[2024-01-24 10:47:06,543] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,548] [INFO] DQC Reference Directory: /var/lib/cwl/stg182bf8a4-aff5-4d25-a344-c3cd2b052d97/dqc_reference
[2024-01-24 10:47:12,099] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,104] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg31194931-68e7-48ba-bea8-f235c3cd785b/GCF_003660455.1_ASM366045v1_genomic.fna.gz | prodigal -d GCF_003660455.1_ASM366045v1_genomic.fna/cds.fna -a GCF_003660455.1_ASM366045v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:24,823] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:24,823] [INFO] Task started: HMMsearch
[2024-01-24 10:47:24,823] [INFO] Running command: hmmsearch --tblout GCF_003660455.1_ASM366045v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg182bf8a4-aff5-4d25-a344-c3cd2b052d97/dqc_reference/reference_markers.hmm GCF_003660455.1_ASM366045v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:25,110] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:25,112] [INFO] Found 6/6 markers.
[2024-01-24 10:47:25,153] [INFO] Query marker FASTA was written to GCF_003660455.1_ASM366045v1_genomic.fna/markers.fasta
[2024-01-24 10:47:25,154] [INFO] Task started: Blastn
[2024-01-24 10:47:25,154] [INFO] Running command: blastn -query GCF_003660455.1_ASM366045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg182bf8a4-aff5-4d25-a344-c3cd2b052d97/dqc_reference/reference_markers.fasta -out GCF_003660455.1_ASM366045v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:26,392] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:26,395] [INFO] Selected 25 target genomes.
[2024-01-24 10:47:26,395] [INFO] Target genome list was writen to GCF_003660455.1_ASM366045v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:26,420] [INFO] Task started: fastANI
[2024-01-24 10:47:26,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg31194931-68e7-48ba-bea8-f235c3cd785b/GCF_003660455.1_ASM366045v1_genomic.fna.gz --refList GCF_003660455.1_ASM366045v1_genomic.fna/target_genomes.txt --output GCF_003660455.1_ASM366045v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:52,728] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:52,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg182bf8a4-aff5-4d25-a344-c3cd2b052d97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:52,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg182bf8a4-aff5-4d25-a344-c3cd2b052d97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:52,748] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:52,749] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:52,749] [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 ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	100.0	1551	1554	95	conclusive
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	82.3844	857	1554	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	82.2334	867	1554	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	82.2204	875	1554	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	82.0934	876	1554	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	82.063	865	1554	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	82.0463	869	1554	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	82.0389	887	1554	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	82.0304	887	1554	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	82.0021	828	1554	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	81.9264	824	1554	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	81.7572	863	1554	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	81.6179	790	1554	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	81.5915	854	1554	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	81.5267	929	1554	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	81.5127	922	1554	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	81.302	730	1554	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	81.0886	789	1554	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.9728	666	1554	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	80.8359	755	1554	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.8035	726	1554	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.7707	759	1554	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.3298	734	1554	95	below_threshold
Nocardioides acrostichi	strain=CBS4Y-1	GCA_015319165.1	2784339	2784339	type	True	80.2626	703	1554	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	80.0108	722	1554	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:52,751] [INFO] DFAST Taxonomy check result was written to GCF_003660455.1_ASM366045v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:52,751] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:52,751] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:52,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg182bf8a4-aff5-4d25-a344-c3cd2b052d97/dqc_reference/checkm_data
[2024-01-24 10:47:52,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:52,797] [INFO] Task started: CheckM
[2024-01-24 10:47:52,798] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003660455.1_ASM366045v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003660455.1_ASM366045v1_genomic.fna/checkm_input GCF_003660455.1_ASM366045v1_genomic.fna/checkm_result
[2024-01-24 10:48:52,850] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:52,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:52,875] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:52,875] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:52,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003660455.1_ASM366045v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:52,876] [INFO] Task started: Blastn
[2024-01-24 10:48:52,876] [INFO] Running command: blastn -query GCF_003660455.1_ASM366045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg182bf8a4-aff5-4d25-a344-c3cd2b052d97/dqc_reference/reference_markers_gtdb.fasta -out GCF_003660455.1_ASM366045v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:54,827] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:54,831] [INFO] Selected 24 target genomes.
[2024-01-24 10:48:54,831] [INFO] Target genome list was writen to GCF_003660455.1_ASM366045v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:54,851] [INFO] Task started: fastANI
[2024-01-24 10:48:54,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg31194931-68e7-48ba-bea8-f235c3cd785b/GCF_003660455.1_ASM366045v1_genomic.fna.gz --refList GCF_003660455.1_ASM366045v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003660455.1_ASM366045v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:20,151] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:20,169] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:20,169] [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_003660455.1	s__Nocardioides ferulae	100.0	1551	1554	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_014127485.1	s__Nocardioides sp014127485	82.385	856	1554	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	82.2241	905	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_011250565.1	s__Nocardioides sp011250565	82.2201	859	1554	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	82.2153	869	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016907435.1	s__Nocardioides salarius	82.0865	878	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003710085.1	s__Nocardioides sp003710085	82.0414	815	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.05	99.05	0.97	0.97	2	-
GCF_013466785.1	s__Nocardioides marinisabuli	82.0175	871	1554	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	81.9602	833	1554	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	81.8108	820	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014191495.1	s__Nocardioides soli	81.793	857	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_000015265.1	s__Nocardioides sp000015265	81.7797	908	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002117935.1	s__Nocardioides sp002117935	81.7491	867	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014212315.1	s__Nocardioides luti	81.5322	861	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101465.1	s__Nocardioides lianchengensis	81.5239	926	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001425175.1	s__Nocardioides sp001425175	81.5185	865	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000620705.1	s__Nocardioides sp000620705	81.3472	831	1554	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	81.134	784	1554	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	80.8691	751	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013624435.2	s__Nocardioides sp013624415	80.5676	737	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.04	99.04	0.95	0.95	2	-
GCF_015319165.1	s__Nocardioides acrostichi	80.258	702	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006494815.1	s__Nocardioides sambongensis	80.2247	719	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272695.1	s__Nocardioides sp012272695	80.0585	652	1554	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	79.7845	610	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	99.75	99.75	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:20,171] [INFO] GTDB search result was written to GCF_003660455.1_ASM366045v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:20,171] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:20,176] [INFO] DFAST_QC result json was written to GCF_003660455.1_ASM366045v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:20,176] [INFO] DFAST_QC completed!
[2024-01-24 10:49:20,176] [INFO] Total running time: 0h2m14s