Error executing process > 'NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1)'

Caused by:
  Process `NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1)` terminated with an error exit status (1)


Command executed:

  FusionInspector \
          --fusions HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1.fusionreport.tsv \
          --genome_lib ctat_genome_lib_build_dir \
          --left_fq HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz --right_fq HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz \
          --CPU 24 \
          -O . \
          --out_prefix HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1 \
          --vis  --annotate --examine_coding_effect
  
      cat <<-END_VERSIONS > versions.yml
      "NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR":
          STAR-Fusion: $(STAR-Fusion --version 2>&1 | grep -i 'version' | sed 's/STAR-Fusion version: //')
  END_VERSIONS

Command exit status:
  1

Command output:
  Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.9aNutTXGPv/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.9aNutTXGPv/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.9aNutTXGPv/HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1 --shrink_introns --max_intron_length 1000 
  Error: Command '/usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.9aNutTXGPv/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.9aNutTXGPv/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.9aNutTXGPv/HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1 --shrink_introns --max_intron_length 1000 ' returned non-zero exit status 25., exit val: 25
  Error, command: [ /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.9aNutTXGPv/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.9aNutTXGPv/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.9aNutTXGPv/HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1 --shrink_introns --max_intron_length 1000  ] failed, stack trace: [ st: file:/usr/local/src/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86
  st: file:/usr/local/src/STAR-Fusion/FusionInspector/FusionInspector, lineno:654
  st: file:/usr/local/src/STAR-Fusion/FusionInspector/FusionInspector, lineno:1942
   ] 

Command error:
  WARNING, no gtf annotations found for [IGHA1]
  Done.
  Error, no fusion contigs written at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 251.
  Traceback (most recent call last):
    File "/usr/local/src/STAR-Fusion/FusionInspector/FusionInspector", line 1942, in <module>
      FusionInspector().run()
    File "/usr/local/src/STAR-Fusion/FusionInspector/FusionInspector", line 1516, in run
      pipeliner.run()
    File "/usr/local/src/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py", line 71, in run
      cmd.run(checkpoint_dir)
    File "/usr/local/src/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py", line 132, in run
      raise RuntimeError(errmsg)
  RuntimeError: Error, command: [ /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.9aNutTXGPv/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.9aNutTXGPv/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.9aNutTXGPv/HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1 --shrink_introns --max_intron_length 1000  ] failed, stack trace: [ st: file:/usr/local/src/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86
  st: file:/usr/local/src/STAR-Fusion/FusionInspector/FusionInspector, lineno:654
  st: file:/usr/local/src/STAR-Fusion/FusionInspector/FusionInspector, lineno:1942
   ] 

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/f01084a7e1c81d849fc035a08c3330

Container:
  docker.io/trinityctat/starfusion:1.12.0

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`