[2024-01-24 11:09:50,750] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:09:50,751] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:09:50,752] [INFO] DQC Reference Directory: /var/lib/cwl/stgd07d1bff-36e3-4790-9995-ec1250ba830c/dqc_reference
[2024-01-24 11:09:53,302] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:09:53,303] [INFO] Task started: Prodigal
[2024-01-24 11:09:53,303] [INFO] Running command: gunzip -c /var/lib/cwl/stge63e4c9d-6267-44e9-bea0-0902c41772a8/GCF_003967355.1_ASM396735v1_genomic.fna.gz | prodigal -d GCF_003967355.1_ASM396735v1_genomic.fna/cds.fna -a GCF_003967355.1_ASM396735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:10:38,002] [INFO] Task succeeded: Prodigal
[2024-01-24 11:10:38,002] [INFO] Task started: HMMsearch
[2024-01-24 11:10:38,003] [INFO] Running command: hmmsearch --tblout GCF_003967355.1_ASM396735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd07d1bff-36e3-4790-9995-ec1250ba830c/dqc_reference/reference_markers.hmm GCF_003967355.1_ASM396735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:10:38,444] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:10:38,446] [INFO] Found 6/6 markers.
[2024-01-24 11:10:38,532] [INFO] Query marker FASTA was written to GCF_003967355.1_ASM396735v1_genomic.fna/markers.fasta
[2024-01-24 11:10:38,533] [INFO] Task started: Blastn
[2024-01-24 11:10:38,533] [INFO] Running command: blastn -query GCF_003967355.1_ASM396735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd07d1bff-36e3-4790-9995-ec1250ba830c/dqc_reference/reference_markers.fasta -out GCF_003967355.1_ASM396735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:39,904] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:39,908] [INFO] Selected 31 target genomes.
[2024-01-24 11:10:39,908] [INFO] Target genome list was writen to GCF_003967355.1_ASM396735v1_genomic.fna/target_genomes.txt
[2024-01-24 11:10:39,965] [INFO] Task started: fastANI
[2024-01-24 11:10:39,965] [INFO] Running command: fastANI --query /var/lib/cwl/stge63e4c9d-6267-44e9-bea0-0902c41772a8/GCF_003967355.1_ASM396735v1_genomic.fna.gz --refList GCF_003967355.1_ASM396735v1_genomic.fna/target_genomes.txt --output GCF_003967355.1_ASM396735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:11:33,344] [INFO] Task succeeded: fastANI
[2024-01-24 11:11:33,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd07d1bff-36e3-4790-9995-ec1250ba830c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:11:33,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd07d1bff-36e3-4790-9995-ec1250ba830c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:11:33,370] [INFO] Found 31 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:11:33,370] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:11:33,370] [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
Embleya hyalina	strain=NBRC 13850	GCA_003967355.1	516124	516124	type	True	100.0	3965	3983	95	conclusive
Embleya scabrispora	strain=DSM 41855	GCA_000372745.1	159449	159449	type	True	86.9942	2563	3983	95	below_threshold
Peterkaempfera bronchialis	strain=DSM 106435	GCA_003258605.2	2126346	2126346	type	True	77.8627	937	3983	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	77.8366	976	3983	95	below_threshold
Kitasatospora cheerisanensis	strain=KCTC 2395	GCA_000696185.1	81942	81942	type	True	77.6532	1169	3983	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	77.6417	871	3983	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	77.6388	1269	3983	95	below_threshold
Streptacidiphilus albus	strain=NBRC 100918	GCA_000787755.1	105425	105425	type	True	77.5723	1092	3983	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	77.5638	877	3983	95	below_threshold
Streptacidiphilus albus	strain=JL83	GCA_000744705.1	105425	105425	type	True	77.5502	1118	3983	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_019880305.1	249567	249567	type	True	77.5404	910	3983	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	77.5233	985	3983	95	below_threshold
Streptomyces kasugaensis	strain=BCRC 12349	GCA_002261115.1	1946	1946	type	True	77.4825	1063	3983	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	77.4467	996	3983	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	77.4374	995	3983	95	below_threshold
Streptomyces chromofuscus	strain=DSM 40273	GCA_015160875.1	42881	42881	type	True	77.3436	889	3983	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	77.3237	1050	3983	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	77.3208	998	3983	95	below_threshold
Streptomyces chromofuscus	strain=JCM 4354	GCA_014649435.1	42881	42881	type	True	77.284	926	3983	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	77.2772	1082	3983	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	77.2188	890	3983	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	77.2125	1002	3983	95	below_threshold
Streptomyces inusitatus	strain=JCM 4988	GCA_014651115.1	68221	68221	type	True	77.1968	922	3983	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	77.1882	1049	3983	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	76.892	1049	3983	95	below_threshold
Nocardiopsis ganjiahuensis	strain=DSM 45031	GCA_000341085.1	239984	239984	type	True	76.3667	660	3983	95	below_threshold
Actinomadura atramentaria	strain=SF2197	GCA_000381885.1	1990	1990	type	True	76.1515	910	3983	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	76.017	212	3983	95	below_threshold
Nakamurella flava	strain=N5BH11	GCA_005298075.1	2576308	2576308	type	True	75.9681	492	3983	95	below_threshold
Quadrisphaera setariae	strain=DD2A	GCA_008041935.1	2593304	2593304	type	True	75.8878	547	3983	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	75.8742	320	3983	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:11:33,372] [INFO] DFAST Taxonomy check result was written to GCF_003967355.1_ASM396735v1_genomic.fna/tc_result.tsv
[2024-01-24 11:11:33,372] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:11:33,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:11:33,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd07d1bff-36e3-4790-9995-ec1250ba830c/dqc_reference/checkm_data
[2024-01-24 11:11:33,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:11:33,488] [INFO] Task started: CheckM
[2024-01-24 11:11:33,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003967355.1_ASM396735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003967355.1_ASM396735v1_genomic.fna/checkm_input GCF_003967355.1_ASM396735v1_genomic.fna/checkm_result
[2024-01-24 11:15:03,045] [INFO] Task succeeded: CheckM
[2024-01-24 11:15:03,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:15:03,073] [INFO] ===== Completeness check finished =====
[2024-01-24 11:15:03,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:15:03,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003967355.1_ASM396735v1_genomic.fna/markers.fasta)
[2024-01-24 11:15:03,075] [INFO] Task started: Blastn
[2024-01-24 11:15:03,075] [INFO] Running command: blastn -query GCF_003967355.1_ASM396735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd07d1bff-36e3-4790-9995-ec1250ba830c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003967355.1_ASM396735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:15:05,315] [INFO] Task succeeded: Blastn
[2024-01-24 11:15:05,319] [INFO] Selected 24 target genomes.
[2024-01-24 11:15:05,319] [INFO] Target genome list was writen to GCF_003967355.1_ASM396735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:15:05,363] [INFO] Task started: fastANI
[2024-01-24 11:15:05,363] [INFO] Running command: fastANI --query /var/lib/cwl/stge63e4c9d-6267-44e9-bea0-0902c41772a8/GCF_003967355.1_ASM396735v1_genomic.fna.gz --refList GCF_003967355.1_ASM396735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003967355.1_ASM396735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:48,861] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:48,887] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:48,888] [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_003967355.1	s__Embleya hyalina	100.0	3962	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Embleya	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002024165.1	s__Embleya scabrispora_A	94.1729	2929	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Embleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372745.1	s__Embleya scabrispora	86.9769	2565	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Embleya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003144095.1	s__Streptomyces sp003144095	77.9477	930	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205575.1	s__Kitasatospora tateyamensis	77.9157	1005	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717655.1	s__Streptomyces katrae_B	77.6442	963	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.60	96.50	0.86	0.86	4	-
GCF_001270575.1	s__Streptomyces decoyicus	77.5627	875	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_000719095.1	s__Streptacidiphilus jeojiense	77.5163	1050	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016916835.1	s__Streptomyces bryophytorum	77.5065	991	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_001514125.1	s__Streptomyces longwoodensis	77.4788	1052	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.86	0.86	2	-
GCF_001941845.1	s__Streptomyces sp001941845	77.3843	940	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.45	99.45	0.96	0.96	2	-
GCF_015160875.1	s__Streptomyces chromofuscus	77.3619	882	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
GCF_009852415.1	s__Streptomyces sp009852415	77.3543	1105	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720135.1	s__Streptomyces sp000720135	77.3375	1058	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.69	98.69	0.94	0.94	2	-
GCF_008974245.1	s__Streptomyces abyssomicinicus	77.323	997	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443735.1	s__Streptomyces sviceus	77.3006	947	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0589	99.86	99.86	0.99	0.99	3	-
GCF_000744815.1	s__Streptacidiphilus_A oryzae	77.2941	1044	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866665.1	s__Streptomyces monashensis	77.2934	1076	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.78	0.78	2	-
GCF_014651115.1	s__Streptomyces inusitatus	77.2293	911	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111245.1	s__Streptomyces qinglanensis	77.209	892	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900101335.1	s__Quadrisphaera sp900101335	76.1231	506	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688475.1	s__Cellulomonas sp000688475	76.0773	361	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008041935.1	s__Quadrisphaera sp008041935	75.9006	542	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402535.1	s__Cryobacterium sp004402535	75.7679	209	3983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:48,890] [INFO] GTDB search result was written to GCF_003967355.1_ASM396735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:48,890] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:48,896] [INFO] DFAST_QC result json was written to GCF_003967355.1_ASM396735v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:48,896] [INFO] DFAST_QC completed!
[2024-01-24 11:15:48,896] [INFO] Total running time: 0h5m58s