fix #676

workflow/rules/assemble.smk

@@ -51,7 +51,7 @@ if SKIP_QC & (len(MULTIFILE_FRACTIONS) < 3):
             "%s/required_packages.yaml" % CONDAENV
         threads: config.get("simplejob_threads", 1)
         resources:
-            mem=config["simplejob_mem"],
+            mem_mb=config["simplejob_mem"]*1024,
             java_mem=int(config["simplejob_mem"] * JAVA_MEM_FRACTION),
         shell:
             """
@@ -128,7 +128,7 @@ rule normalize_reads:
         "%s/required_packages.yaml" % CONDAENV
     threads: config.get("threads", 1)
     resources:
-        mem=config["mem"],
+        mem_mb=config["mem"]*1024,
         java_mem=int(config["mem"] * JAVA_MEM_FRACTION),
     shell:
         " bbnorm.sh {params.inputs} "
@@ -165,7 +165,7 @@ rule error_correction:
     conda:
         "%s/required_packages.yaml" % CONDAENV
     resources:
-        mem=config["mem"],
+        mem_mb=config["mem"]*1024,
         java_mem=int(config["mem"] * JAVA_MEM_FRACTION),
     params:
         inputs=lambda wc, input: io_params_for_tadpole(input),
@@ -212,7 +212,7 @@ rule merge_pairs:
         ),
     threads: config.get("threads", 1)
     resources:
-        mem=config["mem"],
+        mem_mb=config["mem"]*1024,
         java_mem=int(config["mem"] * JAVA_MEM_FRACTION),
     conda:
         "%s/required_packages.yaml" % CONDAENV
@@ -312,7 +312,7 @@ if config.get("assembler", "megahit") == "megahit":
             "../envs/megahit.yaml"
         threads: config["assembly_threads"]
         resources:
-            mem_mb=config["assembly_memory"]*1000,
+            mem_mb=config["assembly_memory"] * 1000,
             time=config["runtime"]["assembly"],
         shell:
             """
@@ -431,7 +431,7 @@ else:
             "../envs/spades.yaml"
         threads: config["assembly_threads"]
         resources:
-            mem=config["assembly_memory"],
+            mem_mb=config["assembly_memory"]*1024,
             time=config["runtime"]["assembly"],
         shell:
             # remove pipeline_state file to create all output files again
@@ -474,7 +474,7 @@ rule rename_contigs:
         mapping_table="{sample}/assembly/old2new_contig_names.tsv",
     threads: config.get("simplejob_threads", 1)
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=config["simplejob_mem"]*1024,
         time=config["runtime"]["default"],
     log:
         "{sample}/logs/assembly/post_process/rename_and_filter_size.log",
@@ -552,7 +552,7 @@ if config["filter_contigs"]:
             "%s/required_packages.yaml" % CONDAENV
         threads: 1
         resources:
-            mem=config["simplejob_mem"],
+            mem_mb=config["simplejob_mem"]*1024,
             java_mem=int(config["simplejob_mem"] * JAVA_MEM_FRACTION),
         shell:
             """filterbycoverage.sh in={input.fasta} \
@@ -610,7 +610,7 @@ rule calculate_contigs_stats:
         "{sample}/logs/assembly/post_process/contig_stats_final.log",
     threads: 1
     resources:
-        mem=1,
+        mem_mb=1024,
         time=config["runtime"]["simplejob"],
     shell:
         "stats.sh in={input} format=3 out={output} &> {log}"
@@ -660,7 +660,7 @@ rule pileup_contigs_sample:
         "%s/required_packages.yaml" % CONDAENV
     threads: config.get("threads", 1)
     resources:
-        mem=config["mem"],
+        mem_mb=config["mem"]*1024,
         java_mem=int(config["mem"] * JAVA_MEM_FRACTION),
     shell:
         "pileup.sh "
@@ -686,7 +686,7 @@ rule create_bam_index:
         "../envs/required_packages.yaml"
     threads: 1
     resources:
-        mem=2 * config["simplejob_threads"],
+        mem_mb=2 * config["simplejob_threads"] *1024,
     shell:
         "samtools index {input}"
 
@@ -706,7 +706,7 @@ rule predict_genes:
         "logs/benchmarks/prodigal/{sample}.txt"
     threads: 1
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=config["simplejob_mem"]*1024,
         time=config["runtime"]["simplejob"],
     shell:
         """

workflow/rules/binning.smk

@@ -94,7 +94,7 @@ rule run_concoct:
         "%s/concoct.yaml" % CONDAENV
     threads: 10  # concoct uses 10 threads by default, wit for update: https://github.com/BinPro/CONCOCT/issues/177
     resources:
-        mem=config["mem"],
+        mem_mb=config["mem"]*1024,
     shell:
         """
         concoct -c {params.Nexpected_clusters} \
@@ -176,7 +176,7 @@ rule metabat:
         "%s/metabat.yaml" % CONDAENV
     threads: config["threads"]
     resources:
-        mem=config["mem"],
+        mem_mb=config["mem"]*1024,
     shell:
         """
         metabat2 -i {input.contigs} \

workflow/rules/cdhit.smk

@@ -65,7 +65,7 @@ rule cluster_genes:
         "logs/Genecatalog/cluster_genes.log",
     threads: config.get("threads", 1)
     resources:
-        mem=config["mem"],
+        mem_mb=config["mem"]*1024,
     params:
         coverage=config["genecatalog"]["coverage"],
         identity=config["genecatalog"]["minid"],

workflow/rules/cobinning.smk

@@ -19,7 +19,7 @@ rule filter_contigs:
         "../envs/required_packages.yaml"
     threads: 1
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=config["simplejob_mem"]*1024,
         java_mem=int(config["simplejob_mem"] * JAVA_MEM_FRACTION),
     shell:
         " reformat.sh in={input} "
@@ -93,7 +93,7 @@ rule minimap_index:
     params:
         index_size="12G",
     resources:
-        mem=config["mem"],  # limited num of fatnodes (>200g)
+        mem_mb=config["mem"]*1024,  # limited num of fatnodes (>200g)
     threads: config["simplejob_threads"]
     log:
         "logs/cobinning/{bingroup}/minimap_index.log",
@@ -111,7 +111,7 @@ rule samtools_dict:
     output:
         dict="Intermediate/cobinning/{bingroup}/combined_contigs.dict",
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=config["simplejob_mem"]*1024,
         time=config["runtime"]["simplejob"],
     threads: 1
     log:
@@ -131,7 +131,7 @@ rule minimap:
         bam=temp("Intermediate/cobinning/{bingroup}/bams/{sample}.unsorted.bam"),
     threads: config["threads"]
     resources:
-        mem=config["mem"],
+        mem_mb=config["mem"]*1024,
     log:
         "logs/cobinning/{bingroup}/mapping/minimap/{sample}.log",
     benchmark:

workflow/rules/dram.smk

@@ -22,7 +22,7 @@ rule dram_download:
         config=f"{DBDIR}/DRAM/DRAM.config",
     threads: config["threads"]
     resources:
-        mem=config["mem"],
+        mem_mb=config["mem"]*1024,
         time=config["runtime"]["default"],
     log:
         "logs/dram/download_dram.log",
@@ -51,7 +51,7 @@ rule DRAM_annotate:
         outdir=directory("genomes/annotations/dram/intermediate_files/{genome}"),
     threads: config["simplejob_threads"]
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=config["simplejob_mem"]*1024,
         time=config["runtime"]["default"],
     conda:
         "../envs/dram.yaml"
@@ -112,7 +112,7 @@ rule DRAM_destill:
         outdir=directory("genomes/annotations/dram/distil"),
     threads: 1
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=config["simplejob_mem"]*1024,
         ttime=config["runtime"]["simplejob"],
     conda:
         "../envs/dram.yaml"
@@ -134,7 +134,7 @@ rule get_all_modules:
         "genomes/annotations/dram/kegg_modules.tsv",
     threads: 1
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=config["simplejob_mem"]*1024,
         time=config["runtime"]["default"],
     conda:
         "../envs/dram.yaml"

workflow/rules/genecatalog.smk

@@ -150,7 +150,7 @@ if (config["genecatalog"]["clustermethod"] == "linclust") or (
             "../envs/required_packages.yaml"
         threads: 1
         resources:
-            mem=config["mem"],
+            mem_mb=config["mem"]*1024,
             java_mem=int(config["mem"] * JAVA_MEM_FRACTION),
         log:
             "logs/Genecatalog/clustering/get_cds_of_proteins.log",
@@ -218,7 +218,7 @@ rule get_genecatalog_seq_info:
         "../envs/required_packages.yaml"
     threads: 1
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=config["simplejob_mem"]*1024,
         java_mem=int(config["simplejob_mem"] * JAVA_MEM_FRACTION),
     shell:
         "stats.sh gcformat=4 gc={output} in={input} &> {log}"
@@ -283,7 +283,7 @@ rule pileup_Genecatalog:
         "../envs/required_packages.yaml"
     threads: config["threads"]
     resources:
-        mem=config["mem"],
+        mem_mb=config["mem"]*1024,
         java_mem=int(config["mem"] * JAVA_MEM_FRACTION),
     shell:
         " pileup.sh "
@@ -304,7 +304,7 @@ rule gene_pileup_as_parquet:
         "Genecatalog/alignments/{sample}_coverage.parquet",
     threads: 1
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=config["simplejob_mem"]*1024,
         time_min=config["runtime"]["simplejob"] * 60,
     log:
         "logs/Genecatalog/counts/parse_gene_coverages/{sample}.log",
@@ -368,7 +368,7 @@ rule combine_gene_coverages:
         "../envs/hdf.yaml"
     threads: 1
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=config["simplejob_mem"]*1024,
         time_min=get_combine_cov_time(),
     script:
         "../scripts/combine_gene_coverages.py"
@@ -441,7 +441,7 @@ rule eggNOG_homology_search:
         data_dir=EGGNOG_DIR,
         prefix=lambda wc, output: output[0].replace(".emapper.seed_orthologs", ""),
     resources:
-        mem=config["mem"],
+        mem_mb=config["mem"]*1024,
     threads: config["threads"]
     shadow:
         "minimal"
@@ -458,8 +458,8 @@ rule eggNOG_homology_search:
 
 
 def calculate_mem_eggnog():
-    return 2 * config["simplejob_mem"] + (
-        37 if config["eggNOG_use_virtual_disk"] else 0
+    return 1024 *(2 * config["simplejob_mem"] + (
+        37 if config["eggNOG_use_virtual_disk"] )else 0
     )
 
 
@@ -477,7 +477,7 @@ rule eggNOG_annotation:
         copyto_shm="t" if config["eggNOG_use_virtual_disk"] else "f",
     threads: config.get("threads", 1)
     resources:
-        mem=calculate_mem_eggnog(),
+        mem_mb=calculate_mem_eggnog(),
     shadow:
         "minimal"
     conda:
@@ -597,7 +597,7 @@ rule DRAM_annotate_genecatalog:
         genes=temp("Intermediate/genecatalog/annotation/dram/{subset}/genes.faa"),
     threads: config["simplejob_threads"]
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=config["simplejob_mem"]*1024,
         time=config["runtime"]["long"],
     conda:
         "../envs/dram.yaml"
@@ -696,7 +696,7 @@ rule gene2genome:
 #     threads:
 #         12
 #     resources:
-#         mem= 220
+#         mem_mb= 220*1024
 #     shell:
 #         """
 #         canopy -i {input} -o {output.cluster} -c {output.profile} -n {threads} --canopy_size_stats_file {log} {params.canopy_params} 2> {log}

workflow/rules/genomes.smk

@@ -134,7 +134,7 @@ rule predict_genes_genomes:
         "logs/genomes/prodigal/{genome}.txt",
     threads: 1
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=config["simplejob_mem"]*1024,
         time=config["runtime"]["simplejob"],
     shell:
         """
@@ -204,7 +204,7 @@ if config["genome_aligner"] == "minimap":
             index_size="12G",
         threads: 3
         resources:
-            mem=config["mem"],
+            mem_mb=config["mem"]*1024,
         wrapper:
             "v1.19.0/bio/minimap2/index"
 
@@ -221,7 +221,7 @@ if config["genome_aligner"] == "minimap":
             sort="coordinate",
         threads: config["threads"]
         resources:
-            mem=config["mem"],
+            mem_mb=config["mem"]*1024,
             mem_mb=config["mem"] * 1000,
         wrapper:
             "v1.19.0/bio/minimap2/aligner"
@@ -238,7 +238,7 @@ elif config["genome_aligner"] == "bwa":
             "logs/genomes/alignments/bwa_index.log",
         threads: 4
         resources:
-            mem=config["mem"],
+            mem_mb=config["mem"]*1024,
         wrapper:
             "v1.19.0/bio/bwa-mem2/index"
 
@@ -256,7 +256,7 @@ elif config["genome_aligner"] == "bwa":
             sort_order="coordinate",
         threads: config["threads"]
         resources:
-            mem=config["mem"],
+            mem_mb=config["mem"]*1024,
             mem_mb=config["mem"] * 1000,
         wrapper:
             "v1.19.0/bio/bwa-mem2/mem"
@@ -297,7 +297,7 @@ rule mapping_stats_genomes:
         "logs/genomes/alignments/{sample}_stats.log",
     threads: 1
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=config["simplejob_mem"]*1024,
     wrapper:
         "v1.19.0/bio/samtools/stats"
 
@@ -329,7 +329,7 @@ rule pileup_MAGs:
         "../envs/required_packages.yaml"
     threads: config["threads"]
     resources:
-        mem=config["mem"],
+        mem_mb=config["mem"]*1024,
         java_mem=int(config["mem"] * JAVA_MEM_FRACTION),
     shell:
         "pileup.sh in={input.bam} "

workflow/rules/gtdbtk.smk

@@ -53,7 +53,7 @@ rule classify:
         directory(f"{gtdb_dir}/classify"),
     threads: config["threads"]  #pplacer needs much memory for not many threads
     resources:
-        mem=config["large_mem"],
+        mem_mb=config["large_mem"]*1024,
         time=config["runtime"]["long"],
     conda:
         "../envs/gtdbtk.yaml"
@@ -123,7 +123,7 @@ rule root_tree:
         "../envs/tree.yaml"
     threads: 1
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=config["simplejob_mem"]*1024,
         ttime=config["runtime"]["simplejob"],
     log:
         "logs/genomes/tree/root_tree_{msa}.log",

workflow/rules/patch.smk

@@ -4,8 +4,10 @@ localrules:
 
 # Rules that are usefull temporarily to update to new version of atlas
 
+
 ruleorder: copy_assembly > finalize_contigs
 
+
 rule copy_assembly:
     input:
         "{sample}/{sample}_contigs.fasta",