[bam_sort_core] merging from 15 files...

        ==========     _____ _    _ ____  _____  ______          _____  
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          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
	v1.4.6-p5

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P PB_M3_sorted.bam                               ||
||                                                                            ||
||             Output file : PB_M3_featureCounts.out                          ||
||             Annotations : genes.gtf (GTF)                                  ||
||                                                                            ||
||                 Threads : 16                                               ||
||                   Level : meta-feature level                               ||
||              Paired-end : yes                                              ||
||         Strand specific : no                                               ||
||      Multimapping reads : not counted                                      ||
|| Multi-overlapping reads : not counted                                      ||
||       Read orientations : fr                                               ||
||                                                                            ||
||          Chimeric reads : counted                                          ||
||        Both ends mapped : not required                                     ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file genes.gtf ...                                         ||
||    Features : 173784                                                       ||
||    Meta-features : 17337                                                   ||
||    Chromosomes/contigs : 61                                                ||
||                                                                            ||
|| Process BAM file PB_M3_sorted.bam...                                       ||
||    Paired-end reads are included.                                          ||
||    Assign fragments (read pairs) to features...                            ||
||    Found reads that are not properly paired.                               ||
||    (missing mate or the mate is not the next read)                         ||
||    Below are the two reads that are not properly paired:                   ||
||       SRR1177996.4   73   chr4   161811849   50   101M   *   0   0   N     ||
||       #   NH:i:1                                                           ||
||       SRR1177996.5   99   chr14   46643586   50   101M   =   46643759   2  ||
||       74   N   #   NH:i:1                                                  ||
||    2956414 reads have missing mates.                                       ||
||    Input was converted to a format accepted by featureCounts.              ||
||    Total fragments : 18695474                                              ||
||    Successfully assigned fragments : 14518759 (77.7%)                      ||
||    Running time : 5.91 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//