[2023-06-28 01:45:51,964] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:45:51,967] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:45:51,967] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd621306-c623-48d6-a15b-078f51b3d510/dqc_reference
[2023-06-28 01:45:53,193] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:45:53,194] [INFO] Task started: Prodigal
[2023-06-28 01:45:53,194] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c3ab729-e129-4285-a9a8-d466ae2f2cc7/GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna.gz | prodigal -d GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/cds.fna -a GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:46:00,740] [INFO] Task succeeded: Prodigal
[2023-06-28 01:46:00,741] [INFO] Task started: HMMsearch
[2023-06-28 01:46:00,741] [INFO] Running command: hmmsearch --tblout GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd621306-c623-48d6-a15b-078f51b3d510/dqc_reference/reference_markers.hmm GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:46:00,927] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:46:00,929] [INFO] Found 6/6 markers.
[2023-06-28 01:46:00,959] [INFO] Query marker FASTA was written to GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/markers.fasta
[2023-06-28 01:46:00,959] [INFO] Task started: Blastn
[2023-06-28 01:46:00,959] [INFO] Running command: blastn -query GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd621306-c623-48d6-a15b-078f51b3d510/dqc_reference/reference_markers.fasta -out GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:46:02,093] [INFO] Task succeeded: Blastn
[2023-06-28 01:46:02,097] [INFO] Selected 14 target genomes.
[2023-06-28 01:46:02,097] [INFO] Target genome list was writen to GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/target_genomes.txt
[2023-06-28 01:46:02,098] [INFO] Task started: fastANI
[2023-06-28 01:46:02,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c3ab729-e129-4285-a9a8-d466ae2f2cc7/GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna.gz --refList GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/target_genomes.txt --output GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:46:10,950] [INFO] Task succeeded: fastANI
[2023-06-28 01:46:10,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd621306-c623-48d6-a15b-078f51b3d510/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:46:10,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd621306-c623-48d6-a15b-078f51b3d510/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:46:10,961] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:46:10,961] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 01:46:10,961] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Microbacterium testaceum	strain=NBRC 12675	GCA_006539145.1	2033	2033	suspected-type	True	84.5616	514	826	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_900096885.1	993073	993073	type	True	84.2936	492	826	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_001456955.1	993073	993073	type	True	84.2731	493	826	95	below_threshold
Microbacterium proteolyticum	strain=CECT 8356	GCA_014192415.1	1572644	1572644	type	True	83.7728	471	826	95	below_threshold
Microbacterium imperiale	strain=DSM 20530	GCA_017876655.1	33884	33884	type	True	80.141	304	826	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	79.9848	306	826	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	79.8229	325	826	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	79.7098	321	826	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	79.5794	334	826	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	74.9721	78	826	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	74.8423	73	826	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	74.737	85	826	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:46:10,962] [INFO] DFAST Taxonomy check result was written to GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/tc_result.tsv
[2023-06-28 01:46:10,963] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:46:10,963] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:46:10,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd621306-c623-48d6-a15b-078f51b3d510/dqc_reference/checkm_data
[2023-06-28 01:46:10,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:46:10,998] [INFO] Task started: CheckM
[2023-06-28 01:46:10,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/checkm_input GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/checkm_result
[2023-06-28 01:46:38,620] [INFO] Task succeeded: CheckM
[2023-06-28 01:46:38,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.44%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 01:46:38,638] [INFO] ===== Completeness check finished =====
[2023-06-28 01:46:38,638] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:46:38,638] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/markers.fasta)
[2023-06-28 01:46:38,638] [INFO] Task started: Blastn
[2023-06-28 01:46:38,638] [INFO] Running command: blastn -query GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd621306-c623-48d6-a15b-078f51b3d510/dqc_reference/reference_markers_gtdb.fasta -out GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:46:40,436] [INFO] Task succeeded: Blastn
[2023-06-28 01:46:40,439] [INFO] Selected 18 target genomes.
[2023-06-28 01:46:40,439] [INFO] Target genome list was writen to GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:46:40,493] [INFO] Task started: fastANI
[2023-06-28 01:46:40,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c3ab729-e129-4285-a9a8-d466ae2f2cc7/GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna.gz --refList GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/target_genomes_gtdb.txt --output GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:46:52,415] [INFO] Task succeeded: fastANI
[2023-06-28 01:46:52,428] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 01:46:52,429] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_001476655.1	s__Microbacterium testaceum_C	98.0364	699	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000202635.1	s__Microbacterium testaceum_F	89.3801	632	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476285.1	s__Microbacterium testaceum_B	87.6967	608	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.43	98.38	0.88	0.88	4	-
GCF_004854025.1	s__Microbacterium hydrothermale	85.5274	529	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104345.1	s__Microbacterium testaceum_A	84.6169	484	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.34	95.96	0.91	0.90	3	-
GCF_006539145.1	s__Microbacterium testaceum	84.5227	516	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.70	98.67	0.94	0.93	3	-
GCF_900156435.1	s__Microbacterium sp900156435	84.3588	485	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007679045.1	s__Microbacterium sp007679045	84.3153	510	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.00	99.00	0.94	0.94	2	-
GCF_017833635.1	s__Microbacterium sp017833635	84.3075	484	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001792815.1	s__Microbacterium sp001792815	84.2889	515	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.83	97.73	0.90	0.88	7	-
GCF_003075375.1	s__Microbacterium testaceum_E	83.9946	463	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.83	96.83	0.84	0.84	2	-
GCF_001424225.1	s__Microbacterium sp001424225	83.9742	475	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984105.1	s__Microbacterium sp001984105	83.7784	497	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.34	96.71	0.91	0.85	3	-
GCF_014193845.1	s__Sphingomonas sp014193845	74.8689	74	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
GCF_004345855.1	s__Sphingomonas sp004345855	74.8476	86	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014194975.1	s__Sphingomonas sp014194975	74.8267	95	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 01:46:52,430] [INFO] GTDB search result was written to GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/result_gtdb.tsv
[2023-06-28 01:46:52,431] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:46:52,434] [INFO] DFAST_QC result json was written to GCA_913777975.1_SP92_3_metabat2_genome_mining.29_genomic.fna/dqc_result.json
[2023-06-28 01:46:52,434] [INFO] DFAST_QC completed!
[2023-06-28 01:46:52,434] [INFO] Total running time: 0h1m0s