[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 4 files...

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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           S LZ_M29_sorted.bam                              ||
||                                                                            ||
||             Output file : LZ_M29_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 LZ_M29_sorted.bam...                                      ||
||    Single-end reads are included.                                          ||
||    Assign reads to features...                                             ||
||    Total reads : 13612936                                                  ||
||    Successfully assigned reads : 19957 (0.1%)                              ||
||    Running time : 0.19 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//


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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           S LZ_M29_sorted.bam                              ||
||                                                                            ||
||             Output file : LZ_M29_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 LZ_M29_sorted.bam...                                      ||
||    Single-end reads are included.                                          ||
||    Assign reads to features...                                             ||
||    Total reads : 13612936                                                  ||
||    Successfully assigned reads : 1435897 (10.5%)                           ||
||    Running time : 0.19 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//