memory/time fixes

tdayris · Dec 18, 2023 · f3dd770 · f3dd770
1 parent 2dbea37
commit f3dd770
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/workflow/rules/agat/gff2gtf.smk b/workflow/rules/agat/gff2gtf.smk
@@ -5,8 +5,8 @@ rule agat_gff2gtf:
         gtf="reference/{species}.{build}.{release}.gtf",
     threads: 1
     resources:
-        # Reserve 14Gb per attempt (max_vms: 12786.95 on Flamingo)
-        mem_mb=lambda wildcards, attempt: (1024 * 14) * attempt,
+        # Reserve 16Gb per attempt (max_vms: 12786.95 on Flamingo)
+        mem_mb=lambda wildcards, attempt: (1024 * 16) * attempt,
         # Reserve 20min per attempts (hg38: 0:14:50 on Flamingo)
         runtime=lambda wildcards, attempt: 20 * attempt,
         tmpdir="tmp",

diff --git a/workflow/rules/raw_data/genome_variation.smk b/workflow/rules/raw_data/genome_variation.smk
@@ -5,8 +5,8 @@ rule get_genome_vcf_variations:
     resources:
         # Reserve 700Mb per attempt (max_vms: 691.63 on Flamingo)
         mem_mb=lambda wildcards, attempt: 700 * attempt,
-        # Reserve 45min per attempts (hg38: 0:42:53 on Flamingo)
-        runtime=lambda wildcards, attempt: 45 * attempt,
+        # Reserve 1h per attempts (hg38: 0:56:07 on Flamingo)
+        runtime=lambda wildcards, attempt: 60 * attempt,
         tmpdir="tmp",
     log:
         "logs/get_genome/fasta_sequence/{species}.{build}.{release}.{datatype}.log",