File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/cb58c9953d1bed0a2e73facb239694/.command.log
Size
3.6 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-89cc59-R1_B23WHYVLT4_1)
Attempt

Content

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  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/6b/cb58c9953d1bed0a2e73facb239694/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/cb58c9953d1bed0a2e73facb239694/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/41a9964700bf35e6c5837b500db11d/aih-tih-sc-89cc59-R1_B23WHYVLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/41a9964700bf35e6c5837b500db11d/aih-tih-sc-89cc59-R1_B23WHYVLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/1b2ff0c69bb0d568a9340ece81324f/aih-tih-sc-89cc59-R1_B23WHYVLT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-89cc59-R1_B23WHYVLT4_1.fusionreport.tsv --gtf /tmp/nxf.b85KyCCB1A/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.b85KyCCB1A/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.b85KyCCB1A/aih-tih-sc-89cc59-R1_B23WHYVLT4_1 --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 aih-tih-sc-89cc59-R1_B23WHYVLT4_1.fusionreport.tsv --gtf /tmp/nxf.b85KyCCB1A/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.b85KyCCB1A/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.b85KyCCB1A/aih-tih-sc-89cc59-R1_B23WHYVLT4_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 aih-tih-sc-89cc59-R1_B23WHYVLT4_1.fusionreport.tsv --gtf /tmp/nxf.b85KyCCB1A/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.b85KyCCB1A/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.b85KyCCB1A/aih-tih-sc-89cc59-R1_B23WHYVLT4_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
 ] 
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 aih-tih-sc-89cc59-R1_B23WHYVLT4_1.fusionreport.tsv --gtf /tmp/nxf.b85KyCCB1A/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.b85KyCCB1A/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.b85KyCCB1A/aih-tih-sc-89cc59-R1_B23WHYVLT4_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
 ]