[2024-01-24 11:59:13,204] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:13,207] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:13,207] [INFO] DQC Reference Directory: /var/lib/cwl/stg84f8073a-5900-410d-8726-d6674a7e83b8/dqc_reference
[2024-01-24 11:59:14,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:14,571] [INFO] Task started: Prodigal
[2024-01-24 11:59:14,571] [INFO] Running command: gunzip -c /var/lib/cwl/stgc437c822-86cb-4456-88b4-c6888bd7c41f/GCF_001514065.1_ASM151406v1_genomic.fna.gz | prodigal -d GCF_001514065.1_ASM151406v1_genomic.fna/cds.fna -a GCF_001514065.1_ASM151406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:45,125] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:45,125] [INFO] Task started: HMMsearch
[2024-01-24 11:59:45,125] [INFO] Running command: hmmsearch --tblout GCF_001514065.1_ASM151406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84f8073a-5900-410d-8726-d6674a7e83b8/dqc_reference/reference_markers.hmm GCF_001514065.1_ASM151406v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:45,580] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:45,581] [INFO] Found 6/6 markers.
[2024-01-24 11:59:45,658] [INFO] Query marker FASTA was written to GCF_001514065.1_ASM151406v1_genomic.fna/markers.fasta
[2024-01-24 11:59:45,658] [INFO] Task started: Blastn
[2024-01-24 11:59:45,659] [INFO] Running command: blastn -query GCF_001514065.1_ASM151406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84f8073a-5900-410d-8726-d6674a7e83b8/dqc_reference/reference_markers.fasta -out GCF_001514065.1_ASM151406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:47,068] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:47,072] [INFO] Selected 18 target genomes.
[2024-01-24 11:59:47,072] [INFO] Target genome list was writen to GCF_001514065.1_ASM151406v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:47,080] [INFO] Task started: fastANI
[2024-01-24 11:59:47,080] [INFO] Running command: fastANI --query /var/lib/cwl/stgc437c822-86cb-4456-88b4-c6888bd7c41f/GCF_001514065.1_ASM151406v1_genomic.fna.gz --refList GCF_001514065.1_ASM151406v1_genomic.fna/target_genomes.txt --output GCF_001514065.1_ASM151406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:32,350] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:32,351] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84f8073a-5900-410d-8726-d6674a7e83b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:32,351] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84f8073a-5900-410d-8726-d6674a7e83b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:32,370] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:00:32,370] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:00:32,370] [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 antibioticus	strain=DSM 40234	GCA_001514065.1	1890	1890	suspected-type	True	100.0	3360	3365	95	inconclusive
Streptomyces aquilus	strain=GGCR-6	GCA_003955715.1	2548456	2548456	type	True	95.1791	2695	3365	95	inconclusive
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	94.2955	2680	3365	95	below_threshold
Streptomyces griseorubiginosus	strain=DSM 40469	GCA_001514195.1	67304	67304	type	True	86.5154	2259	3365	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	86.4557	2092	3365	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	86.2845	2019	3365	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	86.1008	2030	3365	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	85.9845	2101	3365	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.7763	1794	3365	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.7549	1923	3365	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	84.9732	1934	3365	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	84.9207	1472	3365	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.701	1834	3365	95	below_threshold
Streptomyces fuscichromogenes	strain=CGMCC 4.7110	GCA_014645815.1	1324013	1324013	type	True	84.6236	2055	3365	95	below_threshold
Streptomyces humidus	strain=JCM 4386	GCA_014649655.1	52259	52259	type	True	84.5804	1872	3365	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.5594	1958	3365	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	84.073	1827	3365	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	84.0466	1866	3365	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:32,373] [INFO] DFAST Taxonomy check result was written to GCF_001514065.1_ASM151406v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:32,374] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:32,374] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:32,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84f8073a-5900-410d-8726-d6674a7e83b8/dqc_reference/checkm_data
[2024-01-24 12:00:32,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:32,468] [INFO] Task started: CheckM
[2024-01-24 12:00:32,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001514065.1_ASM151406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001514065.1_ASM151406v1_genomic.fna/checkm_input GCF_001514065.1_ASM151406v1_genomic.fna/checkm_result
[2024-01-24 12:02:58,579] [INFO] Task succeeded: CheckM
[2024-01-24 12:02:58,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:02:58,613] [INFO] ===== Completeness check finished =====
[2024-01-24 12:02:58,613] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:02:58,613] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001514065.1_ASM151406v1_genomic.fna/markers.fasta)
[2024-01-24 12:02:58,614] [INFO] Task started: Blastn
[2024-01-24 12:02:58,614] [INFO] Running command: blastn -query GCF_001514065.1_ASM151406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84f8073a-5900-410d-8726-d6674a7e83b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_001514065.1_ASM151406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:03:00,711] [INFO] Task succeeded: Blastn
[2024-01-24 12:03:00,717] [INFO] Selected 8 target genomes.
[2024-01-24 12:03:00,718] [INFO] Target genome list was writen to GCF_001514065.1_ASM151406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:03:00,725] [INFO] Task started: fastANI
[2024-01-24 12:03:00,725] [INFO] Running command: fastANI --query /var/lib/cwl/stgc437c822-86cb-4456-88b4-c6888bd7c41f/GCF_001514065.1_ASM151406v1_genomic.fna.gz --refList GCF_001514065.1_ASM151406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001514065.1_ASM151406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:03:22,857] [INFO] Task succeeded: fastANI
[2024-01-24 12:03:22,872] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:03:22,872] [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_001514065.1	s__Streptomyces antibioticus	100.0	3360	3365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2614	N/A	N/A	N/A	N/A	1	conclusive
GCF_003955715.1	s__Streptomyces aquilus	95.1714	2696	3365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2614	97.56	95.79	0.89	0.84	3	-
GCA_002027195.1	s__Streptomyces sp002027195	94.9115	2277	3365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0044	N/A	N/A	N/A	N/A	1	-
GCF_015163075.1	s__Streptomyces sp015163075	94.2969	2679	3365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143935.1	s__Streptomyces sp003143935	91.9527	2520	3365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018128905.1	s__Streptomyces sp003814525	86.7322	2264	3365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	99.42	0.94	0.94	2	-
GCF_001514195.1	s__Streptomyces griseorubiginosus	86.5328	2256	3365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.34	95.64	0.90	0.86	7	-
GCF_014645815.1	s__Streptomyces fuscichromogenes	84.6192	2056	3365	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 12:03:22,873] [INFO] GTDB search result was written to GCF_001514065.1_ASM151406v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:03:22,875] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:03:22,878] [INFO] DFAST_QC result json was written to GCF_001514065.1_ASM151406v1_genomic.fna/dqc_result.json
[2024-01-24 12:03:22,879] [INFO] DFAST_QC completed!
[2024-01-24 12:03:22,879] [INFO] Total running time: 0h4m10s