gistfile1.txt

Error executing process > 'featureCounts (TPF-18-103_tu_KAM56A3_S17.1)'

Caused by:
  Process `featureCounts (TPF-18-103_tu_KAM56A3_S17.1)` terminated with an error exit status (255)

Command executed:

  featureCounts -a genes.gtf -g gene_id -t exon -o TPF-18-103_tu_KAM56A3_S17.1.sorted_gene.featureCounts.txt --extraAttributes gene_name -p -s 2 TPF-18-103_tu_KAM56A3_S17.1.sorted.bam
  featureCounts -a genes.gtf -g gene_biotype -o TPF-18-103_tu_KAM56A3_S17.1.sorted_biotype.featureCounts.txt -p -s 2 TPF-18-103_tu_KAM56A3_S17.1.sorted.bam
  cut -f 1,7 TPF-18-103_tu_KAM56A3_S17.1.sorted_biotype.featureCounts.txt | tail -n +3 | cat biotypes_header.txt - >> TPF-18-103_tu_KAM56A3_S17.1.sorted_biotype_counts_mqc.txt && mqc_features_stat.py TPF-18-103_tu_KAM56A3_S17.1.sorted_biotype_counts_mqc.txt -s TPF-18-103_tu_KAM56A3_S17.1.sorted -f rRNA -o TPF-18-103_tu_KAM56A3_S17.1.sorted_biotype_counts_gs_mqc.tsv

Command exit status:
  255

Command output:
  (empty)

Command error:
  ||    Total alignments : 64363814                                             ||
  ||    Successfully assigned alignments : 44914927 (69.8%)                     ||
  ||    Running time : 5.00 minutes                                             ||
  ||                                                                            ||
  ||                                                                            ||
  || Summary of counting results can be found in file "TPF-18-103_tu_KAM56A3_S  ||
  || 17.1.sorted_gene.featureCounts.txt.summary"                                ||
  ||                                                                            ||
  \\============================================================================//
  
  
          ==========     _____ _    _ ____  _____  ______          _____  
          =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
            =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
              ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
                ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
          ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
  ||      v1.6.4
  
  //========================== featureCounts setting ===========================\\
  ||                                                                            ||
  ||             Input files : 1 BAM file                                       ||
  ||                           P TPF-18-103_tu_KAM56A3_S17.1.sorted.bam         ||
  ||                                                                            ||
  ||             Output file : TPF-18-103_tu_KAM56A3_S17.1.sorted_biotype.f ... ||
  ||                 Summary : TPF-18-103_tu_KAM56A3_S17.1.sorted_biotype.f ... ||
  ||              Annotation : genes.gtf (GTF)                                  ||
  ||      Dir for temp files : ./                                               ||
  ||                                                                            ||
  ||                 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 : not required                                     ||
  ||                                                                            ||
  \\============================================================================//
  
  //================================= Running ==================================\\
  ||                                                                            ||
  || Load annotation file genes.gtf ...                                         ||
  
  ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
  The specified gene identifier attribute is 'gene_biotype' 
  An example of attributes included in your GTF annotation is 'gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "rna0"; tss_id "TSS31672";' 
  The program has to terminate.