[2024-01-25 20:26:35,787] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:26:35,795] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:26:35,795] [INFO] DQC Reference Directory: /var/lib/cwl/stgb60cd410-ecf7-4d61-aaee-093496ce3dd1/dqc_reference
[2024-01-25 20:26:36,946] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:26:36,946] [INFO] Task started: Prodigal
[2024-01-25 20:26:36,947] [INFO] Running command: gunzip -c /var/lib/cwl/stgc528d64f-6965-4c01-9a21-3b4adfffd93a/GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/cds.fna -a GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:26:58,819] [INFO] Task succeeded: Prodigal
[2024-01-25 20:26:58,819] [INFO] Task started: HMMsearch
[2024-01-25 20:26:58,819] [INFO] Running command: hmmsearch --tblout GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb60cd410-ecf7-4d61-aaee-093496ce3dd1/dqc_reference/reference_markers.hmm GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:26:59,149] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:26:59,151] [INFO] Found 6/6 markers.
[2024-01-25 20:26:59,236] [INFO] Query marker FASTA was written to GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:26:59,236] [INFO] Task started: Blastn
[2024-01-25 20:26:59,236] [INFO] Running command: blastn -query GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb60cd410-ecf7-4d61-aaee-093496ce3dd1/dqc_reference/reference_markers.fasta -out GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:00,506] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:00,509] [INFO] Selected 26 target genomes.
[2024-01-25 20:27:00,509] [INFO] Target genome list was writen to GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:27:00,524] [INFO] Task started: fastANI
[2024-01-25 20:27:00,524] [INFO] Running command: fastANI --query /var/lib/cwl/stgc528d64f-6965-4c01-9a21-3b4adfffd93a/GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna.gz --refList GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:28:01,394] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:01,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb60cd410-ecf7-4d61-aaee-093496ce3dd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:28:01,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb60cd410-ecf7-4d61-aaee-093496ce3dd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:28:01,410] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:28:01,410] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:28:01,410] [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
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	100.0	3031	3035	95	conclusive
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	84.1247	2034	3035	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	83.9832	1818	3035	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	83.935	1815	3035	95	below_threshold
Nonomuraea wenchangensis	strain=CGMCC 4.5598	GCA_900111685.1	568860	568860	type	True	83.8103	1867	3035	95	below_threshold
Nonomuraea antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	83.7893	1835	3035	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	83.7685	1683	3035	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	83.649	1910	3035	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	83.6004	1916	3035	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	83.5816	2012	3035	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	83.5514	2007	3035	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.5469	1165	3035	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	83.51	1882	3035	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	83.4955	2052	3035	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	83.2777	1830	3035	95	below_threshold
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	83.2725	1834	3035	95	below_threshold
Nonomuraea jiangxiensis	strain=CGMCC 4.6533	GCA_900099965.1	633440	633440	type	True	83.1758	1846	3035	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	82.8434	1729	3035	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	82.7099	1828	3035	95	below_threshold
Microtetraspora malaysiensis	strain=NBRC 100735	GCA_001528665.1	161358	161358	type	True	80.3313	1384	3035	95	below_threshold
Microbispora bryophytorum	strain=NEAU-TX2-2	GCA_014712735.1	1460882	1460882	type	True	79.9401	1230	3035	95	below_threshold
Microbispora bryophytorum	strain=DSM 46710	GCA_006874465.1	1460882	1460882	type	True	79.9254	1234	3035	95	below_threshold
Herbidospora mongoliensis	strain=NBRC 105882	GCA_001570545.1	688067	688067	type	True	78.6344	1171	3035	95	below_threshold
Streptomyces misionensis	strain=DSM 40306	GCA_900104815.1	67331	67331	type	True	76.5052	898	3035	95	below_threshold
Sanguibacter inulinus	strain=DSM 100099	GCA_013415325.1	60922	60922	type	True	75.8543	368	3035	95	below_threshold
Gryllotalpicola protaetiae	strain=2DFW10M-5	GCA_003627055.1	2419771	2419771	type	True	75.8083	307	3035	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:28:01,412] [INFO] DFAST Taxonomy check result was written to GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:28:01,412] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:28:01,412] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:28:01,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb60cd410-ecf7-4d61-aaee-093496ce3dd1/dqc_reference/checkm_data
[2024-01-25 20:28:01,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:28:01,497] [INFO] Task started: CheckM
[2024-01-25 20:28:01,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/checkm_input GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:29:32,904] [INFO] Task succeeded: CheckM
[2024-01-25 20:29:32,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 6.60%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2024-01-25 20:29:32,926] [INFO] ===== Completeness check finished =====
[2024-01-25 20:29:32,926] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:29:32,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:29:32,927] [INFO] Task started: Blastn
[2024-01-25 20:29:32,927] [INFO] Running command: blastn -query GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb60cd410-ecf7-4d61-aaee-093496ce3dd1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:29:35,192] [INFO] Task succeeded: Blastn
[2024-01-25 20:29:35,195] [INFO] Selected 22 target genomes.
[2024-01-25 20:29:35,195] [INFO] Target genome list was writen to GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:29:35,284] [INFO] Task started: fastANI
[2024-01-25 20:29:35,284] [INFO] Running command: fastANI --query /var/lib/cwl/stgc528d64f-6965-4c01-9a21-3b4adfffd93a/GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna.gz --refList GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:30:38,611] [INFO] Task succeeded: fastANI
[2024-01-25 20:30:38,625] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:30:38,625] [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_900109355.1	s__Nonomuraea pusilla	100.0	3031	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.44	99.44	0.97	0.97	2	conclusive
GCA_013362835.1	s__Nonomuraea sp013362835	85.2483	866	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648435.1	s__Nonomuraea spiralis	84.0867	2044	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_000379885.1	s__Nonomuraea coxensis	83.9252	1817	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111685.1	s__Nonomuraea wenchangensis	83.805	1867	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283785.1	s__Nonomuraea sp013283785	83.7714	1838	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236395.1	s__Nonomuraea sp003236395	83.759	1685	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006334985.2	s__Nonomuraea phyllanthi	83.6502	1906	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.34	99.34	0.97	0.97	2	-
GCF_900323885.1	s__Nonomuraea parvosata	83.5938	2084	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_014204795.1	s__Nonomuraea jabiensis	83.5923	1999	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873145.1	s__Nonomuraea angiospora	83.5795	2013	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207985.1	s__Nonomuraea rubra	83.4933	2051	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065375.1	s__Nonomuraea sp008065375	83.3212	1853	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086045.1	s__Nonomuraea sp008086045	83.3142	1994	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011505.1	s__Nonomuraea polychroma	83.2951	1828	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005893125.1	s__Nonomuraea sp005893125	83.2883	1827	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099965.1	s__Nonomuraea jiangxiensis	83.1607	1850	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001528665.1	s__Microtetraspora malaysiensis	80.3212	1387	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001570385.1	s__Microtetraspora glauca	79.9122	1361	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049245.1	s__Streptomyces sp019049245	76.3697	824	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335115.1	s__Quadrisphaera sp006335115	75.8631	633	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627055.1	s__Gryllotalpicola protaetiae	75.8032	308	3035	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gryllotalpicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:30:38,626] [INFO] GTDB search result was written to GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:30:38,627] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:30:38,631] [INFO] DFAST_QC result json was written to GCF_900109355.1_IMG-taxon_2599185218_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:30:38,631] [INFO] DFAST_QC completed!
[2024-01-25 20:30:38,631] [INFO] Total running time: 0h4m3s