[2024-01-24 13:09:41,149] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:41,155] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:41,155] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0009147-9aa0-49a9-bc0f-e70e4bbb8475/dqc_reference
[2024-01-24 13:09:42,324] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:42,325] [INFO] Task started: Prodigal
[2024-01-24 13:09:42,325] [INFO] Running command: gunzip -c /var/lib/cwl/stg444b41da-c448-4801-b32b-af0743c43a06/GCF_000716445.1_ASM71644v1_genomic.fna.gz | prodigal -d GCF_000716445.1_ASM71644v1_genomic.fna/cds.fna -a GCF_000716445.1_ASM71644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:09,078] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:09,078] [INFO] Task started: HMMsearch
[2024-01-24 13:10:09,078] [INFO] Running command: hmmsearch --tblout GCF_000716445.1_ASM71644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0009147-9aa0-49a9-bc0f-e70e4bbb8475/dqc_reference/reference_markers.hmm GCF_000716445.1_ASM71644v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:09,543] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:09,544] [INFO] Found 6/6 markers.
[2024-01-24 13:10:09,619] [INFO] Query marker FASTA was written to GCF_000716445.1_ASM71644v1_genomic.fna/markers.fasta
[2024-01-24 13:10:09,619] [INFO] Task started: Blastn
[2024-01-24 13:10:09,620] [INFO] Running command: blastn -query GCF_000716445.1_ASM71644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0009147-9aa0-49a9-bc0f-e70e4bbb8475/dqc_reference/reference_markers.fasta -out GCF_000716445.1_ASM71644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:11,194] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:11,197] [INFO] Selected 19 target genomes.
[2024-01-24 13:10:11,197] [INFO] Target genome list was writen to GCF_000716445.1_ASM71644v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:11,219] [INFO] Task started: fastANI
[2024-01-24 13:10:11,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg444b41da-c448-4801-b32b-af0743c43a06/GCF_000716445.1_ASM71644v1_genomic.fna.gz --refList GCF_000716445.1_ASM71644v1_genomic.fna/target_genomes.txt --output GCF_000716445.1_ASM71644v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:55,402] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:55,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0009147-9aa0-49a9-bc0f-e70e4bbb8475/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:55,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0009147-9aa0-49a9-bc0f-e70e4bbb8475/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:55,422] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:55,422] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:55,422] [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 wedmorensis	strain=NRRL 3426	GCA_000716445.1	43759	43759	type	True	100.0	3024	3037	95	conclusive
Streptomyces nashvillensis	strain=JCM 4498	GCA_014650095.1	67334	67334	type	True	89.7254	2133	3037	95	below_threshold
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	89.5249	2141	3037	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	89.487	2096	3037	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	89.4288	2101	3037	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000725545.1	1905	1905	type	True	89.2369	1967	3037	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000718175.1	1905	1905	type	True	89.1715	1974	3037	95	below_threshold
Streptomyces gardneri	strain=JCM 4375	GCA_014655085.1	66892	66892	type	True	89.1397	2173	3037	95	below_threshold
Streptomyces narbonensis	strain=JCM 4147	GCA_014649015.1	67333	67333	type	True	89.1088	1980	3037	95	below_threshold
Streptomyces gardneri	strain=NBRC 12865	GCA_006539185.1	66892	66892	type	True	89.0987	2156	3037	95	below_threshold
Streptomyces zaomyceticus	strain=JCM 4864	GCA_014656215.1	68286	68286	type	True	89.0132	1999	3037	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	88.9152	1562	3037	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	86.4063	1956	3037	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	82.6464	1548	3037	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.5803	1516	3037	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.2916	1395	3037	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	81.4745	1405	3037	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	81.4695	1440	3037	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	80.9368	1356	3037	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:55,424] [INFO] DFAST Taxonomy check result was written to GCF_000716445.1_ASM71644v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:55,424] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:55,424] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:55,424] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0009147-9aa0-49a9-bc0f-e70e4bbb8475/dqc_reference/checkm_data
[2024-01-24 13:10:55,425] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:55,509] [INFO] Task started: CheckM
[2024-01-24 13:10:55,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000716445.1_ASM71644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000716445.1_ASM71644v1_genomic.fna/checkm_input GCF_000716445.1_ASM71644v1_genomic.fna/checkm_result
[2024-01-24 13:12:53,355] [INFO] Task succeeded: CheckM
[2024-01-24 13:12:53,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:12:53,419] [INFO] ===== Completeness check finished =====
[2024-01-24 13:12:53,420] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:12:53,420] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000716445.1_ASM71644v1_genomic.fna/markers.fasta)
[2024-01-24 13:12:53,420] [INFO] Task started: Blastn
[2024-01-24 13:12:53,420] [INFO] Running command: blastn -query GCF_000716445.1_ASM71644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0009147-9aa0-49a9-bc0f-e70e4bbb8475/dqc_reference/reference_markers_gtdb.fasta -out GCF_000716445.1_ASM71644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:56,109] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:56,113] [INFO] Selected 17 target genomes.
[2024-01-24 13:12:56,113] [INFO] Target genome list was writen to GCF_000716445.1_ASM71644v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:12:56,158] [INFO] Task started: fastANI
[2024-01-24 13:12:56,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg444b41da-c448-4801-b32b-af0743c43a06/GCF_000716445.1_ASM71644v1_genomic.fna.gz --refList GCF_000716445.1_ASM71644v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000716445.1_ASM71644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:35,543] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:35,566] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:35,567] [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_000716445.1	s__Streptomyces wedmorensis	100.0	3024	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	conclusive
GCF_001426585.1	s__Streptomyces sp001426585	89.6762	1776	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.07	96.69	0.91	0.88	3	-
GCF_900105415.1	s__Streptomyces sp900105415	89.6388	2112	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_014648895.1	s__Streptomyces tanashiensis	89.5178	2142	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	97.78	0.91	0.91	2	-
GCF_000830005.1	s__Streptomyces vietnamensis	89.4997	2095	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386135.1	s__Streptomyces sp003386135	89.3624	2122	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
GCF_014649755.1	s__Streptomyces litmocidini	89.3322	1996	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.07	95.07	0.85	0.85	2	-
GCF_000725545.1	s__Streptomyces exfoliatus	89.1696	1977	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_014649015.1	s__Streptomyces narbonensis	89.1377	1975	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.06	95.06	0.89	0.89	2	-
GCF_006539185.1	s__Streptomyces gardneri	89.1212	2151	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.06	97.41	0.92	0.89	5	-
GCA_000717735.1	s__Streptomyces griseoluteus_A	89.0955	1957	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_001426405.1	s__Streptomyces sp001426405	89.069	1954	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001905665.1	s__Streptomyces sp001905665	88.9333	1945	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905825.1	s__Streptomyces sp001905825	88.6599	2064	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.90	96.90	0.90	0.90	2	-
GCF_001280125.1	s__Streptomyces sp001280125	88.6372	1749	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.57	95.16	0.89	0.81	3	-
GCF_014451325.1	s__Streptomyces sp014451325	88.437	1432	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002911015.1	s__Streptomyces populi	81.5389	1495	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:35,569] [INFO] GTDB search result was written to GCF_000716445.1_ASM71644v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:35,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:35,574] [INFO] DFAST_QC result json was written to GCF_000716445.1_ASM71644v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:35,575] [INFO] DFAST_QC completed!
[2024-01-24 13:13:35,575] [INFO] Total running time: 0h3m54s