[2024-01-24 14:14:44,906] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:44,908] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:44,909] [INFO] DQC Reference Directory: /var/lib/cwl/stgece51f19-772b-4462-a1bf-ba6ecd713645/dqc_reference
[2024-01-24 14:14:46,178] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:46,179] [INFO] Task started: Prodigal
[2024-01-24 14:14:46,179] [INFO] Running command: gunzip -c /var/lib/cwl/stg4978ee8a-45bf-487f-b0d2-5a258e71191f/GCF_000719135.1_ASM71913v1_genomic.fna.gz | prodigal -d GCF_000719135.1_ASM71913v1_genomic.fna/cds.fna -a GCF_000719135.1_ASM71913v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:03,721] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:03,721] [INFO] Task started: HMMsearch
[2024-01-24 14:15:03,722] [INFO] Running command: hmmsearch --tblout GCF_000719135.1_ASM71913v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgece51f19-772b-4462-a1bf-ba6ecd713645/dqc_reference/reference_markers.hmm GCF_000719135.1_ASM71913v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:04,064] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:04,065] [INFO] Found 6/6 markers.
[2024-01-24 14:15:04,127] [INFO] Query marker FASTA was written to GCF_000719135.1_ASM71913v1_genomic.fna/markers.fasta
[2024-01-24 14:15:04,127] [INFO] Task started: Blastn
[2024-01-24 14:15:04,127] [INFO] Running command: blastn -query GCF_000719135.1_ASM71913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgece51f19-772b-4462-a1bf-ba6ecd713645/dqc_reference/reference_markers.fasta -out GCF_000719135.1_ASM71913v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:05,579] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:05,583] [INFO] Selected 22 target genomes.
[2024-01-24 14:15:05,584] [INFO] Target genome list was writen to GCF_000719135.1_ASM71913v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:05,606] [INFO] Task started: fastANI
[2024-01-24 14:15:05,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg4978ee8a-45bf-487f-b0d2-5a258e71191f/GCF_000719135.1_ASM71913v1_genomic.fna.gz --refList GCF_000719135.1_ASM71913v1_genomic.fna/target_genomes.txt --output GCF_000719135.1_ASM71913v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:42,086] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:42,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgece51f19-772b-4462-a1bf-ba6ecd713645/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:42,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgece51f19-772b-4462-a1bf-ba6ecd713645/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:42,109] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:42,109] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:42,109] [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 specialis	strain=type strain: GW41-1564	GCA_001493375.1	498367	498367	type	True	81.6852	1057	2140	95	below_threshold
Streptomyces hainanensis	strain=DSM 41900	GCA_004348415.1	402648	402648	type	True	81.3163	1079	2140	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	81.2289	1154	2140	95	below_threshold
Streptomyces radicis	strain=DS1-2	GCA_003626575.1	1750517	1750517	type	True	81.1776	1196	2140	95	below_threshold
Streptomyces hoynatensis	strain=KCTC 29097	GCA_003626535.1	1141874	1141874	type	True	81.116	1217	2140	95	below_threshold
Streptomyces triticirhizae	strain=NEAU-YY642	GCA_003696235.1	2483353	2483353	type	True	80.815	1040	2140	95	below_threshold
Streptomyces mimosae	strain=3MP-10	GCA_006334995.2	2586635	2586635	type	True	80.7787	1167	2140	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	80.6072	1083	2140	95	below_threshold
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	80.5945	1086	2140	95	below_threshold
Streptomyces pathocidini	strain=NRRL B-24287	GCA_001418495.1	1650571	1650571	type	True	79.9591	684	2140	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	79.6648	862	2140	95	below_threshold
Streptomyces calidiresistens	strain=DSM 42108	GCA_014141525.1	1485586	1485586	type	True	79.5716	593	2140	95	below_threshold
Streptomyces carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	79.3904	925	2140	95	below_threshold
Streptomyces boncukensis	strain=SB3404	GCA_011045075.1	2711219	2711219	type	True	79.1829	817	2140	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	79.0338	939	2140	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	78.9893	969	2140	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	78.9778	957	2140	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	78.9059	967	2140	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	78.8593	880	2140	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	78.6727	969	2140	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	78.647	950	2140	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	78.4548	964	2140	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:42,111] [INFO] DFAST Taxonomy check result was written to GCF_000719135.1_ASM71913v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:42,111] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:42,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:42,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgece51f19-772b-4462-a1bf-ba6ecd713645/dqc_reference/checkm_data
[2024-01-24 14:15:42,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:42,172] [INFO] Task started: CheckM
[2024-01-24 14:15:42,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000719135.1_ASM71913v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000719135.1_ASM71913v1_genomic.fna/checkm_input GCF_000719135.1_ASM71913v1_genomic.fna/checkm_result
[2024-01-24 14:17:05,872] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:05,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:05,899] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:05,899] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:05,899] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000719135.1_ASM71913v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:05,900] [INFO] Task started: Blastn
[2024-01-24 14:17:05,900] [INFO] Running command: blastn -query GCF_000719135.1_ASM71913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgece51f19-772b-4462-a1bf-ba6ecd713645/dqc_reference/reference_markers_gtdb.fasta -out GCF_000719135.1_ASM71913v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:08,402] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:08,406] [INFO] Selected 18 target genomes.
[2024-01-24 14:17:08,406] [INFO] Target genome list was writen to GCF_000719135.1_ASM71913v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:08,427] [INFO] Task started: fastANI
[2024-01-24 14:17:08,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg4978ee8a-45bf-487f-b0d2-5a258e71191f/GCF_000719135.1_ASM71913v1_genomic.fna.gz --refList GCF_000719135.1_ASM71913v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000719135.1_ASM71913v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:37,531] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:37,546] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:37,546] [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_000719135.1	s__Streptomyces avicenniae	100.0	2139	2140	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_004193175.1	s__Streptomyces sp004193175	83.6333	1281	2140	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	81.6847	1058	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083795.1	s__Streptomyces sp001083795	81.6142	1124	2140	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	81.4567	1098	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348415.1	s__Streptomyces hainanensis	81.2627	1089	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002128305.1	s__Streptomyces sp002128305	81.2531	1119	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626575.1	s__Streptomyces sp003626575	81.1616	1199	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001984575.1	s__Streptomyces sp001984575	81.096	1220	2140	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	81.093	1220	2140	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	80.8462	1034	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.35	0.89	0.89	3	-
GCF_900230195.1	s__Streptomyces zhaozhouensis	80.6506	1076	2140	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	80.187	1088	2140	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	79.6874	858	2140	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	79.3426	925	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112575.1	s__Streptomyces ardesiacus	79.0198	940	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_014596915.1	s__Streptomyces sp014596915	78.9118	939	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001906585.1	s__Streptomyces kebangsaanensis	78.871	880	2140	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:37,548] [INFO] GTDB search result was written to GCF_000719135.1_ASM71913v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:37,549] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:37,553] [INFO] DFAST_QC result json was written to GCF_000719135.1_ASM71913v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:37,554] [INFO] DFAST_QC completed!
[2024-01-24 14:17:37,554] [INFO] Total running time: 0h2m53s