[2024-01-24 15:10:54,354] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:54,356] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:54,356] [INFO] DQC Reference Directory: /var/lib/cwl/stgc115693b-f800-4305-8940-106704fabe82/dqc_reference
[2024-01-24 15:10:56,637] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,638] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,638] [INFO] Running command: gunzip -c /var/lib/cwl/stg487e0241-7786-45fd-803f-3f03c3b62037/GCF_009184865.1_ASM918486v1_genomic.fna.gz | prodigal -d GCF_009184865.1_ASM918486v1_genomic.fna/cds.fna -a GCF_009184865.1_ASM918486v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:26,914] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:26,915] [INFO] Task started: HMMsearch
[2024-01-24 15:11:26,915] [INFO] Running command: hmmsearch --tblout GCF_009184865.1_ASM918486v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc115693b-f800-4305-8940-106704fabe82/dqc_reference/reference_markers.hmm GCF_009184865.1_ASM918486v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:27,354] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:27,355] [INFO] Found 6/6 markers.
[2024-01-24 15:11:27,433] [INFO] Query marker FASTA was written to GCF_009184865.1_ASM918486v1_genomic.fna/markers.fasta
[2024-01-24 15:11:27,433] [INFO] Task started: Blastn
[2024-01-24 15:11:27,434] [INFO] Running command: blastn -query GCF_009184865.1_ASM918486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc115693b-f800-4305-8940-106704fabe82/dqc_reference/reference_markers.fasta -out GCF_009184865.1_ASM918486v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:28,723] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:28,728] [INFO] Selected 14 target genomes.
[2024-01-24 15:11:28,729] [INFO] Target genome list was writen to GCF_009184865.1_ASM918486v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:28,740] [INFO] Task started: fastANI
[2024-01-24 15:11:28,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg487e0241-7786-45fd-803f-3f03c3b62037/GCF_009184865.1_ASM918486v1_genomic.fna.gz --refList GCF_009184865.1_ASM918486v1_genomic.fna/target_genomes.txt --output GCF_009184865.1_ASM918486v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:12:04,962] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:04,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc115693b-f800-4305-8940-106704fabe82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:12:04,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc115693b-f800-4305-8940-106704fabe82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:12:04,974] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:12:04,974] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:12:04,974] [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 phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	100.0	3389	3391	95	conclusive
Streptomyces brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	92.3169	2352	3391	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	90.5983	2423	3391	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	90.3087	2235	3391	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	90.2854	2261	3391	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	90.239	2456	3391	95	below_threshold
Streptomyces stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	90.0482	2363	3391	95	below_threshold
Streptomyces adelaidensis	strain=CAP261	GCA_016598475.1	2796465	2796465	type	True	89.2222	2232	3391	95	below_threshold
Streptomyces tailanensis	strain=TRM68348	GCA_008386495.1	2569858	2569858	type	True	88.0244	2216	3391	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	87.5014	1767	3391	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	87.475	2137	3391	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	84.271	1959	3391	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.0789	1966	3391	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	79.6668	906	3391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:12:04,976] [INFO] DFAST Taxonomy check result was written to GCF_009184865.1_ASM918486v1_genomic.fna/tc_result.tsv
[2024-01-24 15:12:04,976] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:12:04,976] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:12:04,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc115693b-f800-4305-8940-106704fabe82/dqc_reference/checkm_data
[2024-01-24 15:12:04,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:12:05,083] [INFO] Task started: CheckM
[2024-01-24 15:12:05,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009184865.1_ASM918486v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009184865.1_ASM918486v1_genomic.fna/checkm_input GCF_009184865.1_ASM918486v1_genomic.fna/checkm_result
[2024-01-24 15:14:56,583] [INFO] Task succeeded: CheckM
[2024-01-24 15:14:56,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.29%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 15:14:56,612] [INFO] ===== Completeness check finished =====
[2024-01-24 15:14:56,613] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:14:56,613] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009184865.1_ASM918486v1_genomic.fna/markers.fasta)
[2024-01-24 15:14:56,614] [INFO] Task started: Blastn
[2024-01-24 15:14:56,614] [INFO] Running command: blastn -query GCF_009184865.1_ASM918486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc115693b-f800-4305-8940-106704fabe82/dqc_reference/reference_markers_gtdb.fasta -out GCF_009184865.1_ASM918486v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:14:58,549] [INFO] Task succeeded: Blastn
[2024-01-24 15:14:58,554] [INFO] Selected 16 target genomes.
[2024-01-24 15:14:58,554] [INFO] Target genome list was writen to GCF_009184865.1_ASM918486v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:14:58,579] [INFO] Task started: fastANI
[2024-01-24 15:14:58,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg487e0241-7786-45fd-803f-3f03c3b62037/GCF_009184865.1_ASM918486v1_genomic.fna.gz --refList GCF_009184865.1_ASM918486v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009184865.1_ASM918486v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:15:39,179] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:39,197] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:15:39,197] [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_009184865.1	s__Streptomyces phaeolivaceus	100.0	3388	3391	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_018927715.1	s__Streptomyces brasiliscabiei	92.3237	2351	3391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550375.1	s__Streptomyces europaeiscabiei	90.7811	2104	3391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.72	96.30	0.83	0.82	3	-
GCF_900114955.1	s__Streptomyces sp900114955	90.4106	2372	3391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.68	97.04	0.90	0.85	10	-
GCF_000772895.1	s__Streptomyces galbus_A	90.3354	2342	3391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383595.1	s__Streptomyces bottropensis	90.3076	2259	3391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	-
GCF_014873495.1	s__Streptomyces stelliscabiei	90.1025	2355	3391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.87	99.68	0.98	0.96	4	-
GCF_014203845.1	s__Streptomyces scabiei_E	90.0608	2276	3391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
GCF_000091305.1	s__Streptomyces scabiei	89.711	2339	3391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.37	97.09	0.94	0.86	16	-
GCF_016598475.1	s__Streptomyces adelaidensis	89.2159	2233	3391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386495.1	s__Streptomyces tailanensis	88.0065	2219	3391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418645.1	s__Streptomyces neyagawaensis	87.3383	1576	3391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4249	N/A	N/A	N/A	N/A	1	-
GCA_002027195.1	s__Streptomyces sp002027195	84.3252	1693	3391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0044	N/A	N/A	N/A	N/A	1	-
GCF_001514305.1	s__Streptomyces dysideae	84.2856	1955	3391	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	83.9333	1895	3391	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	83.2034	1644	3391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:15:39,199] [INFO] GTDB search result was written to GCF_009184865.1_ASM918486v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:15:39,199] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:15:39,203] [INFO] DFAST_QC result json was written to GCF_009184865.1_ASM918486v1_genomic.fna/dqc_result.json
[2024-01-24 15:15:39,203] [INFO] DFAST_QC completed!
[2024-01-24 15:15:39,203] [INFO] Total running time: 0h4m45s