[2024-01-24 12:21:55,375] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:55,378] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:55,378] [INFO] DQC Reference Directory: /var/lib/cwl/stg44464a51-b6e9-4361-ab13-010862ffe52b/dqc_reference
[2024-01-24 12:21:56,582] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:56,583] [INFO] Task started: Prodigal
[2024-01-24 12:21:56,583] [INFO] Running command: gunzip -c /var/lib/cwl/stg933c6e0e-dabe-4a3d-8805-a464ef831ffb/GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/cds.fna -a GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:20,279] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:20,279] [INFO] Task started: HMMsearch
[2024-01-24 12:22:20,279] [INFO] Running command: hmmsearch --tblout GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44464a51-b6e9-4361-ab13-010862ffe52b/dqc_reference/reference_markers.hmm GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:20,671] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:20,673] [INFO] Found 6/6 markers.
[2024-01-24 12:22:20,723] [INFO] Query marker FASTA was written to GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:22:20,724] [INFO] Task started: Blastn
[2024-01-24 12:22:20,724] [INFO] Running command: blastn -query GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg44464a51-b6e9-4361-ab13-010862ffe52b/dqc_reference/reference_markers.fasta -out GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:22,005] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:22,011] [INFO] Selected 28 target genomes.
[2024-01-24 12:22:22,011] [INFO] Target genome list was writen to GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:22:22,022] [INFO] Task started: fastANI
[2024-01-24 12:22:22,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg933c6e0e-dabe-4a3d-8805-a464ef831ffb/GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna.gz --refList GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:07,077] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:07,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44464a51-b6e9-4361-ab13-010862ffe52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:07,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44464a51-b6e9-4361-ab13-010862ffe52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:07,099] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:07,099] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:07,100] [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
Spongiactinospora rosea	strain=LHW63015	GCA_003315795.1	2248750	2248750	type	True	80.5835	1076	1995	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	80.4291	1082	1995	95	below_threshold
Thermopolyspora flexuosa	strain=DSM 43186	GCA_006716785.1	103836	103836	type	True	80.3339	957	1995	95	below_threshold
Thermopolyspora flexuosa	strain=JCM 3056	GCA_014647775.1	103836	103836	type	True	80.246	931	1995	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.1094	1098	1995	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	80.0555	982	1995	95	below_threshold
Microbispora rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	79.9886	988	1995	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.8356	760	1995	95	below_threshold
Sphaerisporangium melleum	strain=JCM 13064	GCA_014646695.1	321316	321316	type	True	79.7999	1024	1995	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	79.7708	947	1995	95	below_threshold
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	79.7655	1036	1995	95	below_threshold
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	79.7481	1014	1995	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	79.69	1034	1995	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	79.6859	978	1995	95	below_threshold
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	79.6764	1054	1995	95	below_threshold
Microbispora corallina	strain=NBRC 16416	GCA_016863035.1	83302	83302	type	True	79.6454	970	1995	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	79.644	951	1995	95	below_threshold
Microbispora rosea	strain=ATCC 12950	GCA_900156315.1	58117	58117	type	True	79.6083	992	1995	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	79.6073	1057	1995	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	79.5988	998	1995	95	below_threshold
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	79.5971	993	1995	95	below_threshold
Sphaerisporangium album	strain=CCTCC AA 208026	GCA_003323745.1	509200	509200	type	True	79.5829	981	1995	95	below_threshold
Microbispora camponoti	strain=2C-HV3	GCA_014712745.1	1677852	1677852	type	True	79.5658	968	1995	95	below_threshold
Microtetraspora malaysiensis	strain=NBRC 100735	GCA_001528665.1	161358	161358	type	True	79.4911	927	1995	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.4368	1039	1995	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	79.3294	1030	1995	95	below_threshold
Herbidospora solisilvae	strain=NEAU-GS84	GCA_009901565.1	2696284	2696284	type	True	79.0083	912	1995	95	below_threshold
Herbidospora galbida	strain=NEAU-GS14	GCA_005233835.1	2575442	2575442	type	True	78.8775	921	1995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:07,101] [INFO] DFAST Taxonomy check result was written to GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:23:07,102] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:07,102] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:07,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44464a51-b6e9-4361-ab13-010862ffe52b/dqc_reference/checkm_data
[2024-01-24 12:23:07,104] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:07,159] [INFO] Task started: CheckM
[2024-01-24 12:23:07,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/checkm_input GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:24:23,682] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:23,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.36%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2024-01-24 12:24:23,707] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:23,707] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:23,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:24:23,708] [INFO] Task started: Blastn
[2024-01-24 12:24:23,708] [INFO] Running command: blastn -query GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg44464a51-b6e9-4361-ab13-010862ffe52b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:25,668] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:25,673] [INFO] Selected 23 target genomes.
[2024-01-24 12:24:25,673] [INFO] Target genome list was writen to GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:25,685] [INFO] Task started: fastANI
[2024-01-24 12:24:25,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg933c6e0e-dabe-4a3d-8805-a464ef831ffb/GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna.gz --refList GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:00,612] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:00,629] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:00,630] [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_900099985.1	s__Thermostaphylospora chromogena	100.0	1989	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermostaphylospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014202315.1	s__Thermocatellispora tengchongensis	81.6359	1337	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermocatellispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315795.1	s__Desertactinospora sp003315795	80.5392	1085	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Desertactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236385.1	s__Desertactinospora gelatinilytica	80.4634	907	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Desertactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716785.1	s__Thermopolyspora flexuosa	80.3076	961	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermopolyspora	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014648175.1	s__Planobispora rosea	80.3043	1051	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
GCF_002093975.1	s__Nonomuraea rubra_A	80.2051	1074	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647835.1	s__Microbispora aerata	79.9734	990	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014646695.1	s__Sphaerisporangium melleum	79.8113	1021	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_006334915.2	s__Microbispora catharanthi	79.7602	1011	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.79	95.45	0.89	0.84	4	-
GCF_014205275.1	s__Sphaerisporangium siamense	79.7392	950	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016863395.1	s__Sphaerisporangium rufum	79.709	1030	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200435.1	s__Sphaerisporangium krabiense	79.7001	977	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003260025.2	s__Microbispora triticiradicis	79.656	906	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.16	96.98	0.92	0.88	7	-
GCF_016863035.1	s__Microbispora corallina	79.6282	973	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.01	97.01	0.91	0.91	2	-
GCF_900156315.1	s__Microbispora rosea	79.628	987	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.16	98.33	0.97	0.94	3	-
GCF_006874465.1	s__Microbispora bryophytorum	79.6246	958	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.22	97.66	0.97	0.91	4	-
GCF_016863095.1	s__Microbispora siamensis	79.6107	1057	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.99	95.83	0.88	0.87	3	-
GCF_003323745.1	s__Sphaerisporangium album	79.6093	975	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012999535.1	s__Microbispora sp012999535	79.5348	940	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001528665.1	s__Microtetraspora malaysiensis	79.5052	924	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100605.1	s__Sinosporangium album	79.4285	765	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sinosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863435.1	s__Sinosporangium siamense	79.1117	809	1995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sinosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:00,631] [INFO] GTDB search result was written to GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:00,632] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:00,637] [INFO] DFAST_QC result json was written to GCF_900099985.1_IMG-taxon_2634166206_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:25:00,637] [INFO] DFAST_QC completed!
[2024-01-24 12:25:00,637] [INFO] Total running time: 0h3m5s