Error #8
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Can you send me the content of And ~/.config/snakemake/cluster/cluster_config.yaml |
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################################################################### _______ _ _____/\ |__ __| | | /\ / ____|/ \ | | | | / \ | (___/ /\ \ | | | | / /\ \ ___ \/ ____ \ | | | |____ / ____ \ ____) |// _\ || || // _\ |/################################################################### For more details about the config values see:https://metagenome-atlas.rtfd.io######################## Execution parameters######################## threads and memory (GB) for most jobs especially from BBtools, which are memory demandingthreads: 8 threads and memory for jobs needing high amount of memory. e.g GTDB-tk,checkm or assemblylarge_mem: 250 #Runtime only for cluster execution Local directory for temp files, useful for cluster execution without shared file systemtmpdir: /local_scratch/student198 directory where databases are downloaded with 'atlas download'database_dir: /scratch/project_2004930/databases ######################## Quality control######################## remove (PCR)-duplicated reads using clumpifydeduplicate: true used to trim adapters from reads and read endspreprocess_adapters: /scratch/project_2004930/databases/adapters.fa 0.05 requires at least 5 percent of each nucleotide per sequencepreprocess_minimum_base_frequency: 0.05 error correction where PE reads overlaperror_correction_overlapping_pairs: true ######################## Pre-assembly-processing######################## error_correction_before_assembly: true join R1 and R2 at overlap; unjoined reads are still utilizedmerge_pairs_before_assembly: true extend reads while merging to this many nucleotidesmerging_extend2: 40 Iterations are performed until extend2 x iterationsmerging_flags: ecct iterations=5 ######################## Assembly######################## megahit OR spadesassembler: spades Megahit#----------- 2 is for metagenomes, 3 for genomes with 30x coveragemegahit_min_count: 2 ['default','meta-large','meta-sensitive']megahit_preset: default Spades#------------ Preprocessed long reads can be defined in the sample table with 'longreads' , for more info see the spades manualFiltering#------------ filter out assembled noisethis is more important for assemblys from megahitfilter_contigs: true trim contig tipscontig_trim_bp: 0 require contigs to have read supportminimum_average_coverage: 1 after filteringminimum_contig_length: 500 ######################## Quantification######################## Mapping reads to contigs#-------------------------- ######################## Binning######################## final_binner: DASTool # [DASTool or one of the binner, e.g. maxbin] binner: # If DASTool is used as final_binner, use predictions of this binners
metabat: maxbin: DASTool: genome_dereplication: rename_mags_contigs: true #Rename contigs of representative MAGs ######################## Annotations####################### annotations:
- checkm_taxonomy- checkm_tree######################## Gene catalog####################### eggNOG_use_virtual_disk: false # coping the eggNOG DB to a virtual disk can sppeed up the annotation |
This is a yaml file, defining options for specific rules or by default.The '#' defines a comment.the two spaces at the beginning of rows below rulenames are important.## For more information see https://snakemake.readthedocs.io/en/stable/executing/cluster-cloud.html#cluster-execution Overwrite/Define arguments for all rulesdefault: rename_contigs: queue: normalYou can overwrite values for specific rulesrulename: |
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What is this error about? snakemake.exceptions.WorkflowError: Config file is not valid JSON or YAML. In case of YAML, make sure to not mix whitespace and tab indentation. |
snakemake: error: unrecognized arguments: --threads=8 --mem=60 --large_mem=250 --large_threads=8 --assembly_threads=8 --assembly_memory=250 --tmpdir=/local_scratch/student198 --database_dir=/scratch/project_2004930/databases --data_type=metagenome --interleaved_fastqs=False --deduplicate=True --duplicates_only_optical=False --duplicates_allow_substitutions=2 --preprocess_adapters=/scratch/project_2004930/databases/adapters.fa --preprocess_minimum_base_quality=10 --preprocess_minimum_passing_read_length=51 --preprocess_minimum_base_frequency=0.05 --preprocess_adapter_min_k=8 --preprocess_allowable_kmer_mismatches=1 --preprocess_reference_kmer_match_length=27 --error_correction_overlapping_pairs=True --contaminant_max_indel=20 --contaminant_min_ratio=0.65 --contaminant_kmer_length=13 --contaminant_minimum_hits=1 --contaminant_ambiguous=best --error_correction_before_assembly=True --merge_pairs_before_assembly=True --merging_k=62 --merging_extend2=40 --merging_flags=ecct iterations=5 --assembler=spades --megahit_min_count=2 --megahit_k_min=21 --megahit_k_max=121 --megahit_k_step=20 --megahit_merge_level=20,0.98 --megahit_prune_level=2 --megahit_low_local_ratio=0.2 --megahit_preset=default --spades_skip_BayesHammer=True --spades_use_scaffolds=True --spades_k=auto --spades_preset=meta --spades_extra= --longread_type=none --filter_contigs=True --prefilter_minimum_contig_length=300 --contig_trim_bp=0 --minimum_average_coverage=1 --minimum_percent_covered_bases=20 --minimum_mapped_reads=0 --minimum_contig_length=500 --contig_min_id=0.9 --contig_map_paired_only=True --contig_max_distance_between_pairs=1000 --maximum_counted_map_sites=10 --final_binner=DASTool --binner=metabat --binner=maxbin --metabat={'sensitivity': 'sensitive', 'min_contig_length': 1500} --maxbin={'max_iteration': 50, 'prob_threshold': 0.9, 'min_contig_length': 1000} --DASTool={'search_engine': 'diamond', 'score_threshold': 0.5} --genome_dereplication={'ANI': 0.95, 'overlap': 0.6, 'opt_parameters': '', 'filter': {'noFilter': False, 'length': 5000, 'completeness': 50, 'contamination': 10}, 'score': {'completeness': 1, 'contamination': 5, 'N50': 0.5, 'length': 0}} --rename_mags_contigs=True --annotations=gtdb_tree --annotations=gtdb_taxonomy --annotations=genes --genecatalog={'source': 'contigs', 'clustermethod': 'linclust', 'minlength_nt': 100, 'minid': 0.95, 'coverage': 0.9, 'extra': '', 'SubsetSize': 500000} --eggNOG_use_virtual_disk=False --virtual_disk=/dev/shm assembly
[2021-09-27 14:20 CRITICAL] Command 'snakemake --snakefile /scratch/project_2004930/miniconda3/envs/atlasenv/lib/python3.8/site-packages/atlas/Snakefile --directory /users/student198/First_Run --jobs 40 --rerun-incomplete --configfile '/users/student198/First_Run/config.yaml' --nolock --profile cluster --use-conda --conda-prefix /scratch/project_2004930/databases/conda_envs --scheduler greedy assembly ' returned non-zero exit status 2.
(atlasenv) [student198@puhti-login1 First_Run]$
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