[2024-01-24 13:21:47,207] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:47,209] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:47,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a398a9d-7c1d-4ebc-8a56-b2bcf29946e4/dqc_reference
[2024-01-24 13:21:48,698] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:48,699] [INFO] Task started: Prodigal
[2024-01-24 13:21:48,699] [INFO] Running command: gunzip -c /var/lib/cwl/stga011b483-2daa-4c01-8cb6-bc4e3444fd61/GCF_015160855.1_ASM1516085v1_genomic.fna.gz | prodigal -d GCF_015160855.1_ASM1516085v1_genomic.fna/cds.fna -a GCF_015160855.1_ASM1516085v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:19,276] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:19,276] [INFO] Task started: HMMsearch
[2024-01-24 13:22:19,276] [INFO] Running command: hmmsearch --tblout GCF_015160855.1_ASM1516085v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a398a9d-7c1d-4ebc-8a56-b2bcf29946e4/dqc_reference/reference_markers.hmm GCF_015160855.1_ASM1516085v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:19,763] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:19,768] [INFO] Found 6/6 markers.
[2024-01-24 13:22:19,856] [INFO] Query marker FASTA was written to GCF_015160855.1_ASM1516085v1_genomic.fna/markers.fasta
[2024-01-24 13:22:19,857] [INFO] Task started: Blastn
[2024-01-24 13:22:19,857] [INFO] Running command: blastn -query GCF_015160855.1_ASM1516085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a398a9d-7c1d-4ebc-8a56-b2bcf29946e4/dqc_reference/reference_markers.fasta -out GCF_015160855.1_ASM1516085v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:21,469] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:21,475] [INFO] Selected 20 target genomes.
[2024-01-24 13:22:21,475] [INFO] Target genome list was writen to GCF_015160855.1_ASM1516085v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:21,489] [INFO] Task started: fastANI
[2024-01-24 13:22:21,490] [INFO] Running command: fastANI --query /var/lib/cwl/stga011b483-2daa-4c01-8cb6-bc4e3444fd61/GCF_015160855.1_ASM1516085v1_genomic.fna.gz --refList GCF_015160855.1_ASM1516085v1_genomic.fna/target_genomes.txt --output GCF_015160855.1_ASM1516085v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:12,272] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:12,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a398a9d-7c1d-4ebc-8a56-b2bcf29946e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:12,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a398a9d-7c1d-4ebc-8a56-b2bcf29946e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:12,289] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:12,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:12,289] [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
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	100.0	3319	3319	95	conclusive
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	90.7524	2528	3319	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	90.0588	2385	3319	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	90.027	2356	3319	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	89.8944	2170	3319	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	89.7475	2401	3319	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	89.5892	2298	3319	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	87.3135	1950	3319	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	86.3284	2171	3319	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.2927	2041	3319	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	86.2677	1871	3319	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.7099	1862	3319	95	below_threshold
Streptomyces chromofuscus	strain=DSM 40273	GCA_015160875.1	42881	42881	type	True	85.5552	1761	3319	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.4269	1848	3319	95	below_threshold
Streptomyces chromofuscus	strain=JCM 4354	GCA_014649435.1	42881	42881	type	True	85.3312	1782	3319	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.5272	1811	3319	95	below_threshold
Streptomyces yokosukanensis	strain=DSM 40224	GCA_001514035.1	67386	67386	type	True	84.4674	1827	3319	95	below_threshold
Streptomyces capitiformicae	strain=1H-SSA4	GCA_002214185.1	2014920	2014920	type	True	84.4608	2008	3319	95	below_threshold
Streptomyces acidicola	strain=K1PN6	GCA_009377235.1	2596892	2596892	type	True	84.2216	1786	3319	95	below_threshold
Streptomyces abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	80.5964	1218	3319	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:12,291] [INFO] DFAST Taxonomy check result was written to GCF_015160855.1_ASM1516085v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:12,292] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:12,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:12,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a398a9d-7c1d-4ebc-8a56-b2bcf29946e4/dqc_reference/checkm_data
[2024-01-24 13:23:12,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:12,391] [INFO] Task started: CheckM
[2024-01-24 13:23:12,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015160855.1_ASM1516085v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015160855.1_ASM1516085v1_genomic.fna/checkm_input GCF_015160855.1_ASM1516085v1_genomic.fna/checkm_result
[2024-01-24 13:26:17,982] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:17,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 13:26:18,013] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:18,014] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:18,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015160855.1_ASM1516085v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:18,015] [INFO] Task started: Blastn
[2024-01-24 13:26:18,015] [INFO] Running command: blastn -query GCF_015160855.1_ASM1516085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a398a9d-7c1d-4ebc-8a56-b2bcf29946e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_015160855.1_ASM1516085v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:20,445] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:20,449] [INFO] Selected 19 target genomes.
[2024-01-24 13:26:20,450] [INFO] Target genome list was writen to GCF_015160855.1_ASM1516085v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:20,486] [INFO] Task started: fastANI
[2024-01-24 13:26:20,487] [INFO] Running command: fastANI --query /var/lib/cwl/stga011b483-2daa-4c01-8cb6-bc4e3444fd61/GCF_015160855.1_ASM1516085v1_genomic.fna.gz --refList GCF_015160855.1_ASM1516085v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015160855.1_ASM1516085v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:08,152] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:08,170] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:08,171] [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_015160855.1	s__Streptomyces ferrugineus	100.0	3319	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014655715.1	s__Streptomyces lanatus	90.7658	2527	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042075.1	s__Streptomyces sp008042075	90.4317	2328	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028635.1	s__Streptomyces cyaneus	90.0353	2354	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719285.1	s__Streptomyces bicolor	89.9792	2294	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001513975.1	s__Streptomyces curacoi	89.8944	2170	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCF_003963535.1	s__Streptomyces cyaneochromogenes	89.7566	2399	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270495.1	s__Streptomyces viridochromogenes_A	89.7186	2325	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.87	99.75	0.95	0.94	3	-
GCF_019049285.1	s__Streptomyces sp019049285	89.6719	2275	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509475.1	s__Streptomyces regalis	89.6293	2371	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103585.1	s__Streptomyces sp900103585	89.611	2405	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514235.1	s__Streptomyces caeruleatus	89.5825	2299	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003074055.1	s__Streptomyces nigra	87.3283	1947	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.21	97.15	0.92	0.91	4	-
GCF_002291145.1	s__Streptomyces sp002291145	86.4554	2091	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754715.1	s__Streptomyces sp002754715	85.876	2147	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160875.1	s__Streptomyces chromofuscus	85.538	1766	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
GCF_900105755.1	s__Streptomyces sp900105755	84.8164	1891	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650035.1	s__Streptomyces lucensis	84.5695	1664	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377235.1	s__Streptomyces acidicola	84.201	1789	3319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.86	96.86	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:08,172] [INFO] GTDB search result was written to GCF_015160855.1_ASM1516085v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:08,173] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:08,177] [INFO] DFAST_QC result json was written to GCF_015160855.1_ASM1516085v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:08,177] [INFO] DFAST_QC completed!
[2024-01-24 13:27:08,177] [INFO] Total running time: 0h5m21s