[2024-01-24 12:06:14,626] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg41a0719b-13eb-4fca-b12d-e49c4d4293f3/dqc_reference
[2024-01-24 12:06:16,061] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:16,062] [INFO] Task started: Prodigal
[2024-01-24 12:06:16,062] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ed2d454-18b7-4493-bf2d-c9d8f92ed06b/GCF_014069875.1_ASM1406987v1_genomic.fna.gz | prodigal -d GCF_014069875.1_ASM1406987v1_genomic.fna/cds.fna -a GCF_014069875.1_ASM1406987v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:23,192] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:23,192] [INFO] Task started: HMMsearch
[2024-01-24 12:06:23,192] [INFO] Running command: hmmsearch --tblout GCF_014069875.1_ASM1406987v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41a0719b-13eb-4fca-b12d-e49c4d4293f3/dqc_reference/reference_markers.hmm GCF_014069875.1_ASM1406987v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:23,441] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:23,442] [INFO] Found 6/6 markers.
[2024-01-24 12:06:23,473] [INFO] Query marker FASTA was written to GCF_014069875.1_ASM1406987v1_genomic.fna/markers.fasta
[2024-01-24 12:06:23,474] [INFO] Task started: Blastn
[2024-01-24 12:06:23,474] [INFO] Running command: blastn -query GCF_014069875.1_ASM1406987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41a0719b-13eb-4fca-b12d-e49c4d4293f3/dqc_reference/reference_markers.fasta -out GCF_014069875.1_ASM1406987v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:24,403] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:24,408] [INFO] Selected 20 target genomes.
[2024-01-24 12:06:24,408] [INFO] Target genome list was writen to GCF_014069875.1_ASM1406987v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:24,419] [INFO] Task started: fastANI
[2024-01-24 12:06:24,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ed2d454-18b7-4493-bf2d-c9d8f92ed06b/GCF_014069875.1_ASM1406987v1_genomic.fna.gz --refList GCF_014069875.1_ASM1406987v1_genomic.fna/target_genomes.txt --output GCF_014069875.1_ASM1406987v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:36,329] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:36,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41a0719b-13eb-4fca-b12d-e49c4d4293f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:36,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41a0719b-13eb-4fca-b12d-e49c4d4293f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:36,350] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:36,350] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:36,351] [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
Flaviflexus equikiangi	strain=dk850	GCA_014069875.1	2758573	2758573	type	True	100.0	781	781	95	conclusive
Flaviflexus salsibiostraticola	strain=KCTC 33148	GCA_003952265.1	1282737	1282737	type	True	80.4224	443	781	95	below_threshold
Flaviflexus ciconiae	strain=H23T48	GCA_003971195.1	2496867	2496867	type	True	79.4635	323	781	95	below_threshold
Flaviflexus huanghaiensis	strain=CICC 10486	GCA_014118685.1	1111473	1111473	type	True	79.066	350	781	95	below_threshold
Flaviflexus massiliensis	strain=SIT4	GCA_001375495.1	1522309	1522309	type	True	79.0657	276	781	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.7324	135	781	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	77.6591	125	781	95	below_threshold
Actinomyces viscosus	strain=NCTC10951	GCA_900637975.1	1656	1656	type	True	77.6044	96	781	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	77.3666	132	781	95	below_threshold
Peptidiphaga gingivicola	strain=BA112	GCA_001652275.1	2741497	2741497	type	True	77.3368	79	781	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.1084	87	781	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	76.9748	87	781	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	76.9259	83	781	95	below_threshold
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	76.9155	88	781	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	76.8987	85	781	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	76.8742	87	781	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	76.4397	55	781	95	below_threshold
Glycomyces terrestris	strain=YIM 121974	GCA_003933745.1	2493553	2493553	type	True	75.817	69	781	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	75.7815	69	781	95	below_threshold
Microbispora rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	75.6352	71	781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:36,361] [INFO] DFAST Taxonomy check result was written to GCF_014069875.1_ASM1406987v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:36,361] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:36,361] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:36,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41a0719b-13eb-4fca-b12d-e49c4d4293f3/dqc_reference/checkm_data
[2024-01-24 12:06:36,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:36,417] [INFO] Task started: CheckM
[2024-01-24 12:06:36,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014069875.1_ASM1406987v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014069875.1_ASM1406987v1_genomic.fna/checkm_input GCF_014069875.1_ASM1406987v1_genomic.fna/checkm_result
[2024-01-24 12:07:04,862] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:04,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:04,887] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:04,888] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:04,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014069875.1_ASM1406987v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:04,889] [INFO] Task started: Blastn
[2024-01-24 12:07:04,889] [INFO] Running command: blastn -query GCF_014069875.1_ASM1406987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41a0719b-13eb-4fca-b12d-e49c4d4293f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014069875.1_ASM1406987v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:06,126] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:06,130] [INFO] Selected 18 target genomes.
[2024-01-24 12:07:06,131] [INFO] Target genome list was writen to GCF_014069875.1_ASM1406987v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:06,155] [INFO] Task started: fastANI
[2024-01-24 12:07:06,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ed2d454-18b7-4493-bf2d-c9d8f92ed06b/GCF_014069875.1_ASM1406987v1_genomic.fna.gz --refList GCF_014069875.1_ASM1406987v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014069875.1_ASM1406987v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:16,893] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:16,911] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:16,912] [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_014069875.1	s__Flaviflexus sp014069875	100.0	781	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	99.13	99.13	0.93	0.93	3	conclusive
GCF_003952265.1	s__Flaviflexus salsibiostraticola	80.4066	445	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971195.1	s__Flaviflexus sp003971195	79.4635	323	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001375495.1	s__Flaviflexus massiliensis	79.1754	278	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014118685.1	s__Flaviflexus huanghaiensis	79.066	350	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002564025.1	s__Flavimobilis soli	77.9827	95	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563695.1	s__Georgenia soli	77.6753	125	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001462455.1	s__Cellulomonas sp001462455	77.3169	82	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636275.1	s__Actinotalea carbonis	77.1426	94	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	100.00	100.00	0.97	0.97	2	-
GCF_009733795.1	s__Pseudactinotalea caeni	77.1345	107	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631615.1	s__Tsukamurella paurometabola_A	77.0018	63	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	76.9619	98	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_013004695.1	s__Promicromonospora citrea	76.9004	86	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	99.97	99.97	0.99	0.99	2	-
GCF_014635665.1	s__Isoptericola cucumis	76.8593	91	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114185.1	s__Cellulomonas sp900114185	76.7899	90	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000385135.1	s__Promicromonospora sukumoe_B	76.777	82	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	95.99	95.99	0.93	0.93	2	-
GCA_905373325.1	s__Peptidiphaga sp905373325	76.5596	54	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Peptidiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001865245.1	s__Streptomyces sp001865245	76.0192	64	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.88	98.02	0.87	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:16,914] [INFO] GTDB search result was written to GCF_014069875.1_ASM1406987v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:16,914] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:16,941] [INFO] DFAST_QC result json was written to GCF_014069875.1_ASM1406987v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:16,941] [INFO] DFAST_QC completed!
[2024-01-24 12:07:16,941] [INFO] Total running time: 0h1m2s