[2024-01-25 18:15:20,940] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:20,942] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:20,942] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bb6f1cc-8f47-4c3c-a9b1-6bd07d98d559/dqc_reference
[2024-01-25 18:15:22,077] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:22,078] [INFO] Task started: Prodigal
[2024-01-25 18:15:22,078] [INFO] Running command: gunzip -c /var/lib/cwl/stga8d0d574-3e5e-4abd-bf8a-8df35ca45e25/GCF_003047295.1_ASM304729v1_genomic.fna.gz | prodigal -d GCF_003047295.1_ASM304729v1_genomic.fna/cds.fna -a GCF_003047295.1_ASM304729v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:32,718] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:32,719] [INFO] Task started: HMMsearch
[2024-01-25 18:15:32,719] [INFO] Running command: hmmsearch --tblout GCF_003047295.1_ASM304729v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bb6f1cc-8f47-4c3c-a9b1-6bd07d98d559/dqc_reference/reference_markers.hmm GCF_003047295.1_ASM304729v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:32,941] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:32,943] [INFO] Found 6/6 markers.
[2024-01-25 18:15:32,980] [INFO] Query marker FASTA was written to GCF_003047295.1_ASM304729v1_genomic.fna/markers.fasta
[2024-01-25 18:15:32,980] [INFO] Task started: Blastn
[2024-01-25 18:15:32,980] [INFO] Running command: blastn -query GCF_003047295.1_ASM304729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bb6f1cc-8f47-4c3c-a9b1-6bd07d98d559/dqc_reference/reference_markers.fasta -out GCF_003047295.1_ASM304729v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:34,154] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:34,156] [INFO] Selected 21 target genomes.
[2024-01-25 18:15:34,157] [INFO] Target genome list was writen to GCF_003047295.1_ASM304729v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:34,178] [INFO] Task started: fastANI
[2024-01-25 18:15:34,178] [INFO] Running command: fastANI --query /var/lib/cwl/stga8d0d574-3e5e-4abd-bf8a-8df35ca45e25/GCF_003047295.1_ASM304729v1_genomic.fna.gz --refList GCF_003047295.1_ASM304729v1_genomic.fna/target_genomes.txt --output GCF_003047295.1_ASM304729v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:15:55,047] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:55,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bb6f1cc-8f47-4c3c-a9b1-6bd07d98d559/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:15:55,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bb6f1cc-8f47-4c3c-a9b1-6bd07d98d559/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:15:55,061] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:15:55,061] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:15:55,061] [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 sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	100.0	1416	1416	95	conclusive
Nocardioides terrigena	strain=KCTC 19217	GCA_003047265.1	424797	424797	type	True	87.1627	1056	1416	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	83.0892	904	1416	95	below_threshold
Nocardioides allogilvus	strain=KCTC 49020	GCA_003047285.1	2072017	2072017	type	True	83.0152	829	1416	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	82.721	839	1416	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	82.6683	886	1416	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	82.6108	850	1416	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	82.6049	833	1416	95	below_threshold
Nocardioides alpinus	strain=DSM 23325	GCA_002836395.1	748909	748909	type	True	82.3365	833	1416	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	82.3239	847	1416	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	82.2787	799	1416	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	82.2436	840	1416	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	82.2222	854	1416	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	82.1041	811	1416	95	below_threshold
Nocardioides piscis	strain=HDW12A	GCA_011300215.1	2714938	2714938	type	True	82.0284	760	1416	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	81.4813	737	1416	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	81.4194	740	1416	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	81.415	738	1416	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	81.1219	753	1416	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	81.0404	729	1416	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	80.8722	687	1416	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:15:55,067] [INFO] DFAST Taxonomy check result was written to GCF_003047295.1_ASM304729v1_genomic.fna/tc_result.tsv
[2024-01-25 18:15:55,068] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:15:55,068] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:15:55,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bb6f1cc-8f47-4c3c-a9b1-6bd07d98d559/dqc_reference/checkm_data
[2024-01-25 18:15:55,069] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:15:55,110] [INFO] Task started: CheckM
[2024-01-25 18:15:55,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003047295.1_ASM304729v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003047295.1_ASM304729v1_genomic.fna/checkm_input GCF_003047295.1_ASM304729v1_genomic.fna/checkm_result
[2024-01-25 18:16:56,200] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:56,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:56,224] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:56,225] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:56,227] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003047295.1_ASM304729v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:56,227] [INFO] Task started: Blastn
[2024-01-25 18:16:56,227] [INFO] Running command: blastn -query GCF_003047295.1_ASM304729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bb6f1cc-8f47-4c3c-a9b1-6bd07d98d559/dqc_reference/reference_markers_gtdb.fasta -out GCF_003047295.1_ASM304729v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:58,227] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:58,230] [INFO] Selected 17 target genomes.
[2024-01-25 18:16:58,230] [INFO] Target genome list was writen to GCF_003047295.1_ASM304729v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:58,249] [INFO] Task started: fastANI
[2024-01-25 18:16:58,249] [INFO] Running command: fastANI --query /var/lib/cwl/stga8d0d574-3e5e-4abd-bf8a-8df35ca45e25/GCF_003047295.1_ASM304729v1_genomic.fna.gz --refList GCF_003047295.1_ASM304729v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003047295.1_ASM304729v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:15,681] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:15,691] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:17:15,692] [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_003047295.1	s__Nocardioides sediminis	100.0	1416	1416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003047265.1	s__Nocardioides terrigena	87.1508	1057	1416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	95.44	95.44	0.86	0.86	2	-
GCF_001429625.1	s__Nocardioides sp001429625	86.9322	1057	1416	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	83.0542	908	1416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047285.1	s__Nocardioides allogilvus	83.0226	828	1416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.72	98.72	0.92	0.92	2	-
GCF_018275325.1	s__Nocardioides sp018275325	82.4858	870	1416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112035.1	s__Nocardioides alpinus	82.3551	843	1416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013410035.1	s__Nocardioides cavernae_A	82.2194	824	1416	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	82.2038	844	1416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076135.1	s__Nocardioides gansuensis	82.1536	786	1416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916455.1	s__Nocardioides sp017916455	82.1311	794	1416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCF_017916425.1	s__Nocardioides sp017916425	82.1153	782	1416	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	82.0856	829	1416	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	81.4905	736	1416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013409645.1	s__Nocardioides panaciterrulae	81.3506	745	1416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907435.1	s__Nocardioides salarius	81.1615	744	1416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004919105.1	s__Nocardioides sp004919105	80.006	629	1416	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 18:17:15,693] [INFO] GTDB search result was written to GCF_003047295.1_ASM304729v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:15,694] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:15,697] [INFO] DFAST_QC result json was written to GCF_003047295.1_ASM304729v1_genomic.fna/dqc_result.json
[2024-01-25 18:17:15,697] [INFO] DFAST_QC completed!
[2024-01-25 18:17:15,697] [INFO] Total running time: 0h1m55s