May 25 06:17:45 ..... Started STAR run
May 25 06:17:45 ..... Loading genome
May 25 06:17:55 ..... Started mapping
May 25 06:27:03 ..... Finished successfully
[E::hts_open_format] Failed to open file SRR6658278.sorted.bam.tmp.0000.bam
samtools sort: failed to create temporary file "SRR6658278.sorted.bam.tmp.0000.bam": File exists
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
samtools index: failed to create index for "SRR6658278.sorted.bam": No such file or directory

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
	  v1.6.3

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P SRR6658278.sorted.bam                          ||
||                                                                            ||
||             Output file : SRR6658278                                       ||
||                 Summary : SRR6658278.summary                               ||
||              Annotation : genes.gtf (GTF)                                  ||
||      Dir for temp files : /gpfs/data/yanailab/public/linda_share/for_d ... ||
||                                                                            ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : yes                                              ||
||      Multimapping reads : not counted                                      ||
|| Multi-overlapping reads : not counted                                      ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
||          Chimeric reads : counted                                          ||
||        Both ends mapped : required                                         ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file genes.gtf ...                                         ||
||    Features : 325154                                                       ||
||    Meta-features : 24421                                                   ||
||    Chromosomes/contigs : 36                                                ||
||                                                                            ||
|| Process BAM file SRR6658278.sorted.bam...                                  ||
||    Paired-end reads are included.                                          ||
||    Assign alignments (paired-end) to features...                           ||
||                                                                            ||
||    WARNING: reads from the same pair were found not adjacent to each       ||
||             other in the input (due to read sorting by location or         ||
||             reporting of multi-mapping read pairs).                        ||
||                                                                            ||
||    Pairing up the read pairs.                                              ||
||                                                                            ||
||    Total alignments : 22376375                                             ||
||    Successfully assigned alignments : 17426376 (77.9%)                     ||
||    Running time : 1.29 minutes                                             ||
||                                                                            ||
||                                                                            ||
|| Summary of counting results can be found in file "/gpfs/data/yanailab/pub  ||
|| lic/linda_share/for_debbie/GSE109972/featurecounts/SRR6658278.summary"     ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//