Job failed, going on with independent jobs.
Exiting because a job execution failed. Look above for error message
Note the path to the log file for debugging.
Documentation is available at: https://metagenome-atlas.readthedocs.io
Issues can be raised at: https://github.com/metagenome-atlas/atlas/issues
Complete log: /users/student223/Human/.snakemake/log/2021-09-27T161441.941750.snakemake.log
[2021-09-27 16:14 CRITICAL] Command 'snakemake --snakefile /scratch/project_2004930/atlas/atlas/Snakefile --directory /users/student223/Human --jobs 10 --rerun-incomplete --configfile '/users/student223/Human/config.yaml' --nolock --profile cluster --use-conda --conda-prefix /scratch/project_2004930/databases/conda_envs --scheduler greedy binning --keep-going ' returned non-zero exit status 1.
SilasK
commented
2 years ago
[2021-09-27 16:14 INFO] Executing: snakemake --snakefile /scratch/project_2004930/atlas/atlas/Snakefile --directory /users/student223/Human --jobs 10 --rerun-incomplete --configfile '/users/student223/Human/config.yaml' --nolock --profile cluster --use-conda --conda-prefix /scratch/project_2004930/databases/conda_envs --scheduler greedy binning --keep-going Building DAG of jobs... Using shell: /usr/bin/bash Provided cluster nodes: 10 Singularity containers: ignored Job stats: job count min threads max threads
align_reads_to_final_contigs 8 8 8 apply_quality_filter 8 8 8 assembly 1 1 1 assembly_one_sample 8 1 1 bam_2_sam_binning 8 8 8 bam_2_sam_contigs 8 4 4 binning 1 1 1 build_assembly_report 1 1 1 build_bin_report 1 1 1 build_decontamination_db 1 8 8 build_qc_report 1 1 1 calculate_contigs_stats 16 1 1 calculate_insert_size 8 4 4 combine_bin_stats 1 1 1 combine_contig_stats 1 1 1 combine_insert_stats 1 1 1 combine_read_counts 1 1 1 combine_read_length_stats 1 1 1 convert_sam_to_bam 8 4 4 deduplicate_reads 8 8 8 do_not_filter_contigs 8 1 1 error_correction 8 8 8 finalize_contigs 8 1 1 finalize_sample_qc 8 1 1 get_bins 8 1 1 get_contig_coverage_from_bb 8 1 1 get_contigs_from_gene_names 8 1 1 get_maxbin_cluster_attribution 8 1 1 get_metabat_depth_file 8 8 8 get_read_stats 40 4 4 get_unique_bin_ids 16 1 1 get_unique_cluster_attribution 16 1 1 init_pre_assembly_processing 8 1 1 initialize_qc 8 4 4 maxbin 8 8 8 merge_checkm 1 1 1 merge_pairs 8 8 8 metabat 8 8 8 pileup 8 8 8 pileup_for_binning 8 8 8 predict_genes 8 1 1 qc 1 1 1 qcreads 8 1 1 rename_contigs 8 4 4 rename_spades_output 8 1 1 run_checkm_lineage_wf 8 8 8 run_checkm_tree_qa 8 1 1 run_das_tool 8 8 8 run_decontamination 8 8 8 run_spades 8 8 8 write_read_counts 8 1 1 total 373 1 8
[Mon Sep 27 16:14:45 2021] rule initialize_qc: input: /users/student223/shared/Human/SAMEA103958164_1.fastq.gz, /users/student223/shared/Human/SAMEA103958164_2.fastq.gz output: SAMEA103958164/sequence_quality_control/SAMEA103958164_raw_R1.fastq.gz, SAMEA103958164/sequence_quality_control/SAMEA103958164_raw_R2.fastq.gz log: SAMEA103958164/logs/QC/init.log jobid: 155 wildcards: sample=SAMEA103958164 priority: 80 threads: 4 resources: tmpdir=/local_scratch/student223, mem=10, java_mem=8, time=1, mem_mb=10000, time_min=60
CLUSTER: 2021-09-27 16:14:45 submit command: sbatch --parsable --output=cluster_log/%j.out --error=cluster_log/%j.out --job-name=initialize_qc --cpus-per-task=4 -n1 --time=60 --mem=10000m /users/student223/Human/.snakemake/tmp.80uen2e6/snakejob.initialize_qc.155.sh CLUSTER: 2021-09-27 16:14:45 Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Error submitting jobscript (exit code 1): Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Job failed, going on with independent jobs.
[Mon Sep 27 16:14:45 2021] rule initialize_qc: input: /users/student223/shared/Human/SAMEA103958163_1.fastq.gz, /users/student223/shared/Human/SAMEA103958163_2.fastq.gz output: SAMEA103958163/sequence_quality_control/SAMEA103958163_raw_R1.fastq.gz, SAMEA103958163/sequence_quality_control/SAMEA103958163_raw_R2.fastq.gz log: SAMEA103958163/logs/QC/init.log jobid: 211 wildcards: sample=SAMEA103958163 priority: 80 threads: 4 resources: tmpdir=/local_scratch/student223, mem=10, java_mem=8, time=1, mem_mb=10000, time_min=60
CLUSTER: 2021-09-27 16:14:46 submit command: sbatch --parsable --output=cluster_log/%j.out --error=cluster_log/%j.out --job-name=initialize_qc --cpus-per-task=4 -n1 --time=60 --mem=10000m /users/student223/Human/.snakemake/tmp.80uen2e6/snakejob.initialize_qc.211.sh CLUSTER: 2021-09-27 16:14:46 Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Error submitting jobscript (exit code 1): Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Job failed, going on with independent jobs.
[Mon Sep 27 16:14:46 2021] rule initialize_qc: input: /users/student223/shared/Human/SAMEA103958167_1.fastq.gz, /users/student223/shared/Human/SAMEA103958167_2.fastq.gz output: SAMEA103958167/sequence_quality_control/SAMEA103958167_raw_R1.fastq.gz, SAMEA103958167/sequence_quality_control/SAMEA103958167_raw_R2.fastq.gz log: SAMEA103958167/logs/QC/init.log jobid: 99 wildcards: sample=SAMEA103958167 priority: 80 threads: 4 resources: tmpdir=/local_scratch/student223, mem=10, java_mem=8, time=1, mem_mb=10000, time_min=60
CLUSTER: 2021-09-27 16:14:46 submit command: sbatch --parsable --output=cluster_log/%j.out --error=cluster_log/%j.out --job-name=initialize_qc --cpus-per-task=4 -n1 --time=60 --mem=10000m /users/student223/Human/.snakemake/tmp.80uen2e6/snakejob.initialize_qc.99.sh CLUSTER: 2021-09-27 16:14:46 Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Error submitting jobscript (exit code 1): Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Job failed, going on with independent jobs.
[Mon Sep 27 16:14:46 2021] rule initialize_qc: input: /users/student223/shared/Human/SAMEA103958160_1.fastq.gz, /users/student223/shared/Human/SAMEA103958160_2.fastq.gz output: SAMEA103958160/sequence_quality_control/SAMEA103958160_raw_R1.fastq.gz, SAMEA103958160/sequence_quality_control/SAMEA103958160_raw_R2.fastq.gz log: SAMEA103958160/logs/QC/init.log jobid: 71 wildcards: sample=SAMEA103958160 priority: 80 threads: 4 resources: tmpdir=/local_scratch/student223, mem=10, java_mem=8, time=1, mem_mb=10000, time_min=60
CLUSTER: 2021-09-27 16:14:46 submit command: sbatch --parsable --output=cluster_log/%j.out --error=cluster_log/%j.out --job-name=initialize_qc --cpus-per-task=4 -n1 --time=60 --mem=10000m /users/student223/Human/.snakemake/tmp.80uen2e6/snakejob.initialize_qc.71.sh CLUSTER: 2021-09-27 16:14:46 Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Error submitting jobscript (exit code 1): Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Job failed, going on with independent jobs.
[Mon Sep 27 16:14:46 2021] rule initialize_qc: input: /users/student223/shared/Human/SAMEA103958165_1.fastq.gz, /users/student223/shared/Human/SAMEA103958165_2.fastq.gz output: SAMEA103958165/sequence_quality_control/SAMEA103958165_raw_R1.fastq.gz, SAMEA103958165/sequence_quality_control/SAMEA103958165_raw_R2.fastq.gz log: SAMEA103958165/logs/QC/init.log jobid: 12 wildcards: sample=SAMEA103958165 priority: 80 threads: 4 resources: tmpdir=/local_scratch/student223, mem=10, java_mem=8, time=1, mem_mb=10000, time_min=60
CLUSTER: 2021-09-27 16:14:47 submit command: sbatch --parsable --output=cluster_log/%j.out --error=cluster_log/%j.out --job-name=initialize_qc --cpus-per-task=4 -n1 --time=60 --mem=10000m /users/student223/Human/.snakemake/tmp.80uen2e6/snakejob.initialize_qc.12.sh CLUSTER: 2021-09-27 16:14:47 Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Error submitting jobscript (exit code 1): Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Job failed, going on with independent jobs.
[Mon Sep 27 16:14:47 2021] rule initialize_qc: input: /users/student223/shared/Human/SAMEA103958162_1.fastq.gz, /users/student223/shared/Human/SAMEA103958162_2.fastq.gz output: SAMEA103958162/sequence_quality_control/SAMEA103958162_raw_R1.fastq.gz, SAMEA103958162/sequence_quality_control/SAMEA103958162_raw_R2.fastq.gz log: SAMEA103958162/logs/QC/init.log jobid: 43 wildcards: sample=SAMEA103958162 priority: 80 threads: 4 resources: tmpdir=/local_scratch/student223, mem=10, java_mem=8, time=1, mem_mb=10000, time_min=60
CLUSTER: 2021-09-27 16:14:47 submit command: sbatch --parsable --output=cluster_log/%j.out --error=cluster_log/%j.out --job-name=initialize_qc --cpus-per-task=4 -n1 --time=60 --mem=10000m /users/student223/Human/.snakemake/tmp.80uen2e6/snakejob.initialize_qc.43.sh CLUSTER: 2021-09-27 16:14:47 Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Error submitting jobscript (exit code 1): Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Job failed, going on with independent jobs.
[Mon Sep 27 16:14:47 2021] rule build_decontamination_db: input: /scratch/project_2004930/databases/phiX174_virus.fa output: ref/genome/1/summary.txt log: logs/QC/build_decontamination_db.log jobid: 14 threads: 8 resources: tmpdir=/local_scratch/student223, mem=90, java_mem=76, time=5, mem_mb=90000, time_min=300
CLUSTER: 2021-09-27 16:14:47 submit command: sbatch --parsable --output=cluster_log/%j.out --error=cluster_log/%j.out --job-name=build_decontamination_db --cpus-per-task=8 -n1 --time=300 --mem=90000m /users/student223/Human/.snakemake/tmp.80uen2e6/snakejob.build_decontamination_db.14.sh CLUSTER: 2021-09-27 16:14:47 Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Error submitting jobscript (exit code 1): Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Job failed, going on with independent jobs.
[Mon Sep 27 16:14:47 2021] rule initialize_qc: input: /users/student223/shared/Human/SAMEA103958166_1.fastq.gz, /users/student223/shared/Human/SAMEA103958166_2.fastq.gz output: SAMEA103958166/sequence_quality_control/SAMEA103958166_raw_R1.fastq.gz, SAMEA103958166/sequence_quality_control/SAMEA103958166_raw_R2.fastq.gz log: SAMEA103958166/logs/QC/init.log jobid: 127 wildcards: sample=SAMEA103958166 priority: 80 threads: 4 resources: tmpdir=/local_scratch/student223, mem=10, java_mem=8, time=1, mem_mb=10000, time_min=60
CLUSTER: 2021-09-27 16:14:47 submit command: sbatch --parsable --output=cluster_log/%j.out --error=cluster_log/%j.out --job-name=initialize_qc --cpus-per-task=4 -n1 --time=60 --mem=10000m /users/student223/Human/.snakemake/tmp.80uen2e6/snakejob.initialize_qc.127.sh CLUSTER: 2021-09-27 16:14:48 Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Error submitting jobscript (exit code 1): Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Job failed, going on with independent jobs.
[Mon Sep 27 16:14:48 2021] rule initialize_qc: input: /users/student223/shared/Human/SAMEA103958161_1.fastq.gz, /users/student223/shared/Human/SAMEA103958161_2.fastq.gz output: SAMEA103958161/sequence_quality_control/SAMEA103958161_raw_R1.fastq.gz, SAMEA103958161/sequence_quality_control/SAMEA103958161_raw_R2.fastq.gz log: SAMEA103958161/logs/QC/init.log jobid: 183 wildcards: sample=SAMEA103958161 priority: 80 threads: 4 resources: tmpdir=/local_scratch/student223, mem=10, java_mem=8, time=1, mem_mb=10000, time_min=60
CLUSTER: 2021-09-27 16:14:48 submit command: sbatch --parsable --output=cluster_log/%j.out --error=cluster_log/%j.out --job-name=initialize_qc --cpus-per-task=4 -n1 --time=60 --mem=10000m /users/student223/Human/.snakemake/tmp.80uen2e6/snakejob.initialize_qc.183.sh CLUSTER: 2021-09-27 16:14:48 Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Error submitting jobscript (exit code 1): Job can't be submitted sbatch: error: AssocMaxSubmitJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
Job failed, going on with independent jobs. Exiting because a job execution failed. Look above for error message Note the path to the log file for debugging. Documentation is available at: https://metagenome-atlas.readthedocs.io Issues can be raised at: https://github.com/metagenome-atlas/atlas/issues Complete log: /users/student223/Human/.snakemake/log/2021-09-27T161441.941750.snakemake.log [2021-09-27 16:14 CRITICAL] Command 'snakemake --snakefile /scratch/project_2004930/atlas/atlas/Snakefile --directory /users/student223/Human --jobs 10 --rerun-incomplete --configfile '/users/student223/Human/config.yaml' --nolock --profile cluster --use-conda --conda-prefix /scratch/project_2004930/databases/conda_envs --scheduler greedy binning --keep-going ' returned non-zero exit status 1.