[2024-01-24 11:58:57,351] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,364] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,364] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc55bd1e-0f6f-4576-91fc-06ac1408a66f/dqc_reference
[2024-01-24 11:58:58,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,726] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,726] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5066afe-083c-45bb-95c9-1c77a48dd6aa/GCF_006539185.1_ASM653918v1_genomic.fna.gz | prodigal -d GCF_006539185.1_ASM653918v1_genomic.fna/cds.fna -a GCF_006539185.1_ASM653918v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:22,474] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:22,474] [INFO] Task started: HMMsearch
[2024-01-24 11:59:22,474] [INFO] Running command: hmmsearch --tblout GCF_006539185.1_ASM653918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc55bd1e-0f6f-4576-91fc-06ac1408a66f/dqc_reference/reference_markers.hmm GCF_006539185.1_ASM653918v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:22,916] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:22,918] [INFO] Found 6/6 markers.
[2024-01-24 11:59:23,000] [INFO] Query marker FASTA was written to GCF_006539185.1_ASM653918v1_genomic.fna/markers.fasta
[2024-01-24 11:59:23,001] [INFO] Task started: Blastn
[2024-01-24 11:59:23,001] [INFO] Running command: blastn -query GCF_006539185.1_ASM653918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc55bd1e-0f6f-4576-91fc-06ac1408a66f/dqc_reference/reference_markers.fasta -out GCF_006539185.1_ASM653918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:24,428] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:24,432] [INFO] Selected 15 target genomes.
[2024-01-24 11:59:24,432] [INFO] Target genome list was writen to GCF_006539185.1_ASM653918v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:24,440] [INFO] Task started: fastANI
[2024-01-24 11:59:24,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5066afe-083c-45bb-95c9-1c77a48dd6aa/GCF_006539185.1_ASM653918v1_genomic.fna.gz --refList GCF_006539185.1_ASM653918v1_genomic.fna/target_genomes.txt --output GCF_006539185.1_ASM653918v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:59,216] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:59,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc55bd1e-0f6f-4576-91fc-06ac1408a66f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:59,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc55bd1e-0f6f-4576-91fc-06ac1408a66f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:59,229] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:59:59,230] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:59,230] [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 gardneri	strain=NBRC 12865	GCA_006539185.1	66892	66892	type	True	100.0	2924	2932	95	conclusive
Streptomyces gardneri	strain=JCM 4375	GCA_014655085.1	66892	66892	type	True	99.993	2925	2932	95	conclusive
Streptomyces narbonensis	strain=JCM 4147	GCA_014649015.1	67333	67333	type	True	94.1973	2170	2932	95	below_threshold
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	89.4993	2154	2932	95	below_threshold
Streptomyces nashvillensis	strain=JCM 4498	GCA_014650095.1	67334	67334	type	True	89.4151	2125	2932	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000718175.1	1905	1905	type	True	89.293	1988	2932	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000725545.1	1905	1905	type	True	89.2454	2000	2932	95	below_threshold
Streptomyces wedmorensis	strain=NRRL 3426	GCA_000716445.1	43759	43759	type	True	89.0873	2137	2932	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	89.021	1573	2932	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	88.9412	1914	2932	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	88.8269	2065	2932	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	86.2973	1908	2932	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.0229	1498	2932	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.4333	1552	2932	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.2454	1281	2932	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:59,232] [INFO] DFAST Taxonomy check result was written to GCF_006539185.1_ASM653918v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:59,232] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:59,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:59,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc55bd1e-0f6f-4576-91fc-06ac1408a66f/dqc_reference/checkm_data
[2024-01-24 11:59:59,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:59,316] [INFO] Task started: CheckM
[2024-01-24 11:59:59,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539185.1_ASM653918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539185.1_ASM653918v1_genomic.fna/checkm_input GCF_006539185.1_ASM653918v1_genomic.fna/checkm_result
[2024-01-24 12:01:38,548] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:38,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:38,570] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:38,570] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:38,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539185.1_ASM653918v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:38,571] [INFO] Task started: Blastn
[2024-01-24 12:01:38,571] [INFO] Running command: blastn -query GCF_006539185.1_ASM653918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc55bd1e-0f6f-4576-91fc-06ac1408a66f/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539185.1_ASM653918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:40,673] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:40,676] [INFO] Selected 14 target genomes.
[2024-01-24 12:01:40,676] [INFO] Target genome list was writen to GCF_006539185.1_ASM653918v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:40,707] [INFO] Task started: fastANI
[2024-01-24 12:01:40,707] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5066afe-083c-45bb-95c9-1c77a48dd6aa/GCF_006539185.1_ASM653918v1_genomic.fna.gz --refList GCF_006539185.1_ASM653918v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539185.1_ASM653918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:11,665] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:11,676] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:02:11,677] [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_006539185.1	s__Streptomyces gardneri	100.0	2924	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.06	97.41	0.92	0.89	5	conclusive
GCF_014649015.1	s__Streptomyces narbonensis	94.2082	2169	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.06	95.06	0.89	0.89	2	-
GCF_001426585.1	s__Streptomyces sp001426585	93.3406	1909	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.07	96.69	0.91	0.88	3	-
GCF_014648895.1	s__Streptomyces tanashiensis	89.5017	2153	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	97.78	0.91	0.91	2	-
GCF_000725545.1	s__Streptomyces exfoliatus	89.278	1996	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCA_000717735.1	s__Streptomyces griseoluteus_A	89.2171	1979	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_000717595.1	s__Streptomyces flavochromogenes	89.2047	2121	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5951	N/A	N/A	N/A	N/A	1	-
GCF_001426405.1	s__Streptomyces sp001426405	89.1935	1977	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105415.1	s__Streptomyces sp900105415	89.1719	2068	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_001905665.1	s__Streptomyces sp001905665	89.0805	1962	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716445.1	s__Streptomyces wedmorensis	89.0672	2140	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	-
GCF_001905825.1	s__Streptomyces sp001905825	88.9295	2092	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.90	96.90	0.90	0.90	2	-
GCF_003386135.1	s__Streptomyces sp003386135	88.9281	2039	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
GCF_001280125.1	s__Streptomyces sp001280125	88.543	1765	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.57	95.16	0.89	0.81	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:02:11,678] [INFO] GTDB search result was written to GCF_006539185.1_ASM653918v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:11,680] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:11,684] [INFO] DFAST_QC result json was written to GCF_006539185.1_ASM653918v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:11,684] [INFO] DFAST_QC completed!
[2024-01-24 12:02:11,684] [INFO] Total running time: 0h3m14s