diff --git a/metagenomics.py b/metagenomics.py index d15e3402f..8106c39be 100755 --- a/metagenomics.py +++ b/metagenomics.py @@ -1244,7 +1244,7 @@ def rpsblast_models(db, inFasta, outReport, orfs=None, numThreads=None): args = [] if int(numThreads) > 1: - args.extend(['-num_threads', '1']) + args.extend(['-num_threads', numThreads]) args.extend(['-db', db, '-outfmt', '6', '-query', orf_fn, '-out', outReport]) diff --git a/pipes/rules/assembly.rules b/pipes/rules/assembly.rules index f4810258c..f4d387795 100644 --- a/pipes/rules/assembly.rules +++ b/pipes/rules/assembly.rules @@ -63,7 +63,7 @@ rule assemble_spades: clipDb = objectify_remote(config["trim_clip_db"]) output: contigs_spades=config["tmp_dir"] +'/'+config["subdirs"]["assembly"]+'/{sample}.assembly1-spades.fasta' resources: - mem=12, + mem=100, threads=int(config.get("number_of_threads", 1)) params: n_reads=str(config["spades_n_reads"]), logid="{sample}" @@ -79,7 +79,7 @@ rule assemble_trinity_spades: contigs_trinity=config["tmp_dir"] +'/'+config["subdirs"]["assembly"]+'/{sample}.assembly1-trinity.fasta' output: contigs_trinity_spades=config["tmp_dir"] +'/'+config["subdirs"]["assembly"]+'/{sample}.assembly1-trinity-spades.fasta' resources: - mem=12, + mem=100, threads=int(config.get("number_of_threads", 1)) params: n_reads=str(config["spades_n_reads"]), logid="{sample}"