[2024-01-25 20:17:50,490] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:50,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:50,492] [INFO] DQC Reference Directory: /var/lib/cwl/stg386e47fc-eaab-42ea-8e88-ac7bdd75d94a/dqc_reference
[2024-01-25 20:17:51,637] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:51,637] [INFO] Task started: Prodigal
[2024-01-25 20:17:51,638] [INFO] Running command: gunzip -c /var/lib/cwl/stg972a6ade-60d6-443e-b3c1-aa0c506c581a/GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/cds.fna -a GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:03,537] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:03,538] [INFO] Task started: HMMsearch
[2024-01-25 20:18:03,538] [INFO] Running command: hmmsearch --tblout GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg386e47fc-eaab-42ea-8e88-ac7bdd75d94a/dqc_reference/reference_markers.hmm GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:03,883] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:03,884] [INFO] Found 6/6 markers.
[2024-01-25 20:18:03,931] [INFO] Query marker FASTA was written to GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:18:03,931] [INFO] Task started: Blastn
[2024-01-25 20:18:03,931] [INFO] Running command: blastn -query GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg386e47fc-eaab-42ea-8e88-ac7bdd75d94a/dqc_reference/reference_markers.fasta -out GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:05,176] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:05,179] [INFO] Selected 22 target genomes.
[2024-01-25 20:18:05,179] [INFO] Target genome list was writen to GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:18:05,193] [INFO] Task started: fastANI
[2024-01-25 20:18:05,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg972a6ade-60d6-443e-b3c1-aa0c506c581a/GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna.gz --refList GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:31,265] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:31,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg386e47fc-eaab-42ea-8e88-ac7bdd75d94a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:31,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg386e47fc-eaab-42ea-8e88-ac7bdd75d94a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:31,279] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:18:31,280] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:18:31,280] [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
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	100.0	1752	1752	95	conclusive
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	99.9965	1748	1752	95	conclusive
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	84.4552	1027	1752	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	82.4807	924	1752	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	82.3662	943	1752	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	82.3025	955	1752	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	82.2953	890	1752	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	82.0865	993	1752	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	81.9142	878	1752	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	81.8957	885	1752	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	81.8913	889	1752	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	81.841	966	1752	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	81.5831	909	1752	95	below_threshold
Nocardioides plantarum	strain=DSM 11054	GCA_006346395.1	29299	29299	type	True	81.3206	944	1752	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	80.8106	823	1752	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	80.6964	862	1752	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.6612	839	1752	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.6061	783	1752	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.548	689	1752	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.1815	861	1752	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.0318	793	1752	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	79.9547	737	1752	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:31,281] [INFO] DFAST Taxonomy check result was written to GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:18:31,282] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:31,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:31,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg386e47fc-eaab-42ea-8e88-ac7bdd75d94a/dqc_reference/checkm_data
[2024-01-25 20:18:31,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:31,331] [INFO] Task started: CheckM
[2024-01-25 20:18:31,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/checkm_input GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:19:30,068] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:30,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:30,092] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:30,092] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:30,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:19:30,094] [INFO] Task started: Blastn
[2024-01-25 20:19:30,094] [INFO] Running command: blastn -query GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg386e47fc-eaab-42ea-8e88-ac7bdd75d94a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:32,254] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:32,258] [INFO] Selected 24 target genomes.
[2024-01-25 20:19:32,258] [INFO] Target genome list was writen to GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:32,308] [INFO] Task started: fastANI
[2024-01-25 20:19:32,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg972a6ade-60d6-443e-b3c1-aa0c506c581a/GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna.gz --refList GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:20:00,995] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:01,009] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:20:01,009] [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_900101465.1	s__Nocardioides lianchengensis	100.0	1752	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014127485.1	s__Nocardioides sp014127485	84.4424	1029	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_011250565.1	s__Nocardioides sp011250565	82.5122	910	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014266025.1	s__Nocardioides deserti	82.4236	930	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002117935.1	s__Nocardioides sp002117935	82.3998	930	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013177455.1	s__Nocardioides sp013177455	82.3048	944	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_001425175.1	s__Nocardioides sp001425175	82.2476	1042	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011420305.2	s__Nocardioides sp011420305	82.2243	845	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_003710085.1	s__Nocardioides sp003710085	82.2207	884	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.05	99.05	0.97	0.97	2	-
GCF_013155365.1	s__Nocardioides sp013155365	82.1932	868	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778305.1	s__Nocardioides sp013778305	82.0575	951	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009557055.1	s__Nocardioides sp009557055	82.0205	862	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013466785.1	s__Nocardioides marinisabuli	82.0085	884	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016907435.1	s__Nocardioides salarius	81.8604	885	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013409645.1	s__Nocardioides panaciterrulae	81.7703	817	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015265.1	s__Nocardioides sp000015265	81.6384	888	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004522105.1	s__Nocardioides sp004522105	81.3998	964	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346395.1	s__Nocardioides plantarum	81.3238	943	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057875.1	s__Nocardioides currus	80.8298	821	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779655.1	s__Nocardioides ganghwensis	80.6637	774	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105585.1	s__Nocardioides exalbidus	80.6608	867	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137255.1	s__Nocardioides oleivorans	80.6425	850	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004919105.1	s__Nocardioides sp004919105	80.4901	794	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018831735.1	s__Nocardioides sp018831735	80.4772	884	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:20:01,011] [INFO] GTDB search result was written to GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:20:01,012] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:20:01,016] [INFO] DFAST_QC result json was written to GCF_900101465.1_IMG-taxon_2675903056_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:20:01,016] [INFO] DFAST_QC completed!
[2024-01-25 20:20:01,016] [INFO] Total running time: 0h2m11s