DAY-EC activated.
DAY-EC activated.
USER=ubuntu
HOST=ip-10-0-0-81
PWD=/home/ubuntu
FSX_RESOURCES=/fsx/resources
FSX_REFERENCES=/fsx/references
--- selected fsx dirs ---
/fsx/resources
drwxr-xr-x 3 root root 33280 Jun  6 00:09 /fsx/resources
/fsx/resources/environments
drwxrwxrwt 6 root root 33280 Jun  6 00:18 /fsx/resources/environments
/fsx/resources/environments/conda
drwxrwxrwt 4 root root 33280 Jun  6 00:18 /fsx/resources/environments/conda
/fsx/references/runtime_assets
dr-xr-xr-x 6 root root 33280 Jun  6 00:15 /fsx/references/runtime_assets
/fsx/references/runtime_assets/cached_envs
drwxr-xr-x 10 root root 33280 Jun  6 00:15 /fsx/references/runtime_assets/cached_envs
/fsx/references/runtime_assets/cluster_boot_config
drwxr-xr-x 3 root root 33280 Jun  6 00:17 /fsx/references/runtime_assets/cluster_boot_config
--- fsx mount ---
10.0.1.131@tcp:/ovxjlb4v on /fsx type lustre (rw,noatime,checksum,flock,user_xattr,lruresize,lazystatfs,nouser_fid2path,verbose,encrypt)
--- daylily cfg grep ---
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:107:    s3_uri: s3://lsmc-dayoa-references-usw2/genomic_data/organism_reads_slim/
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:114:    s3_uri: s3://lsmc-dayoa-control-data-usw2/genomic_data/organism_reads_slim/
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:121:    s3_uri: s3://lsmc-dayoa-control-data-usw2/run_data/
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:134:    source_s3_uri_template: s3://lsmc-dayoa-references-usw2/genomic_data/organism_reads_slim/
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:145:    source_s3_uri_template: s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260514_LH01106_0009_B23TVLGLT4/
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:153:      - "Historical live-validation source was s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260514_LH01106_0009_B23TVLGLT4/ mounted read-only under /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/."
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:157:    source_s3_uri_template: s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260514_LH01106_0009_B23TVLGLT4/
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:169:    source_s3_uri_template: s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/pca100/2026/20260513_ONT_HG003/
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:177:      - "Historical live-validation source was s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/pca100/2026/20260513_ONT_HG003/ mounted read-only under /fsx/run_dir_mounts/20260513_ONT_HG003/."
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:181:    source_s3_uri_template: s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/RUN602221/2026/602221-20260417_2346/
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:189:      - "Historical live-validation source was s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/RUN602221/2026/602221-20260417_2346/ mounted read-only under /fsx/run_dir_mounts/602221-20260417_2346/."
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:211:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:242:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:302:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:333:        artifact_registration: &dayoa_multiqc_artifact_registration
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:413:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:452:        artifact_registration: *dayoa_multiqc_artifact_registration
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:485:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:544:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:574:        artifact_registration: *dayoa_multiqc_artifact_registration
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:587:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:647:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:678:        artifact_registration: *dayoa_multiqc_artifact_registration
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:691:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:751:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:796:            failure_cause: "Dry-run failed while preparing Roche/GATK containers: missing Singularity image /fsx/resources/environments/containers/ubuntu/ip-10-0-0-103/7a424a40c6fd659f4d052893dd3554fa.simg."
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:809:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:872:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:906:        artifact_registration: *dayoa_multiqc_artifact_registration
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:919:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:968:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:1026:        runtime_parameters:
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:1080:        runtime_parameters:
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:1133:        runtime_parameters:
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:1155:        artifact_registration:
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:1202:        runtime_parameters:
/home/ubuntu/.config/daylily/daylily_available_repositories.yaml:1256:        runtime_parameters:
/home/ubuntu/.config/daylily/daylily_cli_global.yaml:7:  sentieon_lic_path: /fsx/references/runtime_assets/cached_envs/Life_Sciences_Manufacturing_Corporation_eval.lic
/home/ubuntu/.config/daylily/daylily_cli_global.yaml:9:  sentieon_install_dir: /fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.02/
/home/ubuntu/.config/daylily/daylily-headnode-bootstrap.sh:23:        conda activate DAY-EC >/dev/null 2>&1 || {
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:107:    s3_uri: s3://lsmc-dayoa-references-usw2/genomic_data/organism_reads_slim/
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:114:    s3_uri: s3://lsmc-dayoa-control-data-usw2/genomic_data/organism_reads_slim/
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:121:    s3_uri: s3://lsmc-dayoa-control-data-usw2/run_data/
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:134:    source_s3_uri_template: s3://lsmc-dayoa-references-usw2/genomic_data/organism_reads_slim/
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:145:    source_s3_uri_template: s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260514_LH01106_0009_B23TVLGLT4/
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:153:      - "Historical live-validation source was s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260514_LH01106_0009_B23TVLGLT4/ mounted read-only under /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/."
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:157:    source_s3_uri_template: s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260514_LH01106_0009_B23TVLGLT4/
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:169:    source_s3_uri_template: s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/pca100/2026/20260513_ONT_HG003/
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:177:      - "Historical live-validation source was s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/pca100/2026/20260513_ONT_HG003/ mounted read-only under /fsx/run_dir_mounts/20260513_ONT_HG003/."
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:181:    source_s3_uri_template: s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/RUN602221/2026/602221-20260417_2346/
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:189:      - "Historical live-validation source was s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/RUN602221/2026/602221-20260417_2346/ mounted read-only under /fsx/run_dir_mounts/602221-20260417_2346/."
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:211:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:242:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:302:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:333:        artifact_registration: &dayoa_multiqc_artifact_registration
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:413:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:452:        artifact_registration: *dayoa_multiqc_artifact_registration
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:485:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:544:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:574:        artifact_registration: *dayoa_multiqc_artifact_registration
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:587:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:647:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:678:        artifact_registration: *dayoa_multiqc_artifact_registration
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:691:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:751:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:796:            failure_cause: "Dry-run failed while preparing Roche/GATK containers: missing Singularity image /fsx/resources/environments/containers/ubuntu/ip-10-0-0-103/7a424a40c6fd659f4d052893dd3554fa.simg."
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:809:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:872:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:906:        artifact_registration: *dayoa_multiqc_artifact_registration
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:919:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:968:        runtime_parameters: {}
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:1026:        runtime_parameters:
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:1080:        runtime_parameters:
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:1133:        runtime_parameters:
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:1155:        artifact_registration:
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:1202:        runtime_parameters:
/home/ubuntu/.config/daylily/daylily_pipeline_command_catalog.yaml:1256:        runtime_parameters:
--- env cache listing ---
/fsx/resources/environments/conda/ubuntu
/fsx/resources/environments/conda/ubuntu/i192-dy-all-7
/fsx/resources/environments/conda/ubuntu/i192mem-dy-all-1
/fsx/resources/environments/conda/ubuntu/i192mem-dy-all-6
/fsx/resources/environments/conda/ubuntu/i192-dy-all-4
/fsx/resources/environments/conda/ubuntu/i192mem-dy-all-2
/fsx/resources/environments/conda/ubuntu/i192mem-dy-all-5
/fsx/resources/environments/conda/ubuntu/i192-dy-all-3
/fsx/resources/environments/conda/ubuntu/i192mem-dy-all-7
/fsx/resources/environments/conda/ubuntu/i192-dy-all-1
/fsx/resources/environments/conda/ubuntu/i192-dy-all-6
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/e16773008a9eb117d91285f7b1cb6ab6_
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/e16773008a9eb117d91285f7b1cb6ab6_/ssl
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/e16773008a9eb117d91285f7b1cb6ab6_/include
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/e16773008a9eb117d91285f7b1cb6ab6_/conda-meta
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/e16773008a9eb117d91285f7b1cb6ab6_/x86_64-conda-linux-gnu
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/e16773008a9eb117d91285f7b1cb6ab6_/sbin
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/e16773008a9eb117d91285f7b1cb6ab6_/compiler_compat
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/e16773008a9eb117d91285f7b1cb6ab6_/bin
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/e16773008a9eb117d91285f7b1cb6ab6_/etc
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/e16773008a9eb117d91285f7b1cb6ab6_/libexec
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/e16773008a9eb117d91285f7b1cb6ab6_/lib
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/e16773008a9eb117d91285f7b1cb6ab6_/share
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3a0e4f206e093d942d8271fad4d35296_
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3a0e4f206e093d942d8271fad4d35296_/ssl
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3a0e4f206e093d942d8271fad4d35296_/libexec
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3a0e4f206e093d942d8271fad4d35296_/sbin
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3a0e4f206e093d942d8271fad4d35296_/man
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3a0e4f206e093d942d8271fad4d35296_/share
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3a0e4f206e093d942d8271fad4d35296_/bin
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3a0e4f206e093d942d8271fad4d35296_/etc
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3a0e4f206e093d942d8271fad4d35296_/include
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3a0e4f206e093d942d8271fad4d35296_/conda-meta
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3a0e4f206e093d942d8271fad4d35296_/lib
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3d0893252281fa51ad1d8a1c220b797a_
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3d0893252281fa51ad1d8a1c220b797a_/include
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3d0893252281fa51ad1d8a1c220b797a_/ssl
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3d0893252281fa51ad1d8a1c220b797a_/conda-meta
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3d0893252281fa51ad1d8a1c220b797a_/libexec
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3d0893252281fa51ad1d8a1c220b797a_/lib
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3d0893252281fa51ad1d8a1c220b797a_/share
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3d0893252281fa51ad1d8a1c220b797a_/sbin
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3d0893252281fa51ad1d8a1c220b797a_/bin
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3d0893252281fa51ad1d8a1c220b797a_/etc
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/8ad11a3ecec11ba3035b130d80e455bf_
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/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/8ad11a3ecec11ba3035b130d80e455bf_/include
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/8ad11a3ecec11ba3035b130d80e455bf_/etc
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/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/7c29ee1ebe032a24169825719f2e1a4d_
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/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/7c29ee1ebe032a24169825719f2e1a4d_/conda-meta
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/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/7c29ee1ebe032a24169825719f2e1a4d_/bin
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/7c29ee1ebe032a24169825719f2e1a4d_/lib
--- references runtime listing ---
/fsx/references/runtime_assets
/fsx/references/runtime_assets/cached_envs
/fsx/references/runtime_assets/cached_envs/sentieon_cli-1.5.2
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