Hi,

I am using featureCounts to count reads for every gene from refSeq annotation file. But it went to error:

featureCounts -a ../refGeneReviewed.gtf -t exon -g gene_id -p -Q 10 -o ../../result/fc_accepted_hits.txt accepted_hits.bam

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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P accepted_hits.bam                              ||
||                                                                            ||
||             Output file : ../../result/fc_accepted_hits.txt                ||
||             Annotations : ../refGeneReviewed.gtf (GTF)                     ||
||                                                                            ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : yes                                              ||
||         Strand specific : no                                               ||
||      Multimapping reads : not counted                                      ||
|| Multi-overlapping reads : not counted                                      ||
||                                                                            ||
||          Chimeric reads : counted                                          ||
||        Both ends mapped : not required                                     ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file ../refGeneReviewed.gtf ...                            ||
||    Features : 304046                                                       ||
||    Meta-features : 24154                                                   ||
||    Chromosomes : 35                                                        ||
||                                                                            ||
|| Process BAM file accepted_hits.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)                         ||
Cannot load read part from the tmp file!
featureCounts: input-files.c:2216: sort_SAM_finalise: Assertion `0' failed.
Aborted

This bam and gtf file should be right, because I have used them to run HTSeq-count

It looks that the current directory has no enough space, or some reads in the SAM file are extremely long (e.g., longer than 1200 bps).