diff --git a/config/slurm/profile/config_plugin_dardel.yaml b/config/slurm/profile/config_plugin_dardel.yaml index 91c39d8..f35a5e5 100644 --- a/config/slurm/profile/config_plugin_dardel.yaml +++ b/config/slurm/profile/config_plugin_dardel.yaml @@ -13,10 +13,10 @@ default-resources: slurm_account: XXX-XX-XXX # update this to your slurm account slurm_partition: shared # use Dardel’s shared partition runtime: 120 # default runtime in minutes - mem_mb: 8000 + mem_mb: 6400 nodes: 1 # one node on Dardel from the shared partition ntasks: 1 # number of concurrent tasks / ranks - cpus_per_task: 8 # number of hyperthreads per task, corresponds to 1 GB RAM + cpus_per_task: 8 # number of hyperthreads per task, corresponds to 0.8 GB RAM ## set-threads: map rule names to threads set-threads: @@ -100,110 +100,110 @@ set-threads: set-resources: repeatmodeler: runtime: 10080 - mem_mb: 128000 + mem_mb: 102400 cpus_per_task: 128 repeatmasker: runtime: 10080 - mem_mb: 128000 + mem_mb: 102400 cpus_per_task: 128 historical_fastq_before_group: runtime: 600 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 fastqc_historical_raw: - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 fastqc_modern_raw: - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 fastp_historical: runtime: 600 - mem_mb: 32000 + mem_mb: 25600 cpus_per_task: 32 fastp_modern: runtime: 600 - mem_mb: 32000 + mem_mb: 25600 cpus_per_task: 32 fastqc_historical_merged: - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 fastqc_historical_unmerged: - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 fastqc_modern_trimmed: - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 map_historical: runtime: 10080 - mem_mb: 64000 + mem_mb: 51200 cpus_per_task: 64 sai2bam: runtime: 10080 - mem_mb: 64000 + mem_mb: 51200 cpus_per_task: 64 map_modern: runtime: 10080 - mem_mb: 64000 + mem_mb: 51200 cpus_per_task: 64 sorted_bam_qualimap: runtime: 5760 - mem_mb: 64000 + mem_mb: 51200 cpus_per_task: 64 merge_historical_bams_per_index: runtime: 2880 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 merge_modern_bams_per_index: runtime: 2880 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 merged_index_bam_qualimap: runtime: 5760 - mem_mb: 64000 + mem_mb: 51200 cpus_per_task: 64 rmdup_historical_bams: runtime: 4320 - mem_mb: 48000 + mem_mb: 38400 cpus_per_task: 48 rmdup_modern_bams: runtime: 4320 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 rmdup_bam_qualimap: runtime: 5760 - mem_mb: 64000 + mem_mb: 51200 cpus_per_task: 64 merge_historical_bams_per_sample: runtime: 2880 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 merge_modern_bams_per_sample: runtime: 2880 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 merged_sample_bam_qualimap: runtime: 5760 - mem_mb: 64000 + mem_mb: 51200 cpus_per_task: 64 indel_realigner_targets: runtime: 7200 - mem_mb: 64000 + mem_mb: 51200 cpus_per_task: 64 indel_realigner: runtime: 7200 - mem_mb: 64000 + mem_mb: 51200 cpus_per_task: 64 realigned_bam_qualimap: runtime: 5760 - mem_mb: 64000 + mem_mb: 51200 cpus_per_task: 64 realigned_bam_group: runtime: 2880 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 rescale_historical: runtime: 4320 - mem_mb: 32000 + mem_mb: 25600 cpus_per_task: 32 rescaled_bam_qualimap: runtime: 5760 @@ -213,21 +213,21 @@ set-resources: runtime: 1440 subsample_bams: runtime: 5760 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 subsampled_bam_qualimap: runtime: 5760 - mem_mb: 48000 + mem_mb: 38400 cpus_per_task: 48 subsampled_bam_group: runtime: 2880 variant_calling: runtime: 2880 - mem_mb: 32000 + mem_mb: 25600 cpus_per_task: 32 sort_vcfs: runtime: 1440 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 sorted_bcf2vcf: runtime: 300 @@ -235,45 +235,45 @@ set-resources: runtime: 1440 CpG_genotype_bed_formatting_group: runtime: 1440 - mem_mb: 32000 + mem_mb: 25600 cpus_per_task: 32 all_CpG_bed_formatting_group: runtime: 1440 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 make_noCpG_bed: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 CpG_repeats_bed_formatting_group: runtime: 1440 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 merge_noCpG_noRepeats_beds: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 make_noCpG_repma_bed: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 make_autosomes_bed: runtime: 300 intersect_sexchr_repma_beds: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 intersect_autos_repma_beds: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 intersect_sexchr_CpG_repma_beds: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 intersect_autos_CpG_repma_beds: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 bam2pro_autos: runtime: 1440 @@ -283,47 +283,47 @@ set-resources: runtime: 1440 remove_CpG_vcf: runtime: 300 - mem_mb: 48000 + mem_mb: 38400 cpus_per_task: 48 CpG_vcf2bcf: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 remove_snps_near_indels: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 filter_vcfs_qual_dp: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 filter_vcfs_allelic_balance: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 remove_repeats_vcf: runtime: 300 - mem_mb: 48000 + mem_mb: 38400 cpus_per_task: 48 filtered_vcf2bcf: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 merge_all_vcfs: runtime: 4320 - mem_mb: 48000 + mem_mb: 38400 cpus_per_task: 48 filter_vcf_biallelic: runtime: 1440 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 filter_vcf_missing: runtime: 1440 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 remove_chromosomes: runtime: 1440 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 extract_historical_samples: runtime: 300 @@ -331,23 +331,23 @@ set-resources: runtime: 300 repmasked_bcf2vcf: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 filter_biallelic_missing_vcf: runtime: 1440 - mem_mb: 48000 + mem_mb: 38400 cpus_per_task: 48 vcf2plink_pca: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 filter_vcf_hwe: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 vcf2plink_hwe: runtime: 300 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 build_snpEff_db: runtime: 300 @@ -355,57 +355,57 @@ set-resources: runtime: 300 outgroup_fastqc: runtime: 16 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 align2target: runtime: 4320 - mem_mb: 64000 + mem_mb: 51200 cpus_per_task: 64 bam2fasta: runtime: 1440 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 concatenate_fasta_per_contig: runtime: 1440 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 compute_gerp: runtime: 1440 - mem_mb: 32000 + mem_mb: 25600 cpus_per_task: 32 gerp2coords: runtime: 1440 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 get_ancestral_state: runtime: 1440 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 produce_contig_out: runtime: 1440 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 merge_per_chunk: runtime: 1440 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 merge_gerp_gz: runtime: 1440 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 gerp_derived_alleles: runtime: 10080 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16 merge_gerp_alleles_per_chunk: runtime: 1440 - mem_mb: 32000 + mem_mb: 25600 cpus_per_task: 32 merge_gerp_alleles_gz: runtime: 1440 - mem_mb: 32000 + mem_mb: 25600 cpus_per_task: 32 relative_mutational_load_per_sample: runtime: 1440 - mem_mb: 16000 + mem_mb: 12800 cpus_per_task: 16