Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/363eba166e988cf76c8e6b793254d1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/29ca77f36ab860afe08eb798428957/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
  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/16/34250df3dd603ae7f96d9b5a6a3d59/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/34250df3dd603ae7f96d9b5a6a3d59/.command.run
==> 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)
[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)
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 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam | bcftools call -c > ./1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.vcf
Generate Data Set from .
using this bed file : /usr/local/NGSCheckMate/SNP/SNP_GRCh38_hg38_wChr.bed