[bam_sort_core] merging from 4 files...

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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P KI12_sorted.bam                                ||
||                                                                            ||
||             Output file : KI12_featureCounts.out                           ||
||             Annotations : ncRNA_exon_for_counting.gtf (GTF)                ||
||                                                                            ||
||                 Threads : 16                                               ||
||                   Level : meta-feature level                               ||
||              Paired-end : yes                                              ||
||         Strand specific : inversed                                         ||
||      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 ncRNA_exon_for_counting.gtf ...                       ||
||    Features : 2365829                                                      ||
||    Meta-features : 37907                                                   ||
||    Chromosomes/contigs : 32                                                ||
||                                                                            ||
|| Process BAM file KI12_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:                   ||
||       SRR5345555.1   137   chr4   45003258   50   43M   *   0   0   N   #  ||
||          NH:i:1                                                            ||
||       SRR5345555.2   83   chr5   90905489   50   43M   =   90904297   -12  ||
||       35   N   #   NH:i:1                                                  ||
||    454256 reads have missing mates.                                        ||
||    Input was converted to a format accepted by featureCounts.              ||
||    Total fragments : 4643095                                               ||
||    Successfully assigned fragments : 4153169 (89.4%)                       ||
||    Running time : 1.85 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//