[2024-01-24 13:36:57,760] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:57,762] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:57,762] [INFO] DQC Reference Directory: /var/lib/cwl/stgff065cfb-2c2c-4b96-8c6f-ddc2911537c3/dqc_reference
[2024-01-24 13:36:58,948] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:58,949] [INFO] Task started: Prodigal
[2024-01-24 13:36:58,949] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe41fbd3-81b5-45f7-91bf-74d3df693f33/GCF_013407765.1_ASM1340776v1_genomic.fna.gz | prodigal -d GCF_013407765.1_ASM1340776v1_genomic.fna/cds.fna -a GCF_013407765.1_ASM1340776v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:17,589] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:17,589] [INFO] Task started: HMMsearch
[2024-01-24 13:37:17,589] [INFO] Running command: hmmsearch --tblout GCF_013407765.1_ASM1340776v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff065cfb-2c2c-4b96-8c6f-ddc2911537c3/dqc_reference/reference_markers.hmm GCF_013407765.1_ASM1340776v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:17,957] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:17,958] [INFO] Found 6/6 markers.
[2024-01-24 13:37:18,010] [INFO] Query marker FASTA was written to GCF_013407765.1_ASM1340776v1_genomic.fna/markers.fasta
[2024-01-24 13:37:18,010] [INFO] Task started: Blastn
[2024-01-24 13:37:18,010] [INFO] Running command: blastn -query GCF_013407765.1_ASM1340776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff065cfb-2c2c-4b96-8c6f-ddc2911537c3/dqc_reference/reference_markers.fasta -out GCF_013407765.1_ASM1340776v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:19,545] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:19,548] [INFO] Selected 25 target genomes.
[2024-01-24 13:37:19,548] [INFO] Target genome list was writen to GCF_013407765.1_ASM1340776v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:19,563] [INFO] Task started: fastANI
[2024-01-24 13:37:19,563] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe41fbd3-81b5-45f7-91bf-74d3df693f33/GCF_013407765.1_ASM1340776v1_genomic.fna.gz --refList GCF_013407765.1_ASM1340776v1_genomic.fna/target_genomes.txt --output GCF_013407765.1_ASM1340776v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:03,336] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:03,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff065cfb-2c2c-4b96-8c6f-ddc2911537c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:03,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff065cfb-2c2c-4b96-8c6f-ddc2911537c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:03,355] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:38:03,355] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:03,356] [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
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	100.0	2214	2214	95	conclusive
Peterkaempfera griseoplana	strain=NRRL B-3064	GCA_001418575.1	66896	66896	type	True	79.1321	872	2214	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	79.081	847	2214	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	79.0767	843	2214	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	79.0224	738	2214	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	78.928	672	2214	95	below_threshold
Streptomyces alkaliterrae	strain=OF1	GCA_007097205.2	2213162	2213162	type	True	78.9005	698	2214	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	78.873	917	2214	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	78.8097	857	2214	95	below_threshold
Streptomyces sparsogenes	strain=ATCC 25498	GCA_001704635.1	67365	67365	type	True	78.7325	1001	2214	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	78.6838	962	2214	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	78.6486	1019	2214	95	below_threshold
Kitasatospora viridis	strain=DSM 44826	GCA_007829815.1	281105	281105	type	True	78.6071	1100	2214	95	below_threshold
Kitasatospora griseola	strain=JCM 3339	GCA_014648555.1	2064	2064	type	True	78.5724	952	2214	95	below_threshold
Streptomyces chromofuscus	strain=DSM 40273	GCA_015160875.1	42881	42881	type	True	78.5589	869	2214	95	below_threshold
Streptomyces chromofuscus	strain=JCM 4354	GCA_014649435.1	42881	42881	type	True	78.434	882	2214	95	below_threshold
Streptomyces buecherae	strain=AC541	GCA_014295035.1	2763006	2763006	type	True	78.4288	976	2214	95	below_threshold
Streptacidiphilus pinicola	strain=MMS16-CNU450	GCA_003258295.1	2219663	2219663	type	True	78.3857	857	2214	95	below_threshold
Streptomyces chumphonensis	strain=KK1-2	GCA_014779715.1	1214925	1214925	type	True	78.3318	795	2214	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	78.3156	874	2214	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	78.2318	942	2214	95	below_threshold
Streptacidiphilus jiangxiensis	strain=NBRC 100920	GCA_000787795.1	235985	235985	type	True	78.1529	913	2214	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	78.1005	923	2214	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	78.1003	918	2214	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	78.0031	934	2214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:03,357] [INFO] DFAST Taxonomy check result was written to GCF_013407765.1_ASM1340776v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:03,358] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:03,358] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:03,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff065cfb-2c2c-4b96-8c6f-ddc2911537c3/dqc_reference/checkm_data
[2024-01-24 13:38:03,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:03,430] [INFO] Task started: CheckM
[2024-01-24 13:38:03,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013407765.1_ASM1340776v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013407765.1_ASM1340776v1_genomic.fna/checkm_input GCF_013407765.1_ASM1340776v1_genomic.fna/checkm_result
[2024-01-24 13:39:37,730] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:37,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:37,758] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:37,758] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:37,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013407765.1_ASM1340776v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:37,759] [INFO] Task started: Blastn
[2024-01-24 13:39:37,759] [INFO] Running command: blastn -query GCF_013407765.1_ASM1340776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff065cfb-2c2c-4b96-8c6f-ddc2911537c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_013407765.1_ASM1340776v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:40,152] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:40,155] [INFO] Selected 22 target genomes.
[2024-01-24 13:39:40,155] [INFO] Target genome list was writen to GCF_013407765.1_ASM1340776v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:40,203] [INFO] Task started: fastANI
[2024-01-24 13:39:40,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe41fbd3-81b5-45f7-91bf-74d3df693f33/GCF_013407765.1_ASM1340776v1_genomic.fna.gz --refList GCF_013407765.1_ASM1340776v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013407765.1_ASM1340776v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:17,241] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:17,264] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:40:17,265] [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_013407765.1	s__Allostreptomyces psammosilenae	100.0	2214	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Allostreptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014083985.1	s__SCUT-3 sp014083985	79.6798	911	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__SCUT-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003144095.1	s__Streptomyces sp003144095	79.2414	847	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684805.1	s__Streptomyces palmae	79.0878	841	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000240165.1	s__Streptomyces cattleya	79.0781	998	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	3	-
GCF_014084125.1	s__Streptacidiphilus sp014084125	78.9627	931	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794255.1	s__Streptomyces carminius	78.9554	932	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097205.2	s__Streptomyces alkaliterrae	78.8614	706	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.63	99.32	0.91	0.86	3	-
GCF_002300355.1	s__Kitasatospora sp002300355	78.6875	1052	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744815.1	s__Streptacidiphilus_A oryzae	78.657	932	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650495.1	s__Streptomyces cinnamoneus	78.6141	861	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829815.1	s__Kitasatospora viridis	78.6089	1097	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642695.1	s__Streptomyces chilikensis	78.5379	934	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701325.1	s__Streptomyces sp000701325	78.5135	881	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015712165.1	s__Streptomyces spinoverrucosus_A	78.4077	919	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258295.1	s__Streptacidiphilus pinicola	78.3874	856	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014295035.1	s__Streptomyces buecherae	78.3781	980	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	96.93	0.96	0.94	7	-
GCF_014779715.1	s__Streptomyces chumphonensis	78.3383	794	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142575.1	s__Streptomyces paucisporeus	78.2537	937	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018114805.1	s__Streptomyces philanthi	78.2403	865	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803845.1	s__Streptomyces lavendulae_C	78.191	946	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.97	0.99	0.99	3	-
GCF_900109465.1	s__Streptacidiphilus jiangxiensis	78.1229	914	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.97	99.97	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:40:17,266] [INFO] GTDB search result was written to GCF_013407765.1_ASM1340776v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:17,267] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:17,271] [INFO] DFAST_QC result json was written to GCF_013407765.1_ASM1340776v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:17,271] [INFO] DFAST_QC completed!
[2024-01-24 13:40:17,271] [INFO] Total running time: 0h3m20s