[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 19 files...

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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P G160_M3_sorted.bam                             ||
||                                                                            ||
||             Output file : G160_M3_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 : 3913                                                         ||
||    Meta-features : 524                                                     ||
||    Chromosomes/contigs : 25                                                ||
||                                                                            ||
|| Process BAM file G160_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:                   ||
||       HWI-D00270:267:CB0DPANXX:4:1101:1213:24394   163   chr17   39984894  ||
||          50   50M   =   39984992   148   N   #   NH:i:1                    ||
||       HWI-D00270:267:CB0DPANXX:4:1101:1213:25417   163   chr4   63006135   ||
||         50   50M   =   63006223   347   N   #   NH:i:1                     ||
||    2647921 reads have missing mates.                                       ||
||    Input was converted to a format accepted by featureCounts.              ||
||    Total fragments : 23784588                                              ||
||    Successfully assigned fragments : 82036 (0.3%)                          ||
||    Running time : 4.88 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//


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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P G160_M3_sorted.bam                             ||
||                                                                            ||
||             Output file : G160_M3_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 : 189176                                                       ||
||    Meta-features : 19957                                                   ||
||    Chromosomes/contigs : 32                                                ||
||                                                                            ||
|| Process BAM file G160_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:                   ||
||       HWI-D00270:267:CB0DPANXX:4:1101:1197:31944   73   chr16   57431525   ||
||         50   50M   *   0   0   N   #   NH:i:1                              ||
||       HWI-D00270:267:CB0DPANXX:4:1101:1197:41966   99   chr6   85818353    ||
||        50   50M   =   85818444   467   N   #   NH:i:1                      ||
||    2647921 reads have missing mates.                                       ||
||    Input was converted to a format accepted by featureCounts.              ||
||    Total fragments : 23784588                                              ||
||    Successfully assigned fragments : 15113304 (63.5%)                      ||
||    Running time : 4.96 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//