DAY-EC activated.
DAY-EC activated.
files
-rw-rw-r-- 1 ubuntu ubuntu 13M Jun  6 10:06 results/day/hg38/reports/DAY_final_multiqc.html
-rw-rw-r-- 1 ubuntu ubuntu 26M Jun  6 10:06 results/day/hg38/reports/DAY_final_multiqc_data/multiqc_data.json
MISSING results/day/hg38/reports/dayoa_evidence_manifest.json
-rw-rw-r-- 1 ubuntu ubuntu 9.9K Jun  6 10:06 results/day/hg38/reports/logs/all__mqc_fin_a.log
MISSING results/day/hg38/logs/produce_multiqc_all.log
controllers
ubuntu    498261   53952  0 10:01 ?        00:00:00 sh -c cat >> /home/ubuntu/daylily-runs/hybonly_ilmn_final_multiqc_file_20260606T100052Z/tmux.log
ubuntu    498749  498258  0 10:01 pts/12   00:00:00 bash bin/day_run produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --config aligners=["sent"] dedupers=["dmd"] snv_callers=["sentd"] htd_callers=["cyrius"] multiqc_qc={"enable_tools":["vep","metagenomics","contam_identity"]} -j 200 -p -k --rerun-triggers mtime
ubuntu    498965  498749  0 10:01 pts/12   00:00:00 bash bin/day_run produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --config aligners=["sent"] dedupers=["dmd"] snv_callers=["sentd"] htd_callers=["cyrius"] multiqc_qc={"enable_tools":["vep","metagenomics","contam_identity"]} -j 200 -p -k --rerun-triggers mtime
ubuntu    498966  498965  1 10:01 pts/12   00:00:06 /home/ubuntu/miniconda3/envs/DAYOA/bin/python /home/ubuntu/miniconda3/envs/DAYOA/bin/snakemake --profile=/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --config aligners=["sent"] dedupers=["dmd"] snv_callers=["sentd"] htd_callers=["cyrius"] multiqc_qc={"enable_tools":["vep","metagenomics","contam_identity"]} -j 200 -p -k --rerun-triggers mtime
ubuntu    498967  498965  0 10:01 pts/12   00:00:00 bash bin/day_run produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --config aligners=["sent"] dedupers=["dmd"] snv_callers=["sentd"] htd_callers=["cyrius"] multiqc_qc={"enable_tools":["vep","metagenomics","contam_identity"]} -j 200 -p -k --rerun-triggers mtime
ubuntu    502270  498966  0 10:06 pts/12   00:00:00 /bin/sh -c cd /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis && /home/ubuntu/miniconda3/envs/DAYOA/bin/python -m snakemake --snakefile '/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/Snakefile' --target-jobs 'write_dayoa_evidence_manifest:' --allowed-rules 'write_dayoa_evidence_manifest' --cores 8 --attempt 1 --force-use-threads  --resources 'mem_mb=3000' 'mem_mib=2862' 'disk_mb=1000' 'disk_mib=954' 'threads=1' 'time=5440' 'vcpu=1' --quiet --force --keep-target-files --keep-remote --max-inventory-time 0 --nocolor --notemp --no-hooks --nolock --ignore-incomplete --rerun-triggers 'mtime' --skip-script-cleanup  --use-conda  --conda-frontend 'conda' --conda-prefix '/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81' --conda-base-path '/home/ubuntu/miniconda3' --use-singularity  --singularity-prefix '/fsx/resources/environments/containers/ubuntu/ip-10-0-0-81' --singularity-args '  -B /fsx:/fsx -B /tmp:/tmp -B $PWD/:$PWD   -B /dev/fd:/dev/fd  -B /dev/shm:$PWD/resources/dev/shm -B /dev/shm:/dev/shm ' --wrapper-prefix 'https://github.com/snakemake/snakemake-wrappers/raw/' --local-groupid 'local' --config 'aligners=["sent"]' 'dedupers=["dmd"]' 'snv_callers=["sentd"]' 'htd_callers=["cyrius"]' 'multiqc_qc={"enable_tools":["vep","metagenomics","contam_identity"]}' --printshellcmds  --latency-wait 100 --scheduler 'greedy' --scheduler-solver-path '/home/ubuntu/miniconda3/envs/DAYOA/bin' --default-resources 'mem_mb=3000' 'disk_mb=1000' 'tmpdir=system_tmpdir' 'threads=1' 'time=5440' 'partition=i192,i128,i192mem,bcl2fq-i384-nvme-test' 'vcpu=1' 'distribution=block' "exclusive=''" "constraint=''" "exclude=''" "include=''" --mode 1
ubuntu    502271  502270 84 10:06 pts/12   00:01:31 /home/ubuntu/miniconda3/envs/DAYOA/bin/python -m snakemake --snakefile /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/Snakefile --target-jobs write_dayoa_evidence_manifest: --allowed-rules write_dayoa_evidence_manifest --cores 8 --attempt 1 --force-use-threads --resources mem_mb=3000 mem_mib=2862 disk_mb=1000 disk_mib=954 threads=1 time=5440 vcpu=1 --quiet --force --keep-target-files --keep-remote --max-inventory-time 0 --nocolor --notemp --no-hooks --nolock --ignore-incomplete --rerun-triggers mtime --skip-script-cleanup --use-conda --conda-frontend conda --conda-prefix /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81 --conda-base-path /home/ubuntu/miniconda3 --use-singularity --singularity-prefix /fsx/resources/environments/containers/ubuntu/ip-10-0-0-81 --singularity-args   -B /fsx:/fsx -B /tmp:/tmp -B $PWD/:$PWD   -B /dev/fd:/dev/fd  -B /dev/shm:$PWD/resources/dev/shm -B /dev/shm:/dev/shm  --wrapper-prefix https://github.com/snakemake/snakemake-wrappers/raw/ --local-groupid local --config aligners=["sent"] dedupers=["dmd"] snv_callers=["sentd"] htd_callers=["cyrius"] multiqc_qc={"enable_tools":["vep","metagenomics","contam_identity"]} --printshellcmds --latency-wait 100 --scheduler greedy --scheduler-solver-path /home/ubuntu/miniconda3/envs/DAYOA/bin --default-resources mem_mb=3000 disk_mb=1000 tmpdir=system_tmpdir threads=1 time=5440 partition=i192,i128,i192mem,bcl2fq-i384-nvme-test vcpu=1 distribution=block exclusive='' constraint='' exclude='' include='' --mode 1
last_workflow_lines
[32mFinished job 1.[0m
[32m5 of 7 steps (71%) done[0m
[32mlocalrule write_dayoa_evidence_manifest:
    reason: Missing output files: results/day/hg38/reports/dayoa_evidence_manifest.json; Input files updated by another job: results/day/hg38/reports/DAY_final_multiqc_data/multiqc_general_stats.txt, results/day/hg38/reports/DAY_final_multiqc_data/multiqc_data.json, results/day/hg38/other_reports/contam_identity_mqc.tsv, results/day/hg38/reports/DAY_final_multiqc_data/multiqc_sources.txt, results/day/hg38/reports/DAY_final_multiqc_data/multiqc.log, results/day/hg38/other_reports/haplocheck_mtdna_mqc.tsv, results/day/hg38/other_reports/read_haps_mqc.tsv, results/day/hg38/other_reports/rules_benchmark_data_mqc.tsv, results/day/hg38/reports/multiqc_inputs/final/manifest.tsv, results/day/hg38/reports/DAY_final_multiqc.html
