[2024-01-24 11:35:34,461] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,463] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,463] [INFO] DQC Reference Directory: /var/lib/cwl/stgb34910c8-dcfb-4f12-a262-928e32ea1009/dqc_reference
[2024-01-24 11:35:35,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,684] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,685] [INFO] Running command: gunzip -c /var/lib/cwl/stg1159a181-a8e1-4d9e-9731-2d5924dc2896/GCF_004028635.1_ASM402863v1_genomic.fna.gz | prodigal -d GCF_004028635.1_ASM402863v1_genomic.fna/cds.fna -a GCF_004028635.1_ASM402863v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:36:03,768] [INFO] Task succeeded: Prodigal
[2024-01-24 11:36:03,769] [INFO] Task started: HMMsearch
[2024-01-24 11:36:03,769] [INFO] Running command: hmmsearch --tblout GCF_004028635.1_ASM402863v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb34910c8-dcfb-4f12-a262-928e32ea1009/dqc_reference/reference_markers.hmm GCF_004028635.1_ASM402863v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:36:04,150] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:36:04,152] [INFO] Found 6/6 markers.
[2024-01-24 11:36:04,225] [INFO] Query marker FASTA was written to GCF_004028635.1_ASM402863v1_genomic.fna/markers.fasta
[2024-01-24 11:36:04,226] [INFO] Task started: Blastn
[2024-01-24 11:36:04,226] [INFO] Running command: blastn -query GCF_004028635.1_ASM402863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb34910c8-dcfb-4f12-a262-928e32ea1009/dqc_reference/reference_markers.fasta -out GCF_004028635.1_ASM402863v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:05,515] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:05,519] [INFO] Selected 21 target genomes.
[2024-01-24 11:36:05,520] [INFO] Target genome list was writen to GCF_004028635.1_ASM402863v1_genomic.fna/target_genomes.txt
[2024-01-24 11:36:05,529] [INFO] Task started: fastANI
[2024-01-24 11:36:05,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg1159a181-a8e1-4d9e-9731-2d5924dc2896/GCF_004028635.1_ASM402863v1_genomic.fna.gz --refList GCF_004028635.1_ASM402863v1_genomic.fna/target_genomes.txt --output GCF_004028635.1_ASM402863v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:52,396] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:52,397] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb34910c8-dcfb-4f12-a262-928e32ea1009/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:52,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb34910c8-dcfb-4f12-a262-928e32ea1009/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:52,415] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:36:52,415] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:52,415] [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 cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	100.0	3255	3261	95	conclusive
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	90.6201	2510	3261	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	90.6172	2271	3261	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	90.1217	2433	3261	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	89.9562	2375	3261	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	89.3062	2394	3261	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	89.2971	2431	3261	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	86.5388	2224	3261	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.3513	2062	3261	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	86.2778	1863	3261	95	below_threshold
Streptomyces iakyrus	strain=NRRL ISP-5482	GCA_000717055.1	68219	68219	type	True	85.8454	2053	3261	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	85.7606	1901	3261	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	85.4858	1795	3261	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.4298	1801	3261	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	84.6712	1713	3261	95	below_threshold
Streptomyces alanosinicus	strain=JCM 4714	GCA_014650595.1	68171	68171	type	True	84.2392	1868	3261	95	below_threshold
Actinacidiphila alni	strain=CGMCC 4.3510	GCA_900112845.1	380248	380248	type	True	79.5768	1194	3261	95	below_threshold
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	79.1881	1199	3261	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	79.1062	1150	3261	95	below_threshold
Actinacidiphila yanglinensis	strain=CGMCC 4.2023	GCA_900107965.1	310779	310779	type	True	78.948	1175	3261	95	below_threshold
Kitasatospora gansuensis	strain=DSM 44786	GCA_014203705.1	258050	258050	type	True	78.2915	1047	3261	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:52,417] [INFO] DFAST Taxonomy check result was written to GCF_004028635.1_ASM402863v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:52,417] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:52,417] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:52,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb34910c8-dcfb-4f12-a262-928e32ea1009/dqc_reference/checkm_data
[2024-01-24 11:36:52,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:52,505] [INFO] Task started: CheckM
[2024-01-24 11:36:52,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004028635.1_ASM402863v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004028635.1_ASM402863v1_genomic.fna/checkm_input GCF_004028635.1_ASM402863v1_genomic.fna/checkm_result
[2024-01-24 11:38:33,168] [INFO] Task succeeded: CheckM
[2024-01-24 11:38:33,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 11:38:33,192] [INFO] ===== Completeness check finished =====
[2024-01-24 11:38:33,193] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:38:33,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004028635.1_ASM402863v1_genomic.fna/markers.fasta)
[2024-01-24 11:38:33,194] [INFO] Task started: Blastn
[2024-01-24 11:38:33,194] [INFO] Running command: blastn -query GCF_004028635.1_ASM402863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb34910c8-dcfb-4f12-a262-928e32ea1009/dqc_reference/reference_markers_gtdb.fasta -out GCF_004028635.1_ASM402863v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:38:35,243] [INFO] Task succeeded: Blastn
[2024-01-24 11:38:35,247] [INFO] Selected 18 target genomes.
[2024-01-24 11:38:35,247] [INFO] Target genome list was writen to GCF_004028635.1_ASM402863v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:38:35,261] [INFO] Task started: fastANI
[2024-01-24 11:38:35,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg1159a181-a8e1-4d9e-9731-2d5924dc2896/GCF_004028635.1_ASM402863v1_genomic.fna.gz --refList GCF_004028635.1_ASM402863v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004028635.1_ASM402863v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:39:18,741] [INFO] Task succeeded: fastANI
[2024-01-24 11:39:18,761] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:39:18,761] [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_004028635.1	s__Streptomyces cyaneus	100.0	3255	3261	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_001509475.1	s__Streptomyces regalis	92.8516	2456	3261	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	90.6659	2404	3261	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	90.6385	2268	3261	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	90.6254	2509	3261	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	90.5324	2529	3261	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049285.1	s__Streptomyces sp019049285	90.2444	2330	3261	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	90.0845	2439	3261	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160855.1	s__Streptomyces ferrugineus	89.9767	2372	3261	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	89.9073	2404	3261	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362785.1	s__Streptomyces sp013362785	89.8324	1826	3261	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655715.1	s__Streptomyces lanatus	89.3014	2431	3261	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651035.1	s__Streptomyces lomondensis	86.3603	2071	3261	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001282115.1	s__Streptomyces sp001282115	86.052	1786	3261	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	0.95	0.95	2	-
GCF_001896135.2	s__Streptomyces phaeoluteigriseus	85.1146	1874	3261	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003261055.1	s__Streptomyces cadmiisoli	84.9571	1831	3261	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.22	99.22	0.88	0.88	2	-
GCF_014650595.1	s__Streptomyces alanosinicus	84.2534	1866	3261	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278075.1	s__Streptomyces pristinaespiralis	81.2145	1462	3261	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.86	99.72	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:39:18,763] [INFO] GTDB search result was written to GCF_004028635.1_ASM402863v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:39:18,763] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:39:18,768] [INFO] DFAST_QC result json was written to GCF_004028635.1_ASM402863v1_genomic.fna/dqc_result.json
[2024-01-24 11:39:18,768] [INFO] DFAST_QC completed!
[2024-01-24 11:39:18,768] [INFO] Total running time: 0h3m44s