File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/a938ea94ce0ffbc3244385d220c2b3/.command.log
Size
46.9 KB
Task
NFCORE_RNAFUSION:RNAFUSION:RNA_CONTAMINATION_DETECTION_WORKFLOW:NGSCheckMATE (tih_rna_sample_00115_23H5VFLT4_s35)
Attempt

Content

View in new tab 
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/a938ea94ce0ffbc3244385d220c2b3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/a938ea94ce0ffbc3244385d220c2b3/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/7cd2061c1c16e215b06cb192370845/tih_rna_sample_00115_23H5VFLT4_s35.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/da47d93bf4d914f2e2abc11162b7d0/tih_rna_sample_00115_23H5VFLT4_s35.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

Set the path to your reference file with the NCM_REF environment variable
eg. export NCM_REF=/<path>/<to>/<reference>

ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
[warning] samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future.
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
[mpileup] 1 samples in 1 input files
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by ps)
ps: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ps)
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1.14
samtools mpileup -uf $NCM_REF -l /usr/local/NGSCheckMate/SNP/SNP_GRCh38_hg38_wChr.bed tih_rna_sample_00115_23H5VFLT4_s35.Aligned.sortedByCoord.out.bam | bcftools call -c > ./tih_rna_sample_00115_23H5VFLT4_s35.Aligned.sortedByCoord.out.vcf
Generate Data Set from .
using this bed file : /usr/local/NGSCheckMate/SNP/SNP_GRCh38_hg38_wChr.bed