Bam sort memory, fix #404 (#407)

vanheeringen-lab · Jun 16, 2020 · 4580785 · 4580785
1 parent db24671
commit 4580785
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Showing 3 changed files with 17 additions and 8 deletions.
diff --git a/seq2science/rules/alignment.smk b/seq2science/rules/alignment.smk
@@ -295,11 +295,11 @@ rule samtools_presort:
         expand("{benchmark_dir}/samtools_presort/{{assembly}}-{{sample}}.benchmark.txt", **config)[0]
     params:
         threads=lambda wildcards, input, output, threads: max([1, threads - 1]),
-        sort_order="-n" if not sieve_bam(config) and config.get("bam_sort_order") == "queryname" else "",
-        out_dir=f"{config['result_dir']}/{config['aligner']}"
+        out_dir=f"{config['result_dir']}/{config['aligner']}",
+        memory=lambda wildcards, input, output, threads: f"-m {int(1000 * round(config['bam_sort_mem']/threads, 3))}M"
     threads: 2
     resources:
-        mem_mb=2500
+        mem_gb=config['bam_sort_mem']
     conda:
         "../envs/samtools.yaml"
     shell:
@@ -308,6 +308,6 @@ rule samtools_presort:
         trap "rm -f {params.out_dir}/{wildcards.assembly}-{wildcards.sample}.tmp*bam" INT;
         rm -f {params.out_dir}/{wildcards.assembly}-{wildcards.sample}.tmp*bam 2> {log}
         
-        samtools sort {params.sort_order} -@ {params.threads} {input} -o {output} \
+        samtools sort -@ {params.threads} {params.memory} {input} -o {output} \
         -T {params.out_dir}/{wildcards.assembly}-{wildcards.sample}.tmp 2> {log}
         """
diff --git a/seq2science/rules/bam_cleaning.smk b/seq2science/rules/bam_cleaning.smk
@@ -120,10 +120,13 @@ rule sambamba_sort:
     benchmark:
         expand("{benchmark_dir}/sambamba_sort/{{assembly}}-{{sample}}-{{sorting}}{{sieve}}.benchmark.txt", **config)[0]
     params:
-        lambda wildcards: "-n" if 'queryname' in wildcards.sorting else '',
+        sort_order=lambda wildcards: "-n" if 'queryname' in wildcards.sorting else '',
+        memory=f"-m {config['bam_sort_mem']}G"
     threads: 2
     conda:
         "../envs/sambamba.yaml"
+    resources:
+        mem_gb=config['bam_sort_mem']
     shell:
         """
         sambamba view --nthreads {threads} -f bam  {input} -o /dev/stdout  2> {log} |
@@ -146,10 +149,11 @@ rule samtools_sort:
     params:
         sort_order=lambda wildcards: "-n" if wildcards.sorting == 'queryname' else '',
         threads=lambda wildcards, input, output, threads: max([1, threads - 1]),
-        out_dir=f"{config['result_dir']}/{config['aligner']}"
+        out_dir=f"{config['result_dir']}/{config['aligner']}",
+        memory=lambda wildcards, input, output, threads: f"-m {int(1000 * round(config['bam_sort_mem']/threads, 3))}M"
     threads: 2
     resources:
-        mem_mb=2500
+        mem_gb=config['bam_sort_mem']
     conda:
         "../envs/samtools.yaml"
     shell:
@@ -158,7 +162,7 @@ rule samtools_sort:
         trap "rm -f {params.out_dir}/{wildcards.assembly}-{wildcards.sample}.tmp*bam" INT;
         rm -f {params.out_dir}/{wildcards.assembly}-{wildcards.sample}.tmp*bam 2> {log}
         
-        samtools sort {params.sort_order} -@ {params.threads} {input} -o {output} \
+        samtools sort {params.sort_order} -@ {params.threads} {params.memory} {input} -o {output} \
         -T {params.out_dir}/{wildcards.assembly}-{wildcards.sample}.tmp 2> {log}
         """
 

diff --git a/seq2science/schemas/config/alignment_general.schema.yaml b/seq2science/schemas/config/alignment_general.schema.yaml
@@ -129,3 +129,8 @@ properties:
     description: whether or not to generate a multiqc report
     default: True
     type: boolean
+
+  bam_sort_mem:
+    description: The max memory used in gigabytes by samtools/sambamba when sorting bams
+    default: 2
+    type: integer