[bam_sort_core] merging from 10 files...

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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P G123_M16_sorted.bam                            ||
||                                                                            ||
||             Output file : G123_M16_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 : 5739                                                         ||
||    Meta-features : 1725                                                    ||
||    Chromosomes/contigs : 25                                                ||
||                                                                            ||
|| Process BAM file G123_M16_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:                   ||
||       HWI-D00311:109:C8TK0ANXX:8:1101:1308:81689   145   chr12   13245934  ||
||          50   50M   =   13242909   -3075   N   #   NH:i:1                  ||
||       HWI-D00311:109:C8TK0ANXX:8:1101:1308:92965   73   chr1   172888750   ||
||         50   50M   *   0   0   N   #   NH:i:1                              ||
||    4138877 reads have missing mates.                                       ||
||    Input was converted to a format accepted by featureCounts.              ||
||    Total fragments : 14090747                                              ||
||    Successfully assigned fragments : 54819 (0.4%)                          ||
||    Running time : 3.00 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//


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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P G123_M16_sorted.bam                            ||
||                                                                            ||
||             Output file : G123_M16_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 : 206368                                                       ||
||    Meta-features : 22472                                                   ||
||    Chromosomes/contigs : 32                                                ||
||                                                                            ||
|| Process BAM file G123_M16_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:                   ||
||       HWI-D00311:109:C8TK0ANXX:8:1101:1346:31741   129   chrX   3846748    ||
||        50   50M   chr13   97960497   0   N   #   NH:i:1                    ||
||       HWI-D00311:109:C8TK0ANXX:8:1101:1346:50544   83   chr14   18869319   ||
||         50   50M   =   18869231   -138   N   #   NH:i:1                    ||
||    4138877 reads have missing mates.                                       ||
||    Input was converted to a format accepted by featureCounts.              ||
||    Total fragments : 14090747                                              ||
||    Successfully assigned fragments : 11771810 (83.5%)                      ||
||    Running time : 3.25 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//