[2024-01-24 13:18:46,494] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:46,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:46,498] [INFO] DQC Reference Directory: /var/lib/cwl/stg3cf2fffa-ab0a-45da-aaa2-e4b3dc147f3d/dqc_reference
[2024-01-24 13:18:47,825] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,826] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg7364b418-6ec3-4176-827e-a635badbe1aa/GCF_008868685.1_ASM886868v1_genomic.fna.gz | prodigal -d GCF_008868685.1_ASM886868v1_genomic.fna/cds.fna -a GCF_008868685.1_ASM886868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:17,617] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:17,617] [INFO] Task started: HMMsearch
[2024-01-24 13:19:17,617] [INFO] Running command: hmmsearch --tblout GCF_008868685.1_ASM886868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3cf2fffa-ab0a-45da-aaa2-e4b3dc147f3d/dqc_reference/reference_markers.hmm GCF_008868685.1_ASM886868v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:17,979] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:17,980] [INFO] Found 6/6 markers.
[2024-01-24 13:19:18,053] [INFO] Query marker FASTA was written to GCF_008868685.1_ASM886868v1_genomic.fna/markers.fasta
[2024-01-24 13:19:18,054] [INFO] Task started: Blastn
[2024-01-24 13:19:18,054] [INFO] Running command: blastn -query GCF_008868685.1_ASM886868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cf2fffa-ab0a-45da-aaa2-e4b3dc147f3d/dqc_reference/reference_markers.fasta -out GCF_008868685.1_ASM886868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:19,473] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:19,476] [INFO] Selected 27 target genomes.
[2024-01-24 13:19:19,476] [INFO] Target genome list was writen to GCF_008868685.1_ASM886868v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:19,503] [INFO] Task started: fastANI
[2024-01-24 13:19:19,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg7364b418-6ec3-4176-827e-a635badbe1aa/GCF_008868685.1_ASM886868v1_genomic.fna.gz --refList GCF_008868685.1_ASM886868v1_genomic.fna/target_genomes.txt --output GCF_008868685.1_ASM886868v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:20:17,024] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:17,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3cf2fffa-ab0a-45da-aaa2-e4b3dc147f3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:20:17,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3cf2fffa-ab0a-45da-aaa2-e4b3dc147f3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:20:17,056] [INFO] Found 27 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:20:17,056] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:20:17,057] [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 triticiradicis	strain=NEAU-H2	GCA_008868685.1	2651189	2651189	type	True	100.0	3230	3240	95	inconclusive
Streptomyces populi	strain=A249	GCA_002911015.1	2058924	2058924	type	True	95.0763	2528	3240	95	inconclusive
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	86.458	2047	3240	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	86.4112	1730	3240	95	below_threshold
Streptomyces mirabilis	strain=JCM 4551	GCA_014650275.1	68239	68239	suspected-type	True	85.855	2007	3240	95	below_threshold
Streptomyces olivochromogenes	strain=DSM 40451	GCA_001514115.1	1963	1963	type	True	85.731	2058	3240	95	below_threshold
Streptomyces fagopyri	strain=QMT-28	GCA_009498275.1	2662397	2662397	type	True	85.6698	1923	3240	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	85.0788	1873	3240	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	85.0645	1863	3240	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.9083	1945	3240	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	83.9161	1906	3240	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.7757	1881	3240	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	83.6751	1651	3240	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	83.6707	1874	3240	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.5257	1601	3240	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.5172	1787	3240	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	83.5039	1676	3240	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	83.3563	1772	3240	95	below_threshold
Streptomyces geranii	strain=A301	GCA_002954775.1	2058923	2058923	type	True	83.2691	1603	3240	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	81.9709	1530	3240	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	81.6161	1530	3240	95	below_threshold
Streptomyces albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	80.5171	1295	3240	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	75.7184	159	3240	95	below_threshold
Bifidobacterium miconis	strain=82T10	GCA_019331735.1	2834435	2834435	type	True	75.6477	144	3240	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	75.6311	158	3240	95	below_threshold
Bifidobacterium simiiventris	strain=81T8	GCA_019331715.1	2834434	2834434	type	True	75.6126	121	3240	95	below_threshold
Bifidobacterium phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	75.5228	203	3240	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:20:17,059] [INFO] DFAST Taxonomy check result was written to GCF_008868685.1_ASM886868v1_genomic.fna/tc_result.tsv
[2024-01-24 13:20:17,060] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:20:17,060] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:20:17,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3cf2fffa-ab0a-45da-aaa2-e4b3dc147f3d/dqc_reference/checkm_data
[2024-01-24 13:20:17,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:20:17,156] [INFO] Task started: CheckM
[2024-01-24 13:20:17,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008868685.1_ASM886868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008868685.1_ASM886868v1_genomic.fna/checkm_input GCF_008868685.1_ASM886868v1_genomic.fna/checkm_result
[2024-01-24 13:22:34,493] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:34,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:34,516] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:34,517] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:34,517] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008868685.1_ASM886868v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:34,517] [INFO] Task started: Blastn
[2024-01-24 13:22:34,517] [INFO] Running command: blastn -query GCF_008868685.1_ASM886868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cf2fffa-ab0a-45da-aaa2-e4b3dc147f3d/dqc_reference/reference_markers_gtdb.fasta -out GCF_008868685.1_ASM886868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:36,936] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:36,939] [INFO] Selected 22 target genomes.
[2024-01-24 13:22:36,940] [INFO] Target genome list was writen to GCF_008868685.1_ASM886868v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:36,952] [INFO] Task started: fastANI
[2024-01-24 13:22:36,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg7364b418-6ec3-4176-827e-a635badbe1aa/GCF_008868685.1_ASM886868v1_genomic.fna.gz --refList GCF_008868685.1_ASM886868v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008868685.1_ASM886868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:28,197] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:28,214] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:28,215] [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_002911015.1	s__Streptomyces populi	95.0922	2526	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.82	0.82	2	conclusive
GCF_000725495.1	s__Streptomyces aureus_B	91.5446	2457	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002078175.1	s__Streptomyces sp002078175	87.4895	2059	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.16	97.16	0.90	0.90	2	-
GCF_002300165.1	s__Streptomyces sp002300165	86.6404	1903	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.35	96.35	0.87	0.87	2	-
GCF_014645835.1	s__Streptomyces albiflavescens	86.4573	2047	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002946835.1	s__Streptomyces dengpaensis	86.3809	1734	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014650275.1	s__Streptomyces mirabilis	85.8147	2015	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	96.82	96.27	0.84	0.80	23	-
GCF_001514115.1	s__Streptomyces olivochromogenes	85.7168	2060	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	97.99	96.97	0.89	0.84	4	-
GCF_009498275.1	s__Streptomyces fagopyri	85.699	1917	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042115.1	s__Streptomyces sp008042115	85.2143	1948	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009765.2	s__Streptomyces avermitilis	85.0726	1874	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.91	0.98	0.92	9	-
GCF_000746395.1	s__Streptomyces mirabilis_A	84.3431	1868	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369065.1	s__Streptomyces sp008369065	84.0351	1741	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203845.1	s__Streptomyces scabiei_E	83.3811	1738	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
GCF_002214185.1	s__Streptomyces capitiformicae	83.2434	1714	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	1.00	1.00	2	-
GCF_001514035.1	s__Streptomyces yokosukanensis	83.0845	1755	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386135.1	s__Streptomyces sp003386135	81.6616	1524	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
GCF_900105415.1	s__Streptomyces sp900105415	81.6288	1551	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_014649855.1	s__Streptomyces roseolus	81.5731	1402	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795015.1	s__Streptomyces sp004795015	81.5171	1365	3240	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	81.4645	1519	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	-
GCF_009832925.1	s__Streptomyces sp009832925	81.1899	1399	3240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:28,216] [INFO] GTDB search result was written to GCF_008868685.1_ASM886868v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:28,217] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:28,222] [INFO] DFAST_QC result json was written to GCF_008868685.1_ASM886868v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:28,222] [INFO] DFAST_QC completed!
[2024-01-24 13:23:28,222] [INFO] Total running time: 0h4m42s