                                   ||
||                           150.sorted.bam                                   ||
||                           18.sorted.bam                                    ||
||                           19-G.sorted.bam                                  ||
||                           19.sorted.bam                                    ||
||                           19-S.sorted.bam                                  ||
||                           1.sorted.bam                                     ||
||                           20-G.sorted.bam                                  ||
||                           20.sorted.bam                                    ||
||                           20-S.sorted.bam                                  ||
||                           21.sorted.bam                                    ||
||                           28.sorted.bam                                    ||
||                           29.sorted.bam                                    ||
||                           2.sorted.bam                                     ||
||                           30.sorted.bam                                    ||
||                           31.sorted.bam                                    ||
||                           37.sorted.bam                                    ||
||                           38.sorted.bam                                    ||
||                           39.sorted.bam                                    ||
||                           3.sorted.bam                                     ||
||                           40.sorted.bam                                    ||
||                           41.sorted.bam                                    ||
||                           47.sorted.bam                                    ||
||                           48.sorted.bam                                    ||
||                           49.sorted.bam                                    ||
||                           4.sorted.bam                                     ||
||                           50.sorted.bam                                    ||
||                           57-G.sorted.bam                                  ||
||                           57.sorted.bam                                    ||
||                           57-S.sorted.bam                                  ||
||                           58-G.sorted.bam                                  ||
||                           58.sorted.bam                                    ||
||                           58-S.sorted.bam                                  ||
||                           59.sorted.bam                                    ||
||                           5.sorted.bam                                     ||
||                           60.sorted.bam                                    ||
||                           67.sorted.bam                                    ||
||                           68.sorted.bam                                    ||
||                           69.sorted.bam                                    ||
||                           70.sorted.bam                                    ||
||                           78.sorted.bam                                    ||
||                           79.sorted.bam                                    ||
||                           80.sorted.bam                                    ||
||                           83.sorted.bam                                    ||
||                           88.sorted.bam                                    ||
||                           90.sorted.bam                                    ||
||                           91.sorted.bam                                    ||
||                           97.sorted.bam                                    ||
||                           98.sorted.bam                                    ||
||                           99.sorted.bam                                    ||
||                           RESUB-116.sorted.bam                             ||
||                           RESUB-156.sorted.bam                             ||
||                           RESUB-36.sorted.bam                              ||
||                           RESUB-76.sorted.bam                              ||
||                           RESUB-94.sorted.bam                              ||
||                                                                            ||
||             Output file : featureCounts_matrix.txt                         ||
||                 Summary : featureCounts_matrix.txt.summary                 ||
||              Paired-end : yes                                              ||
||        Count read pairs : yes                                              ||
||              Annotation : genomic.gtf (GTF)                                ||
||      Dir for temp files : ../output/06.2-cod-RNAseq-alignment-genome       ||
||                                                                            ||
||                 Threads : 5                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : not counted                                      ||
|| Multi-overlapping reads : not counted                                      ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file genomic.gtf ...                                       ||
||    Features : 607074                                                       ||
||    Meta-features : 30325                                                   ||
||    Chromosomes/contigs : 24                                                ||
||                                                                            ||
|| Process BAM file 100.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 19056065                                             ||
||    Successfully assigned alignments : 12785884 (67.1%)                     ||
||    Running time : 0.24 minutes                                             ||
||                                                                            ||
|| Process BAM file 107.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 17448988                                             ||
||    Successfully assigned alignments : 11851525 (67.9%)                     ||
||    Running time : 0.25 minutes                                             ||
||                                                                            ||
|| Process BAM file 108.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 24175927                                             ||
||    Successfully assigned alignments : 14080082 (58.2%)                     ||
||    Running time : 0.33 minutes                                             ||
||                                                                            ||
|| Process BAM file 109.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 23613208                                             ||
||    Successfully assigned alignments : 15231173 (64.5%)                     ||
||    Running time : 0.38 minutes                                             ||
||                                                                            ||
|| Process BAM file 10.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 20762104                                             ||
||    Successfully assigned alignments : 12870827 (62.0%)                     ||
||    Running time : 0.29 minutes                                             ||
||                                                                            ||
|| Process BAM file 110.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 22233111                                             ||
||    Successfully assigned alignments : 15465906 (69.6%)                     ||
||    Running time : 0.45 minutes                                             ||
||                                                                            ||
|| Process BAM file 117.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 23609108                                             ||
||    Successfully assigned alignments : 15429859 (65.4%)                     ||
||    Running time : 0.33 minutes                                             ||
||                                                                            ||
|| Process BAM file 118.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 22372646                                             ||
||    Successfully assigned alignments : 15081945 (67.4%)                     ||
||    Running time : 0.34 minutes                                             ||
||                                                                            ||
|| Process BAM file 119.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 23007987                                             ||
||    Successfully assigned alignments : 16523114 (71.8%)                     ||
||    Running time : 0.36 minutes                                             ||
||                                                                            ||
|| Process BAM file 11.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 22428165                                             ||
||    Successfully assigned alignments : 15155871 (67.6%)                     ||
||    Running time : 0.34 minutes                                             ||
||                                                                            ||
|| Process BAM file 120.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 21694475                                             ||
||    Successfully assigned alignments : 14475732 (66.7%)                     ||
||    Running time : 0.31 minutes                                             ||
||                                                                            ||
|| Process BAM file 121.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 21918022                                             ||
||    Successfully assigned alignments : 11763976 (53.7%)                     ||
||    Running time : 0.34 minutes                                             ||
||                                                                            ||
|| Process BAM file 127.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 24409366                                             ||
||    Successfully assigned alignments : 15976812 (65.5%)                     ||
||    Running time : 0.37 minutes                                             ||
||                                                                            ||
|| Process BAM file 128.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 10218416                                             ||
||    Successfully assigned alignments : 6659412 (65.2%)                      ||
||    Running time : 0.15 minutes                                             ||
||                                                                            ||
|| Process BAM file 129.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 16734359                                             ||
||    Successfully assigned alignments : 2671177 (16.0%)                      ||
||    Running time : 0.32 minutes                                             ||
||                                                                            ||
|| Process BAM file 12.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 21591148                                             ||
||    Successfully assigned alignments : 13754085 (63.7%)                     ||
||    Running time : 0.31 minutes                                             ||
||                                                                            ||
|| Process BAM file 131.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 9657596                                              ||
||    Successfully assigned alignments : 5993480 (62.1%)                      ||
||    Running time : 0.14 minutes                                             ||
||                                                                            ||
|| Process BAM file 137.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 8553067                                              ||
||    Successfully assigned alignments : 5525084 (64.6%)                      ||
||    Running time : 0.13 minutes                                             ||
||                                                                            ||
|| Process BAM file 138.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 8652287                                              ||
||    Successfully assigned alignments : 5733285 (66.3%)                      ||
||    Running time : 0.15 minutes                                             ||
||                                                                            ||
|| Process BAM file 139.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 10110465                                             ||
||    Successfully assigned alignments : 6807522 (67.3%)                      ||
||    Running time : 0.15 minutes                                             ||
||                                                                            ||
|| Process BAM file 13.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 19435103                                             ||
||    Successfully assigned alignments : 11548888 (59.4%)                     ||
||    Running time : 0.27 minutes                                             ||
||                                                                            ||
|| Process BAM file 140.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 9800309                                              ||
||    Successfully assigned alignments : 6577903 (67.1%)                      ||
||    Running time : 0.14 minutes                                             ||
||                                                                            ||
|| Process BAM file 147.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 8907043                                              ||
||    Successfully assigned alignments : 5796024 (65.1%)                      ||
||    Running time : 0.13 minutes                                             ||
||                                                                            ||
|| Process BAM file 148.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 25915417                                             ||
||    Successfully assigned alignments : 15203087 (58.7%)                     ||
||    Running time : 0.35 minutes                                             ||
||                                                                            ||
|| Process BAM file 149.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 131957289                                            ||
||    Successfully assigned alignments : 47148428 (35.7%)                     ||
||    Running time : 5.45 minutes                                             ||
||                                                                            ||
|| Process BAM file 150.sorted.bam...                                         ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 28770130                                             ||
||    Successfully assigned alignments : 16582080 (57.6%)                     ||
||    Running time : 0.38 minutes                                             ||
||                                                                            ||
|| Process BAM file 18.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 18678898                                             ||
||    Successfully assigned alignments : 11519670 (61.7%)                     ||
||    Running time : 0.26 minutes                                             ||
||                                                                            ||
|| Process BAM file 19-G.sorted.bam...                                        ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 23227727                                             ||
||    Successfully assigned alignments : 14345804 (61.8%)                     ||
||    Running time : 0.30 minutes                                             ||
||                                                                            ||
|| Process BAM file 19.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 18482829                                             ||
||    Successfully assigned alignments : 12075354 (65.3%)                     ||
||    Running time : 0.27 minutes                                             ||
||                                                                            ||
|| Process BAM file 19-S.sorted.bam...                                        ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 25521079                                             ||
||    Successfully assigned alignments : 16367643 (64.1%)                     ||
||    Running time : 0.35 minutes                                             ||
||                                                                            ||
|| Process BAM file 1.sorted.bam...                                           ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 21765153                                             ||
||    Successfully assigned alignments : 14423095 (66.3%)                     ||
||    Running time : 0.31 minutes                                             ||
||                                                                            ||
|| Process BAM file 20-G.sorted.bam...                                        ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 24522014                                             ||
||    Successfully assigned alignments : 15303048 (62.4%)                     ||
||    Running time : 0.31 minutes                                             ||
||                                                                            ||
|| Process BAM file 20.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 18812942                                             ||
||    Successfully assigned alignments : 10664805 (56.7%)                     ||
||    Running time : 0.28 minutes                                             ||
||                                                                            ||
|| Process BAM file 20-S.sorted.bam...                                        ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 17551460                                             ||
||    Successfully assigned alignments : 10699955 (61.0%)                     ||
||    Running time : 0.24 minutes                                             ||
||                                                                            ||
|| Process BAM file 21.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 18598362                                             ||
||    Successfully assigned alignments : 11420526 (61.4%)                     ||
||    Running time : 0.26 minutes                                             ||
||                                                                            ||
|| Process BAM file 28.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 19634032                                             ||
||    Successfully assigned alignments : 12983935 (66.1%)                     ||
||    Running time : 0.28 minutes                                             ||
||                                                                            ||
|| Process BAM file 29.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 19871083                                             ||
||    Successfully assigned alignments : 11807229 (59.4%)                     ||
||    Running time : 0.28 minutes                                             ||
||                                                                            ||
|| Process BAM file 2.sorted.bam...                                           ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 20241520                                             ||
||    Successfully assigned alignments : 14125489 (69.8%)                     ||
||    Running time : 0.31 minutes                                             ||
||                                                                            ||
|| Process BAM file 30.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 20599422                                             ||
||    Successfully assigned alignments : 13409757 (65.1%)                     ||
||    Running time : 0.29 minutes                                             ||
||                                                                            ||
|| Process BAM file 31.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 19327655                                             ||
||    Successfully assigned alignments : 13162134 (68.1%)                     ||
||    Running time : 0.32 minutes                                             ||
||                                                                            ||
|| Process BAM file 37.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 16548192                                             ||
||    Successfully assigned alignments : 11027236 (66.6%)                     ||
||    Running time : 0.23 minutes                                             ||
||                                                                            ||
|| Process BAM file 38.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 20471986                                             ||
||    Successfully assigned alignments : 11426770 (55.8%)                     ||
||    Running time : 0.31 minutes                                             ||
||                                                                            ||
|| Process BAM file 39.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 18384218                                             ||
||    Successfully assigned alignments : 11682057 (63.5%)                     ||
||    Running time : 0.26 minutes                                             ||
||                                                                            ||
|| Process BAM file 3.sorted.bam...                                           ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 22011011                                             ||
||    Successfully assigned alignments : 13311366 (60.5%)                     ||
||    Running time : 0.32 minutes                                             ||
||                                                                            ||
|| Process BAM file 40.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 19169942                                             ||
||    Successfully assigned alignments : 9933536 (51.8%)                      ||
||    Running time : 0.30 minutes                                             ||
||                                                                            ||
|| Process BAM file 41.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 21009298                                             ||
||    Successfully assigned alignments : 8284903 (39.4%)                      ||
||    Running time : 0.40 minutes                                             ||
||                                                                            ||
|| Process BAM file 47.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 19230750                                             ||
||    Successfully assigned alignments : 12610946 (65.6%)                     ||
||    Running time : 0.26 minutes                                             ||
||                                                                            ||
|| Process BAM file 48.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 20717574                                             ||
||    Successfully assigned alignments : 12942663 (62.5%)                     ||
||    Running time : 0.32 minutes                                             ||
||                                                                            ||
|| Process BAM file 49.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 20720518                                             ||
||    Successfully assigned alignments : 13466176 (65.0%)                     ||
||    Running time : 0.27 minutes                                             ||
||                                                                            ||
|| Process BAM file 4.sorted.bam...                                           ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 21469331                                             ||
||    Successfully assigned alignments : 13796524 (64.3%)                     ||
||    Running time : 0.35 minutes                                             ||
||                                                                            ||
|| Process BAM file 50.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 19414477                                             ||
||    Successfully assigned alignments : 12832153 (66.1%)                     ||
||    Running time : 0.26 minutes                                             ||
||                                                                            ||
|| Process BAM file 57-G.sorted.bam...                                        ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 29264834                                             ||
||    Successfully assigned alignments : 19163066 (65.5%)                     ||
||    Running time : 0.36 minutes                                             ||
||                                                                            ||
|| Process BAM file 57.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 20397646                                             ||
||    Successfully assigned alignments : 13780768 (67.6%)                     ||
||    Running time : 0.28 minutes                                             ||
||                                                                            ||
|| Process BAM file 57-S.sorted.bam...                                        ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 16136380                                             ||
||    Successfully assigned alignments : 3865255 (24.0%)                      ||
||    Running time : 0.20 minutes                                             ||
||                                                                            ||
|| Process BAM file 58-G.sorted.bam...                                        ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 29735701                                             ||
||    Successfully assigned alignments : 19510315 (65.6%)                     ||
||    Running time : 0.37 minutes                                             ||
||                                                                            ||
|| Process BAM file 58.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 20487137                                             ||
||    Successfully assigned alignments : 12498968 (61.0%)                     ||
||    Running time : 0.29 minutes                                             ||
||                                                                            ||
|| Process BAM file 58-S.sorted.bam...                                        ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 16401618                                             ||
||    Successfully assigned alignments : 8900828 (54.3%)                      ||
||    Running time : 0.20 minutes                                             ||
||                                                                            ||
|| Process BAM file 59.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 19048905                                             ||
||    Successfully assigned alignments : 12976245 (68.1%)                     ||
||    Running time : 0.31 minutes                                             ||
||                                                                            ||
|| Process BAM file 5.sorted.bam...                                           ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 21251023                                             ||
||    Successfully assigned alignments : 13435072 (63.2%)                     ||
||    Running time : 0.31 minutes                                             ||
||                                                                            ||
|| Process BAM file 60.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 21401853                                             ||
||    Successfully assigned alignments : 13737507 (64.2%)                     ||
||    Running time : 0.29 minutes                                             ||
||                                                                            ||
|| Process BAM file 67.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 21630139                                             ||
||    Successfully assigned alignments : 14120493 (65.3%)                     ||
||    Running time : 0.31 minutes                                             ||
||                                                                            ||
|| Process BAM file 68.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 21466687                                             ||
||    Successfully assigned alignments : 13669203 (63.7%)                     ||
||    Running time : 0.30 minutes                                             ||
||                                                                            ||
|| Process BAM file 69.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 18046197                                             ||
||    Successfully assigned alignments : 11708441 (64.9%)                     ||
||    Running time : 0.24 minutes                                             ||
||                                                                            ||
|| Process BAM file 70.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 15964922                                             ||
||    Successfully assigned alignments : 10064696 (63.0%)                     ||
||    Running time : 0.21 minutes                                             ||
||                                                                            ||
|| Process BAM file 78.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 19569864                                             ||
||    Successfully assigned alignments : 12078556 (61.7%)                     ||
||    Running time : 0.27 minutes                                             ||
||                                                                            ||
|| Process BAM file 79.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 19833963                                             ||
||    Successfully assigned alignments : 13288089 (67.0%)                     ||
||    Running time : 0.29 minutes                                             ||
||                                                                            ||
|| Process BAM file 80.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 15559637                                             ||
||    Successfully assigned alignments : 9854137 (63.3%)                      ||
||    Running time : 0.21 minutes                                             ||
||                                                                            ||
|| Process BAM file 83.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 17069371                                             ||
||    Successfully assigned alignments : 11595086 (67.9%)                     ||
||    Running time : 0.21 minutes                                             ||
||                                                                            ||
|| Process BAM file 88.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 21410137                                             ||
||    Successfully assigned alignments : 10833097 (50.6%)                     ||
||    Running time : 0.25 minutes                                             ||
||                                                                            ||
|| Process BAM file 90.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 19308153                                             ||
||    Successfully assigned alignments : 11152940 (57.8%)                     ||
||    Running time : 0.22 minutes                                             ||
||                                                                            ||
|| Process BAM file 91.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 21252742                                             ||
||    Successfully assigned alignments : 13538803 (63.7%)                     ||
||    Running time : 0.25 minutes                                             ||
||                                                                            ||
|| Process BAM file 97.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 18633632                                             ||
||    Successfully assigned alignments : 12058202 (64.7%)                     ||
||    Running time : 0.26 minutes                                             ||
||                                                                            ||
|| Process BAM file 98.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 25211921                                             ||
||    Successfully assigned alignments : 13169988 (52.2%)                     ||
||    Running time : 0.37 minutes                                             ||
||                                                                            ||
|| Process BAM file 99.sorted.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 18148493                                             ||
||    Successfully assigned alignments : 10860632 (59.8%)                     ||
||    Running time : 0.21 minutes                                             ||
||                                                                            ||
|| Process BAM file RESUB-116.sorted.bam...                                   ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 16796901                                             ||
||    Successfully assigned alignments : 11345911 (67.5%)                     ||
||    Running time : 0.19 minutes                                             ||
||                                                                            ||
|| Process BAM file RESUB-156.sorted.bam...                                   ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 17152165                                             ||
||    Successfully assigned alignments : 11813894 (68.9%)                     ||
||    Running time : 0.20 minutes                                             ||
||                                                                            ||
|| Process BAM file RESUB-36.sorted.bam...                                    ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 15464864                                             ||
||    Successfully assigned alignments : 10939275 (70.7%)                     ||
||    Running time : 0.20 minutes                                             ||
||                                                                            ||
|| Process BAM file RESUB-76.sorted.bam...                                    ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 15231638                                             ||
||    Successfully assigned alignments : 9925831 (65.2%)                      ||
||    Running time : 0.16 minutes                                             ||
||                                                                            ||
|| Process BAM file RESUB-94.sorted.bam...                                    ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 17516764                                             ||
||    Successfully assigned alignments : 12015596 (68.6%)                     ||
||    Running time : 0.20 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
|| Summary of counting results can be found in file "../output/06.2-cod-RNAs  ||
|| eq-alignment-genome/featureCounts_matrix.txt.summary"                      ||
||                                                                            ||
\\============================================================================//