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Adjust memory to 0.8GB per hyperthread
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@verku
verku committed Nov 20, 2024
1 parent b0c634a commit baf9fb3
Showing 1 changed file with 74 additions and 74 deletions.
148 changes: 74 additions & 74 deletions config/slurm/profile/config_plugin_dardel.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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
Expand All @@ -213,67 +213,67 @@ 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
make_CpG_genotype_bed:
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
Expand All @@ -283,129 +283,129 @@ 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
extract_modern_samples:
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
annotate_vcf:
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

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