[bam_sort_core] merging from 4 files...

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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P WT9_sorted.bam                                 ||
||                                                                            ||
||             Output file : WT9_assign_all_features.out                      ||
||             Annotations : GeneSym_assign_all_features.gtf (GTF)            ||
||                                                                            ||
||                 Threads : 16                                               ||
||                   Level : meta-feature level                               ||
||              Paired-end : yes                                              ||
||         Strand specific : inversed                                         ||
||      Multimapping reads : not counted                                      ||
|| Multi-overlapping reads : counted                                          ||
||       Read orientations : fr                                               ||
||                                                                            ||
||          Chimeric reads : counted                                          ||
||        Both ends mapped : not required                                     ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file GeneSym_assign_all_features.gtf ...                   ||
||    Features : 6105                                                         ||
||    Meta-features : 1713                                                    ||
||    Chromosomes/contigs : 25                                                ||
||                                                                            ||
|| Process BAM file WT9_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:                   ||
||       SRR5345540.6   153   chr5   122022846   50   24M562N18M   *   0   0  ||
||          N   #   NH:i:1                                                    ||
||       SRR5345540.8   153   chr1   121490909   50   41M   *   0   0   N     ||
||       #   NH:i:1                                                           ||
||    492140 reads have missing mates.                                        ||
||    Input was converted to a format accepted by featureCounts.              ||
||    Total fragments : 4444106                                               ||
||    Successfully assigned fragments : 22822 (0.5%)                          ||
||    Running time : 2.20 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//


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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P WT9_sorted.bam                                 ||
||                                                                            ||
||             Output file : WT9_assign_only1_feature.out                     ||
||             Annotations : GeneSym_assign_only1_feature.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 GeneSym_assign_only1_feature.gtf ...                  ||
||    Features : 315218                                                       ||
||    Meta-features : 22484                                                   ||
||    Chromosomes/contigs : 32                                                ||
||                                                                            ||
|| Process BAM file WT9_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:                   ||
||       SRR5345540.241   147   chr18   46753026   50   43M   =   46752932    ||
||        -137   N   #   NH:i:1                                               ||
||       SRR5345540.242   83   chr12   112353136   50   42M   =   112353009   ||
||         -169   N   #   NH:i:1                                              ||
||    492140 reads have missing mates.                                        ||
||    Input was converted to a format accepted by featureCounts.              ||
||    Total fragments : 4444106                                               ||
||    Successfully assigned fragments : 3790288 (85.3%)                       ||
||    Running time : 1.94 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//