Hi I have been trying to run featureCounts on my mapped bam extension files with the command: featureCounts -s 2 -t exon -g gene_id -a /oasis/.../genes_l2.gtf -o /oasis/.../CompleteRNA.txt file.bam

and have been getting:

    ==========     _____ _    _ ____  _____  ______          _____  
    =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
      =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
        ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
          ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
    ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
  v1.5.1

//========================== featureCounts setting ===========================\ || || || Input files : 1 BAM file || || P FF1_1_R.bam || || || || Output file : /oasis/ ... || || Summary : / ... || || Annotation : /oasis/ ... || || Dir for temp files : /oasis/ ... || || || || Threads : 1 || || Level : meta-feature level || || Paired-end : no || || Strand specific : reversely stranded || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Overlapping bases : 0.0% || || || \===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\ || || || Load annotation file /oasis/.../genes_l2. ... || || Features : 690739 || || Meta-features : 46170 || || Chromosomes/contigs : 165 || || || || Process BAM file FF1_1_R.bam... || || Paired-end reads are included. || || Assign reads to features... || featureCounts: readSummary.c:1578: process_pairer_header: Assertion `l_name < 100' failed. /var/spool/torque/mom_priv/jobs/6660772.tscc-mgr.local.SC: line 18: 668 Aborted featureCounts -s 2 -t exon -g gene_id -a /oasis/.../genes_l2.gtf -o /oasis/.../CompleteRun1.txt ${file}

I was wondering about the possible reason for said error. Can it be due to low mapping percentage in bam file.