[2024-01-24 11:13:49,564] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:49,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:49,566] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9637ed8-82cf-4897-a695-ef4d362c0fa8/dqc_reference
[2024-01-24 11:13:50,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:50,778] [INFO] Task started: Prodigal
[2024-01-24 11:13:50,778] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d3018df-8a7f-465b-8e6d-788da2ca0632/GCF_013409225.1_ASM1340922v1_genomic.fna.gz | prodigal -d GCF_013409225.1_ASM1340922v1_genomic.fna/cds.fna -a GCF_013409225.1_ASM1340922v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:14:04,338] [INFO] Task succeeded: Prodigal
[2024-01-24 11:14:04,339] [INFO] Task started: HMMsearch
[2024-01-24 11:14:04,339] [INFO] Running command: hmmsearch --tblout GCF_013409225.1_ASM1340922v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9637ed8-82cf-4897-a695-ef4d362c0fa8/dqc_reference/reference_markers.hmm GCF_013409225.1_ASM1340922v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:14:04,639] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:14:04,641] [INFO] Found 6/6 markers.
[2024-01-24 11:14:04,684] [INFO] Query marker FASTA was written to GCF_013409225.1_ASM1340922v1_genomic.fna/markers.fasta
[2024-01-24 11:14:04,684] [INFO] Task started: Blastn
[2024-01-24 11:14:04,684] [INFO] Running command: blastn -query GCF_013409225.1_ASM1340922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9637ed8-82cf-4897-a695-ef4d362c0fa8/dqc_reference/reference_markers.fasta -out GCF_013409225.1_ASM1340922v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:05,978] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:05,983] [INFO] Selected 22 target genomes.
[2024-01-24 11:14:05,983] [INFO] Target genome list was writen to GCF_013409225.1_ASM1340922v1_genomic.fna/target_genomes.txt
[2024-01-24 11:14:05,992] [INFO] Task started: fastANI
[2024-01-24 11:14:05,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d3018df-8a7f-465b-8e6d-788da2ca0632/GCF_013409225.1_ASM1340922v1_genomic.fna.gz --refList GCF_013409225.1_ASM1340922v1_genomic.fna/target_genomes.txt --output GCF_013409225.1_ASM1340922v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:31,651] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:31,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9637ed8-82cf-4897-a695-ef4d362c0fa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:31,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9637ed8-82cf-4897-a695-ef4d362c0fa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:31,674] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:14:31,674] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:14:31,674] [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_013409225.1	1045774	1045774	type	True	100.0	1764	1765	95	conclusive
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	99.9935	1740	1765	95	conclusive
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	84.5975	1027	1765	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	82.5039	869	1765	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	82.4725	933	1765	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	82.4122	925	1765	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	82.2394	951	1765	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	82.1113	984	1765	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	81.9302	959	1765	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	81.9063	885	1765	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	81.898	893	1765	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	81.8685	897	1765	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	81.5527	911	1765	95	below_threshold
Nocardioides plantarum	strain=DSM 11054	GCA_006346395.1	29299	29299	type	True	81.4239	940	1765	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	80.8836	823	1765	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	80.8195	860	1765	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.8151	844	1765	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.7382	774	1765	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.5695	689	1765	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.1748	870	1765	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.0936	795	1765	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.0512	740	1765	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:31,676] [INFO] DFAST Taxonomy check result was written to GCF_013409225.1_ASM1340922v1_genomic.fna/tc_result.tsv
[2024-01-24 11:14:31,677] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:31,677] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:31,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9637ed8-82cf-4897-a695-ef4d362c0fa8/dqc_reference/checkm_data
[2024-01-24 11:14:31,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:31,726] [INFO] Task started: CheckM
[2024-01-24 11:14:31,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409225.1_ASM1340922v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409225.1_ASM1340922v1_genomic.fna/checkm_input GCF_013409225.1_ASM1340922v1_genomic.fna/checkm_result
[2024-01-24 11:15:41,447] [INFO] Task succeeded: CheckM
[2024-01-24 11:15:41,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:15:41,471] [INFO] ===== Completeness check finished =====
[2024-01-24 11:15:41,471] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:15:41,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409225.1_ASM1340922v1_genomic.fna/markers.fasta)
[2024-01-24 11:15:41,472] [INFO] Task started: Blastn
[2024-01-24 11:15:41,472] [INFO] Running command: blastn -query GCF_013409225.1_ASM1340922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9637ed8-82cf-4897-a695-ef4d362c0fa8/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409225.1_ASM1340922v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:15:43,543] [INFO] Task succeeded: Blastn
[2024-01-24 11:15:43,548] [INFO] Selected 24 target genomes.
[2024-01-24 11:15:43,548] [INFO] Target genome list was writen to GCF_013409225.1_ASM1340922v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:15:43,620] [INFO] Task started: fastANI
[2024-01-24 11:15:43,620] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d3018df-8a7f-465b-8e6d-788da2ca0632/GCF_013409225.1_ASM1340922v1_genomic.fna.gz --refList GCF_013409225.1_ASM1340922v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409225.1_ASM1340922v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:16:11,164] [INFO] Task succeeded: fastANI
[2024-01-24 11:16:11,187] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:16:11,187] [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	99.9935	1740	1765	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	84.566	1030	1765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_013177455.1	s__Nocardioides sp013177455	82.5824	937	1765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_002117935.1	s__Nocardioides sp002117935	82.4858	929	1765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014266025.1	s__Nocardioides deserti	82.4555	920	1765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003710085.1	s__Nocardioides sp003710085	82.4446	880	1765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.05	99.05	0.97	0.97	2	-
GCF_001425175.1	s__Nocardioides sp001425175	82.4431	1022	1765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011250565.1	s__Nocardioides sp011250565	82.4386	913	1765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009557055.1	s__Nocardioides sp009557055	82.2171	849	1765	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	82.2135	850	1765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_013155365.1	s__Nocardioides sp013155365	82.175	875	1765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466785.1	s__Nocardioides marinisabuli	82.0052	893	1765	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	81.9275	891	1765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013778305.1	s__Nocardioides sp013778305	81.8984	962	1765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013409645.1	s__Nocardioides panaciterrulae	81.7687	826	1765	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	81.7559	885	1765	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	81.5034	952	1765	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	81.3507	950	1765	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	80.875	824	1765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105585.1	s__Nocardioides exalbidus	80.7763	866	1765	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	80.6947	776	1765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004137255.1	s__Nocardioides oleivorans	80.589	858	1765	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	80.5889	796	1765	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	80.5022	893	1765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:16:11,188] [INFO] GTDB search result was written to GCF_013409225.1_ASM1340922v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:16:11,189] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:16:11,193] [INFO] DFAST_QC result json was written to GCF_013409225.1_ASM1340922v1_genomic.fna/dqc_result.json
[2024-01-24 11:16:11,193] [INFO] DFAST_QC completed!
[2024-01-24 11:16:11,194] [INFO] Total running time: 0h2m22s