File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/cb5da1871b8100f76ff0f828b694ad/.command.log
Size
3.3 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (dna_s768)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/f9095680fc9dbaa468e61be64b1a39/dna_s768_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/cb5da1871b8100f76ff0f828b694ad/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/cb5da1871b8100f76ff0f828b694ad/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/f9095680fc9dbaa468e61be64b1a39/dna_s768_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/dfe4a857b46613678dfce76ad289f8/dna_s768.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions dna_s768.fusionreport.tsv --gtf /tmp/nxf.4yQVSrulF7/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4yQVSrulF7/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4yQVSrulF7/dna_s768 --shrink_introns --max_intron_length 1000 
Done.
Error, no fusion contigs written at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 251.
Error: Command '/usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions dna_s768.fusionreport.tsv --gtf /tmp/nxf.4yQVSrulF7/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4yQVSrulF7/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4yQVSrulF7/dna_s768 --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 dna_s768.fusionreport.tsv --gtf /tmp/nxf.4yQVSrulF7/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4yQVSrulF7/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4yQVSrulF7/dna_s768 --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
 ] 
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 dna_s768.fusionreport.tsv --gtf /tmp/nxf.4yQVSrulF7/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4yQVSrulF7/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4yQVSrulF7/dna_s768 --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
 ]