[2024-01-25 20:17:20,608] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:20,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:20,609] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7fe219d-3889-4415-985e-3724ca6dbcc4/dqc_reference
[2024-01-25 20:17:21,742] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:21,742] [INFO] Task started: Prodigal
[2024-01-25 20:17:21,743] [INFO] Running command: gunzip -c /var/lib/cwl/stg53847f9b-f809-4ec2-8b53-61973f77a2aa/GCF_014655715.1_ASM1465571v1_genomic.fna.gz | prodigal -d GCF_014655715.1_ASM1465571v1_genomic.fna/cds.fna -a GCF_014655715.1_ASM1465571v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:49,061] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:49,061] [INFO] Task started: HMMsearch
[2024-01-25 20:17:49,061] [INFO] Running command: hmmsearch --tblout GCF_014655715.1_ASM1465571v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7fe219d-3889-4415-985e-3724ca6dbcc4/dqc_reference/reference_markers.hmm GCF_014655715.1_ASM1465571v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:49,439] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:49,440] [INFO] Found 6/6 markers.
[2024-01-25 20:17:49,522] [INFO] Query marker FASTA was written to GCF_014655715.1_ASM1465571v1_genomic.fna/markers.fasta
[2024-01-25 20:17:49,522] [INFO] Task started: Blastn
[2024-01-25 20:17:49,522] [INFO] Running command: blastn -query GCF_014655715.1_ASM1465571v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7fe219d-3889-4415-985e-3724ca6dbcc4/dqc_reference/reference_markers.fasta -out GCF_014655715.1_ASM1465571v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:50,757] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:50,764] [INFO] Selected 14 target genomes.
[2024-01-25 20:17:50,764] [INFO] Target genome list was writen to GCF_014655715.1_ASM1465571v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:50,774] [INFO] Task started: fastANI
[2024-01-25 20:17:50,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg53847f9b-f809-4ec2-8b53-61973f77a2aa/GCF_014655715.1_ASM1465571v1_genomic.fna.gz --refList GCF_014655715.1_ASM1465571v1_genomic.fna/target_genomes.txt --output GCF_014655715.1_ASM1465571v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:26,592] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:26,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7fe219d-3889-4415-985e-3724ca6dbcc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:26,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7fe219d-3889-4415-985e-3724ca6dbcc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:26,603] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:18:26,603] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:18:26,604] [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 lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	100.0	3378	3381	95	conclusive
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	90.6928	2537	3381	95	below_threshold
Streptomyces chartreusis	strain=JCM 4570	GCA_014650315.1	1969	1969	suspected-type	True	90.4187	2492	3381	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	90.3958	2515	3381	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	89.4049	2411	3381	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	89.1967	2486	3381	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	89.1825	2382	3381	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	88.9167	2224	3381	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	86.1359	2202	3381	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.7594	1831	3381	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	85.7034	2097	3381	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.4205	1928	3381	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.3943	1923	3381	95	below_threshold
Streptomyces griseorubiginosus	strain=DSM 40469	GCA_001514195.1	67304	67304	type	True	85.2887	2059	3381	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:26,605] [INFO] DFAST Taxonomy check result was written to GCF_014655715.1_ASM1465571v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:26,605] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:26,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:26,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7fe219d-3889-4415-985e-3724ca6dbcc4/dqc_reference/checkm_data
[2024-01-25 20:18:26,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:26,701] [INFO] Task started: CheckM
[2024-01-25 20:18:26,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014655715.1_ASM1465571v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014655715.1_ASM1465571v1_genomic.fna/checkm_input GCF_014655715.1_ASM1465571v1_genomic.fna/checkm_result
[2024-01-25 20:20:22,737] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:22,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-25 20:20:22,763] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:22,763] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:22,764] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014655715.1_ASM1465571v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:22,764] [INFO] Task started: Blastn
[2024-01-25 20:20:22,764] [INFO] Running command: blastn -query GCF_014655715.1_ASM1465571v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7fe219d-3889-4415-985e-3724ca6dbcc4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014655715.1_ASM1465571v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:24,825] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:24,827] [INFO] Selected 16 target genomes.
[2024-01-25 20:20:24,828] [INFO] Target genome list was writen to GCF_014655715.1_ASM1465571v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:24,847] [INFO] Task started: fastANI
[2024-01-25 20:20:24,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg53847f9b-f809-4ec2-8b53-61973f77a2aa/GCF_014655715.1_ASM1465571v1_genomic.fna.gz --refList GCF_014655715.1_ASM1465571v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014655715.1_ASM1465571v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:08,123] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:08,133] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:08,133] [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_014655715.1	s__Streptomyces lanatus	100.0	3378	3381	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_015160855.1	s__Streptomyces ferrugineus	90.6589	2544	3381	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	90.4424	2447	3381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704715.1	s__Streptomyces chartreusis	90.4148	2512	3381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.83	96.55	0.93	0.86	10	-
GCF_004028635.1	s__Streptomyces cyaneus	89.408	2410	3381	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	89.2962	2509	3381	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	89.2662	2400	3381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.87	99.75	0.95	0.94	3	-
GCA_013362785.1	s__Streptomyces sp013362785	89.2648	1796	3381	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	89.2321	2325	3381	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	89.2053	2381	3381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003963535.1	s__Streptomyces cyaneochromogenes	89.2023	2485	3381	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	89.1498	2388	3381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513975.1	s__Streptomyces curacoi	88.9024	2227	3381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCF_008973465.1	s__Streptomyces sp008973465	86.9203	1929	3381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143935.1	s__Streptomyces sp003143935	85.9845	2100	3381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514195.1	s__Streptomyces griseorubiginosus	85.2784	2061	3381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.34	95.64	0.90	0.86	7	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:08,135] [INFO] GTDB search result was written to GCF_014655715.1_ASM1465571v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:08,135] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:08,138] [INFO] DFAST_QC result json was written to GCF_014655715.1_ASM1465571v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:08,138] [INFO] DFAST_QC completed!
[2024-01-25 20:21:08,138] [INFO] Total running time: 0h3m48s