[2024-01-24 13:13:32,211] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:32,221] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:32,221] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e899d90-6696-4a4f-b972-ce2a437d3381/dqc_reference
[2024-01-24 13:13:33,763] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:33,764] [INFO] Task started: Prodigal
[2024-01-24 13:13:33,764] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e787c1f-8aae-4473-a658-899aa5ceb2a3/GCF_003674065.1_ASM367406v1_genomic.fna.gz | prodigal -d GCF_003674065.1_ASM367406v1_genomic.fna/cds.fna -a GCF_003674065.1_ASM367406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:46,330] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:46,330] [INFO] Task started: HMMsearch
[2024-01-24 13:13:46,330] [INFO] Running command: hmmsearch --tblout GCF_003674065.1_ASM367406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e899d90-6696-4a4f-b972-ce2a437d3381/dqc_reference/reference_markers.hmm GCF_003674065.1_ASM367406v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:46,656] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:46,658] [INFO] Found 6/6 markers.
[2024-01-24 13:13:46,704] [INFO] Query marker FASTA was written to GCF_003674065.1_ASM367406v1_genomic.fna/markers.fasta
[2024-01-24 13:13:46,705] [INFO] Task started: Blastn
[2024-01-24 13:13:46,705] [INFO] Running command: blastn -query GCF_003674065.1_ASM367406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e899d90-6696-4a4f-b972-ce2a437d3381/dqc_reference/reference_markers.fasta -out GCF_003674065.1_ASM367406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:48,001] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:48,006] [INFO] Selected 28 target genomes.
[2024-01-24 13:13:48,007] [INFO] Target genome list was writen to GCF_003674065.1_ASM367406v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:48,040] [INFO] Task started: fastANI
[2024-01-24 13:13:48,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e787c1f-8aae-4473-a658-899aa5ceb2a3/GCF_003674065.1_ASM367406v1_genomic.fna.gz --refList GCF_003674065.1_ASM367406v1_genomic.fna/target_genomes.txt --output GCF_003674065.1_ASM367406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:13,686] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:13,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e899d90-6696-4a4f-b972-ce2a437d3381/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:13,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e899d90-6696-4a4f-b972-ce2a437d3381/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:13,711] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:14:13,712] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:14:13,712] [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
Marmoricola scoriae	strain=DSM 22127	GCA_900104965.1	642780	642780	type	True	80.7631	717	1364	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	80.6326	675	1364	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	80.3907	691	1364	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	80.1143	669	1364	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	80.0875	688	1364	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	80.041	659	1364	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	79.9647	687	1364	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	79.9404	622	1364	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	79.9347	657	1364	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	79.905	652	1364	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	79.8566	677	1364	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	79.8554	739	1364	95	below_threshold
Nocardioides halotolerans	strain=DSM 19273	GCA_000422805.1	433660	433660	type	True	79.7708	642	1364	95	below_threshold
Nocardioides plantarum	strain=DSM 11054	GCA_006346395.1	29299	29299	type	True	79.7618	650	1364	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.7592	615	1364	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.7495	559	1364	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	79.7423	658	1364	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	79.7074	694	1364	95	below_threshold
Nocardioides iriomotensis	strain=NBRC 105384	GCA_004168035.1	715784	715784	type	True	79.6929	657	1364	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	79.6455	608	1364	95	below_threshold
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	79.6446	676	1364	95	below_threshold
Nocardioides rotundus	strain=MCCC 1A10561	GCA_019931675.1	1774216	1774216	type	True	79.5868	577	1364	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	79.5831	608	1364	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	79.5423	640	1364	95	below_threshold
Marmoricola ginsengisoli	strain=Gsoil 097	GCA_003725695.1	661483	661483	type	True	79.4924	588	1364	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	79.4547	615	1364	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.4119	623	1364	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	79.397	639	1364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:13,714] [INFO] DFAST Taxonomy check result was written to GCF_003674065.1_ASM367406v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:13,714] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:13,714] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:13,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e899d90-6696-4a4f-b972-ce2a437d3381/dqc_reference/checkm_data
[2024-01-24 13:14:13,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:13,757] [INFO] Task started: CheckM
[2024-01-24 13:14:13,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003674065.1_ASM367406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003674065.1_ASM367406v1_genomic.fna/checkm_input GCF_003674065.1_ASM367406v1_genomic.fna/checkm_result
[2024-01-24 13:15:12,163] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:12,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:12,189] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:12,189] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:12,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003674065.1_ASM367406v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:12,190] [INFO] Task started: Blastn
[2024-01-24 13:15:12,190] [INFO] Running command: blastn -query GCF_003674065.1_ASM367406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e899d90-6696-4a4f-b972-ce2a437d3381/dqc_reference/reference_markers_gtdb.fasta -out GCF_003674065.1_ASM367406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:14,307] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:14,310] [INFO] Selected 24 target genomes.
[2024-01-24 13:15:14,310] [INFO] Target genome list was writen to GCF_003674065.1_ASM367406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:14,404] [INFO] Task started: fastANI
[2024-01-24 13:15:14,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e787c1f-8aae-4473-a658-899aa5ceb2a3/GCF_003674065.1_ASM367406v1_genomic.fna.gz --refList GCF_003674065.1_ASM367406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003674065.1_ASM367406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:38,133] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:38,156] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:38,157] [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_003674065.1	s__Marmoricola mangrovicus	100.0	1363	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900104965.1	s__Marmoricola scoriae	80.7986	713	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644415.1	s__Marmoricola endophyticus	80.7748	689	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752505.1	s__Marmoricola aurantiacus	80.6784	669	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424755.1	s__Marmoricola sp001424755	80.6373	689	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744365.1	s__Marmoricola sp017744365	80.0986	681	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408145.1	s__Nocardioides marinus	79.9495	621	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCF_015024225.1	s__Nocardioides sp015024225	79.9456	654	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	-
GCF_016924665.1	s__Nocardioides sp016924665	79.9289	675	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519545.1	s__Nocardioides guangzhouensis	79.9009	652	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009823805.1	s__Nocardioides sp009823805	79.8865	697	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001627335.1	s__Nocardioides sp001627335	79.8548	543	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_011046535.1	s__Nocardioides anomalus	79.8537	739	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660455.1	s__Nocardioides ferulae	79.8361	680	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725535.1	s__Marmoricola pocheonensis	79.8173	646	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346395.1	s__Nocardioides plantarum	79.7612	650	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168035.1	s__Nocardioides_B iriomotensis	79.7321	652	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039255.1	s__JABFXA01 sp019039255	79.6519	670	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522105.1	s__Nocardioides sp004522105	79.6208	691	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361955.1	s__JABFXA01 sp013361955	79.5738	602	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	99.75	99.75	0.92	0.92	2	-
GCF_014212315.1	s__Nocardioides luti	79.5435	676	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395785.1	s__Nocardioides_B mesophilus	79.4891	629	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729525.1	s__Nocardioides sp002729525	79.3328	651	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054165.1	s__Nocardioides sp003054165	78.9819	589	1364	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 13:15:38,159] [INFO] GTDB search result was written to GCF_003674065.1_ASM367406v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:38,160] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:38,166] [INFO] DFAST_QC result json was written to GCF_003674065.1_ASM367406v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:38,166] [INFO] DFAST_QC completed!
[2024-01-24 13:15:38,166] [INFO] Total running time: 0h2m6s