[2024-01-24 13:19:01,187] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:01,189] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:01,189] [INFO] DQC Reference Directory: /var/lib/cwl/stgbadc3951-1e4b-41c8-b7a2-c2891e52c3eb/dqc_reference
[2024-01-24 13:19:02,519] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:02,520] [INFO] Task started: Prodigal
[2024-01-24 13:19:02,520] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cca4ccf-5831-4631-96f8-8a27719bb284/GCF_009727065.1_ASM972706v1_genomic.fna.gz | prodigal -d GCF_009727065.1_ASM972706v1_genomic.fna/cds.fna -a GCF_009727065.1_ASM972706v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:10,768] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:10,768] [INFO] Task started: HMMsearch
[2024-01-24 13:19:10,768] [INFO] Running command: hmmsearch --tblout GCF_009727065.1_ASM972706v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbadc3951-1e4b-41c8-b7a2-c2891e52c3eb/dqc_reference/reference_markers.hmm GCF_009727065.1_ASM972706v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:11,027] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:11,028] [INFO] Found 6/6 markers.
[2024-01-24 13:19:11,052] [INFO] Query marker FASTA was written to GCF_009727065.1_ASM972706v1_genomic.fna/markers.fasta
[2024-01-24 13:19:11,052] [INFO] Task started: Blastn
[2024-01-24 13:19:11,052] [INFO] Running command: blastn -query GCF_009727065.1_ASM972706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbadc3951-1e4b-41c8-b7a2-c2891e52c3eb/dqc_reference/reference_markers.fasta -out GCF_009727065.1_ASM972706v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:11,944] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:11,949] [INFO] Selected 24 target genomes.
[2024-01-24 13:19:11,950] [INFO] Target genome list was writen to GCF_009727065.1_ASM972706v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:11,975] [INFO] Task started: fastANI
[2024-01-24 13:19:11,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cca4ccf-5831-4631-96f8-8a27719bb284/GCF_009727065.1_ASM972706v1_genomic.fna.gz --refList GCF_009727065.1_ASM972706v1_genomic.fna/target_genomes.txt --output GCF_009727065.1_ASM972706v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:23,897] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:23,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbadc3951-1e4b-41c8-b7a2-c2891e52c3eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:23,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbadc3951-1e4b-41c8-b7a2-c2891e52c3eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:23,914] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:23,914] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:23,915] [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
Bifidobacterium canis	strain=GSD1FS	GCA_009727065.1	2610880	2610880	type	True	100.0	745	745	95	conclusive
Bifidobacterium animalis subsp. animalis	strain=ATCC 25527	GCA_000260715.1	302912	28025	type	True	81.0404	394	745	95	below_threshold
Bifidobacterium animalis subsp. animalis	strain=LMG 10508	GCA_000741485.1	302912	28025	type	True	81.0289	406	745	95	below_threshold
Bifidobacterium choerinum	strain=DSM 20434	GCA_000484675.1	35760	35760	type	True	80.1627	368	745	95	below_threshold
Bifidobacterium choerinum	strain=DSM 20434	GCA_000771425.1	35760	35760	type	True	80.0398	354	745	95	below_threshold
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_002706665.1	1690	1694	type	True	80.025	334	745	95	below_threshold
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_000687595.1	1690	1694	type	True	79.9857	332	745	95	below_threshold
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_000771145.1	1690	1694	type	True	79.9634	330	745	95	below_threshold
Bifidobacterium pseudolongum subsp. globosum	strain=LMG 11569	GCA_000741295.1	1690	1694	type	True	79.9424	336	745	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.9261	324	745	95	below_threshold
Bifidobacterium adolescentis	strain=NCTC11814	GCA_900445615.1	1680	1680	type	True	79.2564	231	745	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	79.2097	260	745	95	below_threshold
Bifidobacterium ramosum	strain=DSM 100688	GCA_009299505.1	1798158	1798158	type	True	79.0671	257	745	95	below_threshold
Bifidobacterium miconis	strain=82T10	GCA_019331735.1	2834435	2834435	type	True	79.0328	259	745	95	below_threshold
Bifidobacterium ramosum	strain=TREM	GCA_010667665.1	1798158	1798158	type	True	79.0058	259	745	95	below_threshold
Bifidobacterium simiiventris	strain=81T8	GCA_019331715.1	2834434	2834434	type	True	78.9221	269	745	95	below_threshold
Bifidobacterium stellenboschense	strain=DSM 23968	GCA_000741785.1	762211	762211	type	True	78.8345	260	745	95	below_threshold
Bifidobacterium biavatii	strain=DSM 23969	GCA_000771645.1	762212	762212	type	True	78.754	261	745	95	below_threshold
Bifidobacterium biavatii	strain=DSM 23969	GCA_000741165.1	762212	762212	type	True	78.7488	262	745	95	below_threshold
Bifidobacterium pongonis	strain=64T4	GCA_019331805.1	2834432	2834432	type	True	78.6211	235	745	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:23,916] [INFO] DFAST Taxonomy check result was written to GCF_009727065.1_ASM972706v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:23,917] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:23,917] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:23,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbadc3951-1e4b-41c8-b7a2-c2891e52c3eb/dqc_reference/checkm_data
[2024-01-24 13:19:23,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:23,946] [INFO] Task started: CheckM
[2024-01-24 13:19:23,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009727065.1_ASM972706v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009727065.1_ASM972706v1_genomic.fna/checkm_input GCF_009727065.1_ASM972706v1_genomic.fna/checkm_result
[2024-01-24 13:19:53,729] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:53,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:53,749] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:53,749] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:53,749] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009727065.1_ASM972706v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:53,750] [INFO] Task started: Blastn
[2024-01-24 13:19:53,750] [INFO] Running command: blastn -query GCF_009727065.1_ASM972706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbadc3951-1e4b-41c8-b7a2-c2891e52c3eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_009727065.1_ASM972706v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:55,004] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:55,007] [INFO] Selected 21 target genomes.
[2024-01-24 13:19:55,007] [INFO] Target genome list was writen to GCF_009727065.1_ASM972706v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:55,037] [INFO] Task started: fastANI
[2024-01-24 13:19:55,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cca4ccf-5831-4631-96f8-8a27719bb284/GCF_009727065.1_ASM972706v1_genomic.fna.gz --refList GCF_009727065.1_ASM972706v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009727065.1_ASM972706v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:05,163] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:05,183] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:05,183] [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_009727065.1	s__Bifidobacterium canis	100.0	745	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.79	99.79	0.97	0.97	2	conclusive
GCF_000741575.1	s__Bifidobacterium cuniculi	81.5255	299	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000260715.1	s__Bifidobacterium animalis	81.0571	393	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	95.76	0.92	0.88	104	-
GCF_002860345.1	s__Bifidobacterium anseris	80.1652	354	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.21	99.21	0.95	0.95	2	-
GCF_004155535.1	s__Bifidobacterium pseudolongum_C	80.1522	357	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286915.1	s__Bifidobacterium italicum	80.1482	351	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741135.1	s__Bifidobacterium choerinum	80.099	375	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.70	99.15	0.96	0.91	4	-
GCF_003952025.1	s__Bifidobacterium castoris	80.024	370	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741295.1	s__Bifidobacterium globosum	79.959	335	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.22	96.02	0.90	0.78	79	-
GCF_000010425.1	s__Bifidobacterium adolescentis	79.1722	235	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCF_009299505.1	s__Bifidobacterium ramosum	79.0363	257	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_018555335.1	s__Bifidobacterium sp018555335	79.0059	258	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	78.9886	225	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002451435.1	s__Bifidobacterium sp002451435	78.9395	206	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	78.8345	260	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014898155.1	s__Bifidobacterium eulemuris	78.8264	232	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012932675.1	s__Bifidobacterium sp012932675	78.7927	217	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860365.1	s__Bifidobacterium parmae	78.768	253	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741165.1	s__Bifidobacterium biavatii	78.7488	262	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_018555385.1	s__Bifidobacterium sp018555385	78.7244	261	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009371885.1	s__Bifidobacterium tibiigranuli	78.254	176	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:05,185] [INFO] GTDB search result was written to GCF_009727065.1_ASM972706v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:05,186] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:05,191] [INFO] DFAST_QC result json was written to GCF_009727065.1_ASM972706v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:05,191] [INFO] DFAST_QC completed!
[2024-01-24 13:20:05,191] [INFO] Total running time: 0h1m4s