[2024-01-24 13:18:27,658] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:27,662] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:27,662] [INFO] DQC Reference Directory: /var/lib/cwl/stg859e5bde-300f-47f4-aee5-b4184d372194/dqc_reference
[2024-01-24 13:18:29,006] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:29,007] [INFO] Task started: Prodigal
[2024-01-24 13:18:29,008] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc1db5c7-53bd-4d91-9334-d39f3c31e519/GCF_000718165.1_ASM71816v1_genomic.fna.gz | prodigal -d GCF_000718165.1_ASM71816v1_genomic.fna/cds.fna -a GCF_000718165.1_ASM71816v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:01,990] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:01,991] [INFO] Task started: HMMsearch
[2024-01-24 13:19:01,991] [INFO] Running command: hmmsearch --tblout GCF_000718165.1_ASM71816v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg859e5bde-300f-47f4-aee5-b4184d372194/dqc_reference/reference_markers.hmm GCF_000718165.1_ASM71816v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:02,494] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:02,496] [INFO] Found 6/6 markers.
[2024-01-24 13:19:02,605] [INFO] Query marker FASTA was written to GCF_000718165.1_ASM71816v1_genomic.fna/markers.fasta
[2024-01-24 13:19:02,606] [INFO] Task started: Blastn
[2024-01-24 13:19:02,606] [INFO] Running command: blastn -query GCF_000718165.1_ASM71816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg859e5bde-300f-47f4-aee5-b4184d372194/dqc_reference/reference_markers.fasta -out GCF_000718165.1_ASM71816v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:03,936] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:03,941] [INFO] Selected 28 target genomes.
[2024-01-24 13:19:03,941] [INFO] Target genome list was writen to GCF_000718165.1_ASM71816v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:03,953] [INFO] Task started: fastANI
[2024-01-24 13:19:03,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc1db5c7-53bd-4d91-9334-d39f3c31e519/GCF_000718165.1_ASM71816v1_genomic.fna.gz --refList GCF_000718165.1_ASM71816v1_genomic.fna/target_genomes.txt --output GCF_000718165.1_ASM71816v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:20:14,123] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:14,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg859e5bde-300f-47f4-aee5-b4184d372194/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:20:14,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg859e5bde-300f-47f4-aee5-b4184d372194/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:20:14,149] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:20:14,149] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:20:14,150] [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 canus	strain=DSM 40017	GCA_001514145.1	58343	58343	suspected-type	True	87.4599	2452	3771	95	below_threshold
Streptomyces pseudovenezuelae	strain=DSM 40212	GCA_001513955.1	67350	67350	type	True	87.3852	2270	3771	95	below_threshold
Streptomyces resistomycificus	strain=DSM 40133	GCA_001514265.1	67356	67356	type	True	87.2185	2234	3771	95	below_threshold
Streptomyces resistomycificus	strain=NRRL 2290	GCA_001270505.1	67356	67356	type	True	87.2138	2173	3771	95	below_threshold
Streptomyces resistomycificus	strain=NRRL ISP-5133	GCA_000716215.1	67356	67356	type	True	87.1998	2210	3771	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	87.0118	2357	3771	95	below_threshold
Streptomyces aquilus	strain=GGCR-6	GCA_003955715.1	2548456	2548456	type	True	86.8629	2296	3771	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	86.8135	2209	3771	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	86.6611	2305	3771	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	86.046	1934	3771	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.9279	1944	3771	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	85.8958	2251	3771	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	85.8736	2219	3771	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	85.8485	2061	3771	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.8127	2010	3771	95	below_threshold
Streptomyces janthinus	strain=JCM 4387	GCA_014649675.1	67308	67308	type	True	85.6647	2077	3771	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	85.6497	2280	3771	95	below_threshold
Streptomyces violarus	strain=JCM 4534	GCA_014650255.1	67380	67380	type	True	85.5987	2120	3771	95	below_threshold
Streptomyces violarus	strain=CECT 3237	GCA_014191845.1	67380	67380	type	True	85.5577	2120	3771	95	below_threshold
Streptomyces prunicolor	strain=NBRC 13075	GCA_000367365.1	67348	67348	type	True	85.5106	2237	3771	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	85.3236	2088	3771	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	84.8514	1965	3771	95	below_threshold
Streptomyces asoensis	strain=JCM 4185	GCA_014649075.1	249586	249586	type	True	84.7903	1953	3771	95	below_threshold
Streptomyces albaduncus	strain=JCM 4715	GCA_014650615.1	68172	68172	type	True	84.7739	1713	3771	95	below_threshold
Streptomyces albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	84.7675	1734	3771	95	below_threshold
Streptomyces adelaidensis	strain=CAP261	GCA_016598475.1	2796465	2796465	type	True	84.4056	1955	3771	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	84.0662	1610	3771	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	84.0632	1932	3771	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:20:14,152] [INFO] DFAST Taxonomy check result was written to GCF_000718165.1_ASM71816v1_genomic.fna/tc_result.tsv
[2024-01-24 13:20:14,153] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:20:14,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:20:14,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg859e5bde-300f-47f4-aee5-b4184d372194/dqc_reference/checkm_data
[2024-01-24 13:20:14,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:20:14,265] [INFO] Task started: CheckM
[2024-01-24 13:20:14,266] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000718165.1_ASM71816v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000718165.1_ASM71816v1_genomic.fna/checkm_input GCF_000718165.1_ASM71816v1_genomic.fna/checkm_result
[2024-01-24 13:22:12,681] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:12,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 57.14%
--------------------------------------------------------------------------------
[2024-01-24 13:22:12,707] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:12,707] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:12,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000718165.1_ASM71816v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:12,708] [INFO] Task started: Blastn
[2024-01-24 13:22:12,709] [INFO] Running command: blastn -query GCF_000718165.1_ASM71816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg859e5bde-300f-47f4-aee5-b4184d372194/dqc_reference/reference_markers_gtdb.fasta -out GCF_000718165.1_ASM71816v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:15,131] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:15,139] [INFO] Selected 24 target genomes.
[2024-01-24 13:22:15,139] [INFO] Target genome list was writen to GCF_000718165.1_ASM71816v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:15,172] [INFO] Task started: fastANI
[2024-01-24 13:22:15,173] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc1db5c7-53bd-4d91-9334-d39f3c31e519/GCF_000718165.1_ASM71816v1_genomic.fna.gz --refList GCF_000718165.1_ASM71816v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000718165.1_ASM71816v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:20,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:20,278] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:20,278] [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_000718165.1	s__Streptomyces fulvoviolaceus	100.0	3761	3771	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_000745715.1	s__Streptomyces mirabilis_C	87.5754	2319	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010548375.1	s__Streptomyces sp010548375	87.5421	2419	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972385.1	s__Streptomyces sp000972385	87.4942	2278	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514145.1	s__Streptomyces canus	87.4897	2446	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.82	96.31	0.85	0.84	3	-
GCF_002291145.1	s__Streptomyces sp002291145	87.4381	2197	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049245.1	s__Streptomyces sp019049245	87.435	2279	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746295.1	s__Streptomyces sp001746295	87.3565	2377	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013044505.1	s__Streptomyces sp013044505	87.3297	2288	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685355.1	s__Streptomyces lincolnensis	87.2049	2340	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.97	0.95	3	-
GCF_001514265.1	s__Streptomyces resistomycificus	87.2007	2237	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003955715.1	s__Streptomyces aquilus	86.8684	2295	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2614	97.56	95.79	0.89	0.84	3	-
GCF_001514305.1	s__Streptomyces dysideae	86.7812	2215	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720765.1	s__Streptomyces sp000720765	86.6143	2318	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.07	96.07	0.83	0.83	2	-
GCF_000746395.1	s__Streptomyces mirabilis_A	86.5571	2316	3771	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	86.1384	2213	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	85.9057	2204	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013085465.1	s__Streptomyces cacaoi_A	85.8662	2229	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110755.1	s__Streptomyces sp900110755	85.5185	1932	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016860545.1	s__Streptomyces asoensis	84.8353	1967	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.07	98.15	0.93	0.87	3	-
GCF_000721605.1	s__Streptomyces sp000721605	84.6039	1731	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598475.1	s__Streptomyces adelaidensis	84.3865	1958	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091845.1	s__Streptomyces sp900091845	84.3853	1768	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001550375.1	s__Streptomyces europaeiscabiei	84.3213	1864	3771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.72	96.30	0.83	0.82	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:20,280] [INFO] GTDB search result was written to GCF_000718165.1_ASM71816v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:20,281] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:20,288] [INFO] DFAST_QC result json was written to GCF_000718165.1_ASM71816v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:20,289] [INFO] DFAST_QC completed!
[2024-01-24 13:23:20,289] [INFO] Total running time: 0h4m53s