[2024-01-24 13:08:57,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:57,958] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:57,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg09c0e5b2-9d0c-46e7-b1c4-92e86ef28a18/dqc_reference
[2024-01-24 13:08:59,196] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:59,197] [INFO] Task started: Prodigal
[2024-01-24 13:08:59,197] [INFO] Running command: gunzip -c /var/lib/cwl/stg792c6598-beeb-4af2-a004-18167db39c7e/GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/cds.fna -a GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:27,457] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:27,458] [INFO] Task started: HMMsearch
[2024-01-24 13:09:27,458] [INFO] Running command: hmmsearch --tblout GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09c0e5b2-9d0c-46e7-b1c4-92e86ef28a18/dqc_reference/reference_markers.hmm GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:27,808] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:27,809] [INFO] Found 6/6 markers.
[2024-01-24 13:09:27,873] [INFO] Query marker FASTA was written to GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:09:27,874] [INFO] Task started: Blastn
[2024-01-24 13:09:27,874] [INFO] Running command: blastn -query GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg09c0e5b2-9d0c-46e7-b1c4-92e86ef28a18/dqc_reference/reference_markers.fasta -out GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:29,182] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:29,186] [INFO] Selected 14 target genomes.
[2024-01-24 13:09:29,186] [INFO] Target genome list was writen to GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:09:29,259] [INFO] Task started: fastANI
[2024-01-24 13:09:29,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg792c6598-beeb-4af2-a004-18167db39c7e/GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna.gz --refList GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:58,274] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:58,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09c0e5b2-9d0c-46e7-b1c4-92e86ef28a18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:58,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09c0e5b2-9d0c-46e7-b1c4-92e86ef28a18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:58,287] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:09:58,287] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:58,287] [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 griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	100.0	2873	2875	95	conclusive
Streptomyces griseus	strain=NCTC13033	GCA_900460065.1	1911	1911	type	True	99.974	2799	2875	95	conclusive
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	93.4656	2267	2875	95	below_threshold
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	91.4443	2142	2875	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	91.41	1903	2875	95	below_threshold
Streptomyces sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	91.3972	2035	2875	95	below_threshold
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	91.1787	2035	2875	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	90.2113	2079	2875	95	below_threshold
Streptomyces californicus	strain=NRRL B-2098	GCA_000717645.1	67351	67351	type	True	90.141	2029	2875	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	88.544	1628	2875	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.6671	1640	2875	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.3942	1420	2875	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.0714	1236	2875	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	81.0556	1331	2875	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:58,289] [INFO] DFAST Taxonomy check result was written to GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:09:58,289] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:58,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:58,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09c0e5b2-9d0c-46e7-b1c4-92e86ef28a18/dqc_reference/checkm_data
[2024-01-24 13:09:58,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:58,373] [INFO] Task started: CheckM
[2024-01-24 13:09:58,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/checkm_input GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:12:17,962] [INFO] Task succeeded: CheckM
[2024-01-24 13:12:17,963] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:12:17,988] [INFO] ===== Completeness check finished =====
[2024-01-24 13:12:17,989] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:12:17,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:12:17,990] [INFO] Task started: Blastn
[2024-01-24 13:12:17,990] [INFO] Running command: blastn -query GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg09c0e5b2-9d0c-46e7-b1c4-92e86ef28a18/dqc_reference/reference_markers_gtdb.fasta -out GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:20,056] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:20,060] [INFO] Selected 12 target genomes.
[2024-01-24 13:12:20,060] [INFO] Target genome list was writen to GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:12:20,179] [INFO] Task started: fastANI
[2024-01-24 13:12:20,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg792c6598-beeb-4af2-a004-18167db39c7e/GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna.gz --refList GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:12:45,316] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:45,332] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:12:45,332] [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_900460065.1	s__Streptomyces griseus	99.974	2799	2875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.49	99.03	0.95	0.93	10	conclusive
GCF_018619185.1	s__Streptomyces sp018619185	94.1256	2118	2875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650675.1	s__Streptomyces anulatus	93.466	2267	2875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.62	96.42	0.89	0.81	27	-
GCF_000377965.1	s__Streptomyces sp000377965	93.3817	2159	2875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002551245.1	s__Streptomyces sp002551245	92.8563	1874	2875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	91.8757	2123	2875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	-
GCA_002154345.1	s__Streptomyces fimicarius	91.7654	1772	2875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.88	95.22	0.89	0.81	11	-
GCF_001687325.1	s__Streptomyces sp001687325	91.6749	2057	2875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003501885.1	s__Streptomyces globisporus_D	91.6651	1848	2875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6693	N/A	N/A	N/A	N/A	1	-
GCA_014649555.1	s__Streptomyces globisporus	91.6646	2099	2875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.88	97.57	0.92	0.86	14	-
GCF_002910905.1	s__Streptomyces sp002910905	91.6576	1888	2875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648875.1	s__Streptomyces parvus	91.4421	2142	2875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2347	97.39	96.11	0.86	0.79	24	-
--------------------------------------------------------------------------------
[2024-01-24 13:12:45,334] [INFO] GTDB search result was written to GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:12:45,334] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:12:45,337] [INFO] DFAST_QC result json was written to GCF_900105705.1_IMG-taxon_2634166340_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:12:45,338] [INFO] DFAST_QC completed!
[2024-01-24 13:12:45,338] [INFO] Total running time: 0h3m47s