cp: cannot stat `/restricted/projectnb/waxmanlab/kkarri/tabula_muris/GTF_Files/intronic_only_gene_models_ncRNA_for_counting.gtf': No such file or directory
Error: Unable to open file Intron_Only_Regions.gtf. Exiting.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
/var/spool/sge/scc-pg6/job_scripts/8814045: line 315: 109559 Segmentation fault      samtools sort -n ${INPUT_BAM} ${Sample_ID}'_sorted'

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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 unknown file                                   ||
||                           ? O2-MAA000907-3_11_M-1-1_sorted.bam             ||
||                                                                            ||
||             Output file : O2-MAA000907-3_11_M-1-1_featureCounts.out        ||
||             Annotations : exonic_only_gene_models_ncRNA_for_counting.g ... ||
||                                                                            ||
||                 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 exonic_only_gene_models_ncRNA_for_counting.gtf ...    ||
||    Features : 210548                                                       ||
||    Meta-features : 37893                                                   ||
||    Chromosomes/contigs : 32                                                ||
||                                                                            ||
|| Process Unknown file O2-MAA000907-3_11_M-1-1_sorted.bam...                 ||
||    Single-end reads are included.                                          ||
|| Failed to open file O2-MAA000907-3_11_M-1-1_sorted.bam                     ||
|| No counts were generated for this file.                                    ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//