[2024-01-24 14:32:30,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:32:30,651] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:32:30,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg631a6cea-f8c0-48ae-b64d-d80b31aaaf15/dqc_reference
[2024-01-24 14:32:31,927] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:32:31,928] [INFO] Task started: Prodigal
[2024-01-24 14:32:31,928] [INFO] Running command: gunzip -c /var/lib/cwl/stgea0ed09d-09aa-4aea-bfd8-19775b9d6516/GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/cds.fna -a GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:32:48,215] [INFO] Task succeeded: Prodigal
[2024-01-24 14:32:48,216] [INFO] Task started: HMMsearch
[2024-01-24 14:32:48,216] [INFO] Running command: hmmsearch --tblout GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg631a6cea-f8c0-48ae-b64d-d80b31aaaf15/dqc_reference/reference_markers.hmm GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:32:48,569] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:32:48,570] [INFO] Found 6/6 markers.
[2024-01-24 14:32:48,638] [INFO] Query marker FASTA was written to GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:32:48,639] [INFO] Task started: Blastn
[2024-01-24 14:32:48,639] [INFO] Running command: blastn -query GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg631a6cea-f8c0-48ae-b64d-d80b31aaaf15/dqc_reference/reference_markers.fasta -out GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:50,071] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:50,074] [INFO] Selected 22 target genomes.
[2024-01-24 14:32:50,074] [INFO] Target genome list was writen to GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:32:50,085] [INFO] Task started: fastANI
[2024-01-24 14:32:50,086] [INFO] Running command: fastANI --query /var/lib/cwl/stgea0ed09d-09aa-4aea-bfd8-19775b9d6516/GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna.gz --refList GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:33:24,208] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:24,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg631a6cea-f8c0-48ae-b64d-d80b31aaaf15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:33:24,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg631a6cea-f8c0-48ae-b64d-d80b31aaaf15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:33:24,230] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:33:24,230] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:33:24,230] [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 xiamenensis	strain=318	GCA_000993785.3	408015	408015	type	True	88.8837	1569	1917	95	below_threshold
Streptomyces hainanensis	strain=DSM 41900	GCA_004348415.1	402648	402648	type	True	81.4738	1040	1917	95	below_threshold
Streptomyces specialis	strain=type strain: GW41-1564	GCA_001493375.1	498367	498367	type	True	81.385	970	1917	95	below_threshold
Streptomyces triticirhizae	strain=NEAU-YY642	GCA_003696235.1	2483353	2483353	type	True	81.3621	1002	1917	95	below_threshold
Streptomyces mimosae	strain=3MP-10	GCA_006334995.2	2586635	2586635	type	True	81.1056	1112	1917	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	80.9696	1091	1917	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	80.9488	1088	1917	95	below_threshold
Streptomyces hoynatensis	strain=KCTC 29097	GCA_003626535.1	1141874	1141874	type	True	80.8314	1090	1917	95	below_threshold
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	80.8282	1112	1917	95	below_threshold
Streptomyces otsuchiensis	strain=OTB305	GCA_004305975.1	2681388	2681388	type	True	80.7216	905	1917	95	below_threshold
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	80.5215	940	1917	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	80.3435	925	1917	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	80.2999	842	1917	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.9977	977	1917	95	below_threshold
Streptomyces chumphonensis	strain=KK1-2	GCA_014779715.1	1214925	1214925	type	True	79.9782	865	1917	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	79.674	807	1917	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	79.6425	938	1917	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	79.5594	801	1917	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	79.5327	841	1917	95	below_threshold
Streptomyces tirandamycinicus	strain=HNM0039	GCA_003097515.1	2174846	2174846	type	True	79.392	866	1917	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	79.3007	944	1917	95	below_threshold
Streptomyces iranensis	strain=DSM 41954	GCA_017874715.1	576784	576784	type	True	79.2841	1056	1917	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:33:24,233] [INFO] DFAST Taxonomy check result was written to GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:33:24,234] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:33:24,234] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:33:24,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg631a6cea-f8c0-48ae-b64d-d80b31aaaf15/dqc_reference/checkm_data
[2024-01-24 14:33:24,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:33:24,290] [INFO] Task started: CheckM
[2024-01-24 14:33:24,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/checkm_input GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:34:51,610] [INFO] Task succeeded: CheckM
[2024-01-24 14:34:51,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:34:51,636] [INFO] ===== Completeness check finished =====
[2024-01-24 14:34:51,637] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:34:51,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:34:51,637] [INFO] Task started: Blastn
[2024-01-24 14:34:51,638] [INFO] Running command: blastn -query GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg631a6cea-f8c0-48ae-b64d-d80b31aaaf15/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:34:54,550] [INFO] Task succeeded: Blastn
[2024-01-24 14:34:54,554] [INFO] Selected 18 target genomes.
[2024-01-24 14:34:54,555] [INFO] Target genome list was writen to GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:34:54,570] [INFO] Task started: fastANI
[2024-01-24 14:34:54,571] [INFO] Running command: fastANI --query /var/lib/cwl/stgea0ed09d-09aa-4aea-bfd8-19775b9d6516/GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna.gz --refList GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:35:23,194] [INFO] Task succeeded: fastANI
[2024-01-24 14:35:23,221] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:35:23,221] [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_900116145.1	s__Streptomyces harbinensis	100.0	1912	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.20	99.18	0.96	0.96	3	conclusive
GCF_000993785.3	s__Streptomyces xiamenensis	88.9022	1567	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.73	97.97	0.94	0.91	3	-
GCF_004348415.1	s__Streptomyces hainanensis	81.4509	1045	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348315.1	s__Streptomyces sp004348315	81.4233	1042	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001493375.1	s__Streptomyces specialis	81.3886	969	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696235.1	s__Streptomyces triticirhizae	81.3879	998	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.35	0.89	0.89	3	-
GCF_006335015.1	s__Streptomyces sedi	80.9448	1088	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984575.1	s__Streptomyces sp001984575	80.9362	1147	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626535.1	s__Streptomyces hoynatensis	80.8729	1083	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230195.1	s__Streptomyces zhaozhouensis	80.8423	1110	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004305975.1	s__Streptomyces otsuchiensis	80.749	902	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.30	98.24	0.80	0.78	3	-
GCF_000719135.1	s__Streptomyces avicenniae	80.6266	1066	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974485.1	s__Streptomyces sp000974485	80.5514	1104	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709575.1	s__Streptomyces taklimakanensis	80.3938	917	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000968685.2	s__Streptomyces antioxidans	79.5519	952	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649795.1	s__Streptomyces melanogenes	79.2602	915	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCF_002797655.1	s__Streptomyces sp002797655	79.2516	985	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.99	97.30	0.92	0.88	9	-
GCF_002847285.1	s__Streptomyces sp002847285	79.0805	978	1917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.16	95.03	0.85	0.85	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:35:23,223] [INFO] GTDB search result was written to GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:35:23,223] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:35:23,227] [INFO] DFAST_QC result json was written to GCF_900116145.1_IMG-taxon_2675903139_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:35:23,228] [INFO] DFAST_QC completed!
[2024-01-24 14:35:23,228] [INFO] Total running time: 0h2m53s