Warning message:
In rbind(c("gene_id Xkr4", " transcript_id NM_001011874", " gene_name Xkr4" :
  number of columns of result is not a multiple of vector length (arg 665745)

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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P F10-MAA000377-3_9_M-1-1_sorted.bam             ||
||                                                                            ||
||             Output file : F10-MAA000377-3_9_M-1-1_assign_all_features.out  ||
||             Annotations : GeneSym_assign_all_features.gtf (GTF)            ||
||                                                                            ||
||                 Threads : 16                                               ||
||                   Level : meta-feature level                               ||
||              Paired-end : yes                                              ||
||         Strand specific : no                                               ||
||      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 F10-MAA000377-3_9_M-1-1_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:                   ||
||       SRR6575592.161   73   chr17   39983332   50   100M   *   0   0   N   ||
||         #   NH:i:1                                                         ||
||       SRR6575592.163   83   chrX   34338453   50   100M   =   34337868     ||
||       -685   N   #   NH:i:1                                                ||
||    101637 reads have missing mates.                                        ||
||    Input was converted to a format accepted by featureCounts.              ||
||    Total fragments : 534809                                                ||
||    Successfully assigned fragments : 5990 (1.1%)                           ||
||    Running time : 0.45 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//


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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P F10-MAA000377-3_9_M-1-1_sorted.bam             ||
||                                                                            ||
||             Output file : F10-MAA000377-3_9_M-1-1_assign_only1_feature ... ||
||             Annotations : GeneSym_assign_only1_feature.gtf (GTF)           ||
||                                                                            ||
||                 Threads : 16                                               ||
||                   Level : meta-feature level                               ||
||              Paired-end : yes                                              ||
||         Strand specific : no                                               ||
||      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 : 315310                                                       ||
||    Meta-features : 22576                                                   ||
||    Chromosomes/contigs : 124                                               ||
||                                                                            ||
|| Process BAM file F10-MAA000377-3_9_M-1-1_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:                   ||
||       SRR6575592.4   89   chr4   107579934   50   100M   *   0   0   N     ||
||       #   NH:i:1                                                           ||
||       SRR6575592.5   81   chr4   99637318   50   100M   =   99634170   -3  ||
||       248   N   #   NH:i:1                                                 ||
||    101637 reads have missing mates.                                        ||
||    Input was converted to a format accepted by featureCounts.              ||
||    Total fragments : 534809                                                ||
||    Successfully assigned fragments : 523711 (97.9%)                        ||
||    Running time : 0.42 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//