[2024-01-24 11:26:22,711] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:22,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:22,717] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2708d1a-1da3-4dff-a58d-ab4bb4397684/dqc_reference
[2024-01-24 11:26:23,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:23,963] [INFO] Task started: Prodigal
[2024-01-24 11:26:23,963] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb0f5f0a-9bcb-4019-b402-44f82934c2cc/GCF_001751245.1_ASM175124v1_genomic.fna.gz | prodigal -d GCF_001751245.1_ASM175124v1_genomic.fna/cds.fna -a GCF_001751245.1_ASM175124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:46,399] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:46,399] [INFO] Task started: HMMsearch
[2024-01-24 11:26:46,399] [INFO] Running command: hmmsearch --tblout GCF_001751245.1_ASM175124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2708d1a-1da3-4dff-a58d-ab4bb4397684/dqc_reference/reference_markers.hmm GCF_001751245.1_ASM175124v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:46,772] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:46,774] [INFO] Found 6/6 markers.
[2024-01-24 11:26:46,821] [INFO] Query marker FASTA was written to GCF_001751245.1_ASM175124v1_genomic.fna/markers.fasta
[2024-01-24 11:26:46,822] [INFO] Task started: Blastn
[2024-01-24 11:26:46,822] [INFO] Running command: blastn -query GCF_001751245.1_ASM175124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2708d1a-1da3-4dff-a58d-ab4bb4397684/dqc_reference/reference_markers.fasta -out GCF_001751245.1_ASM175124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:48,095] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:48,098] [INFO] Selected 24 target genomes.
[2024-01-24 11:26:48,098] [INFO] Target genome list was writen to GCF_001751245.1_ASM175124v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:48,126] [INFO] Task started: fastANI
[2024-01-24 11:26:48,127] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb0f5f0a-9bcb-4019-b402-44f82934c2cc/GCF_001751245.1_ASM175124v1_genomic.fna.gz --refList GCF_001751245.1_ASM175124v1_genomic.fna/target_genomes.txt --output GCF_001751245.1_ASM175124v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:26,318] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:26,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2708d1a-1da3-4dff-a58d-ab4bb4397684/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:26,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2708d1a-1da3-4dff-a58d-ab4bb4397684/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:26,338] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:26,338] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:26,339] [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 oceani	strain=SCSIO 02100	GCA_001751245.1	1075402	1075402	type	True	99.995	2025	2049	95	conclusive
Streptomyces armeniacus	strain=ATCC 15676	GCA_003355155.1	83291	83291	type	True	81.5476	1219	2049	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	79.7431	801	2049	95	below_threshold
Streptomyces albidus (ex Kaewkla and Franco 2021)	strain=CAP215	GCA_013870515.1	722709	722709	type	True	79.7244	798	2049	95	below_threshold
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	79.7196	893	2049	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	79.6831	878	2049	95	below_threshold
Streptomyces smyrnaeus	strain=DSM 42105	GCA_017676345.1	1387713	1387713	type	True	79.621	960	2049	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	79.59	690	2049	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	79.4954	932	2049	95	below_threshold
Streptomyces daqingensis	strain=CGMCC 4.7178	GCA_014645895.1	1472640	1472640	type	True	79.467	886	2049	95	below_threshold
Streptomyces lycii	strain=TRM 66187	GCA_009735685.1	2654337	2654337	type	True	79.4268	876	2049	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	79.344	737	2049	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	79.3183	728	2049	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	79.2323	841	2049	95	below_threshold
Streptomyces chumphonensis	strain=KK1-2	GCA_014779715.1	1214925	1214925	type	True	79.2044	798	2049	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	79.168	938	2049	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=NRRL ISP-5260	GCA_000717285.1	132474	1927	type	True	79.1414	920	2049	95	below_threshold
Streptomyces albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	79.136	850	2049	95	below_threshold
Streptomyces albofaciens	strain=ATCC 23873	GCA_008634025.1	66866	66866	type	True	79.1311	938	2049	95	below_threshold
Streptomyces thermovulgaris	strain=NRRL B-12375	GCA_002155915.1	1934	1934	type	True	78.9887	683	2049	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	78.8899	979	2049	95	below_threshold
Streptomyces otsuchiensis	strain=OTB305	GCA_004305975.1	2681388	2681388	type	True	78.8176	655	2049	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	78.8105	870	2049	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	78.4816	847	2049	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:26,340] [INFO] DFAST Taxonomy check result was written to GCF_001751245.1_ASM175124v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:26,341] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:26,341] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:26,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2708d1a-1da3-4dff-a58d-ab4bb4397684/dqc_reference/checkm_data
[2024-01-24 11:27:26,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:26,403] [INFO] Task started: CheckM
[2024-01-24 11:27:26,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001751245.1_ASM175124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001751245.1_ASM175124v1_genomic.fna/checkm_input GCF_001751245.1_ASM175124v1_genomic.fna/checkm_result
[2024-01-24 11:28:33,029] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:33,030] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:33,051] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:33,051] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:33,051] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001751245.1_ASM175124v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:33,052] [INFO] Task started: Blastn
[2024-01-24 11:28:33,052] [INFO] Running command: blastn -query GCF_001751245.1_ASM175124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2708d1a-1da3-4dff-a58d-ab4bb4397684/dqc_reference/reference_markers_gtdb.fasta -out GCF_001751245.1_ASM175124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:34,877] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:34,881] [INFO] Selected 17 target genomes.
[2024-01-24 11:28:34,882] [INFO] Target genome list was writen to GCF_001751245.1_ASM175124v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:34,894] [INFO] Task started: fastANI
[2024-01-24 11:28:34,894] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb0f5f0a-9bcb-4019-b402-44f82934c2cc/GCF_001751245.1_ASM175124v1_genomic.fna.gz --refList GCF_001751245.1_ASM175124v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001751245.1_ASM175124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:29:02,767] [INFO] Task succeeded: fastANI
[2024-01-24 11:29:02,788] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:29:02,788] [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_001751245.1	s__Streptomyces oceani	99.995	2025	2049	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_003355155.1	s__Streptomyces armeniacus	81.5096	1226	2049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424825.1	s__Streptomyces sp000424825	81.1273	1050	2049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665095.1	s__Streptomyces sp003665095	81.0735	1079	2049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843305.1	s__Streptomyces barkulensis	79.7547	867	2049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	99.92	99.92	0.99	0.99	2	-
GCF_000718985.1	s__Streptomyces megasporus	79.7199	806	2049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794255.1	s__Streptomyces carminius	79.6944	848	2049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017676385.1	s__Streptomyces sp017676385	79.6738	902	2049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114215.1	s__Streptomyces pini	79.6515	858	2049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	N/A	N/A	N/A	N/A	1	-
GCF_001751255.1	s__Streptomyces nanshensis_A	79.6441	871	2049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.85	97.85	0.86	0.86	2	-
GCF_001751365.1	s__Streptomyces abyssalis	79.6103	872	2049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.91	99.91	0.99	0.99	2	-
GCF_000424965.1	s__Streptomyces sp000424965	79.5128	940	2049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920575.1	s__Streptomyces sp002920575	79.3572	903	2049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704655.1	s__Streptomyces rimosus	79.1488	939	2049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	96.53	0.95	0.89	49	-
GCF_008634025.1	s__Streptomyces albofaciens	79.1135	942	2049	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	78.8073	656	2049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.30	98.24	0.80	0.78	3	-
GCF_900091845.1	s__Streptomyces sp900091845	78.6273	859	2049	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 11:29:02,791] [INFO] GTDB search result was written to GCF_001751245.1_ASM175124v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:29:02,792] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:29:02,944] [INFO] DFAST_QC result json was written to GCF_001751245.1_ASM175124v1_genomic.fna/dqc_result.json
[2024-01-24 11:29:02,944] [INFO] DFAST_QC completed!
[2024-01-24 11:29:02,945] [INFO] Total running time: 0h2m40s