[2024-01-24 14:30:17,132] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:17,134] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:17,134] [INFO] DQC Reference Directory: /var/lib/cwl/stg34dd8f8b-eca9-4142-95e0-410e94a927f9/dqc_reference
[2024-01-24 14:30:18,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:18,560] [INFO] Task started: Prodigal
[2024-01-24 14:30:18,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg705929f6-6505-4849-87dd-37614a063e14/GCF_016755895.1_ASM1675589v1_genomic.fna.gz | prodigal -d GCF_016755895.1_ASM1675589v1_genomic.fna/cds.fna -a GCF_016755895.1_ASM1675589v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:46,156] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:46,156] [INFO] Task started: HMMsearch
[2024-01-24 14:30:46,156] [INFO] Running command: hmmsearch --tblout GCF_016755895.1_ASM1675589v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34dd8f8b-eca9-4142-95e0-410e94a927f9/dqc_reference/reference_markers.hmm GCF_016755895.1_ASM1675589v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:46,636] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:46,638] [INFO] Found 6/6 markers.
[2024-01-24 14:30:46,732] [INFO] Query marker FASTA was written to GCF_016755895.1_ASM1675589v1_genomic.fna/markers.fasta
[2024-01-24 14:30:46,732] [INFO] Task started: Blastn
[2024-01-24 14:30:46,733] [INFO] Running command: blastn -query GCF_016755895.1_ASM1675589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34dd8f8b-eca9-4142-95e0-410e94a927f9/dqc_reference/reference_markers.fasta -out GCF_016755895.1_ASM1675589v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:48,250] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:48,254] [INFO] Selected 19 target genomes.
[2024-01-24 14:30:48,255] [INFO] Target genome list was writen to GCF_016755895.1_ASM1675589v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:48,262] [INFO] Task started: fastANI
[2024-01-24 14:30:48,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg705929f6-6505-4849-87dd-37614a063e14/GCF_016755895.1_ASM1675589v1_genomic.fna.gz --refList GCF_016755895.1_ASM1675589v1_genomic.fna/target_genomes.txt --output GCF_016755895.1_ASM1675589v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:32,310] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:32,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34dd8f8b-eca9-4142-95e0-410e94a927f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:32,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34dd8f8b-eca9-4142-95e0-410e94a927f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:32,327] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:32,327] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:32,328] [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 xanthophaeus	strain=NBRC 12829	GCA_016755895.1	67385	67385	type	True	100.0	2868	2879	95	conclusive
Streptomyces xanthophaeus	strain=NRRL B-5414	GCA_000725805.1	67385	67385	type	True	99.9602	2786	2879	95	conclusive
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	88.1882	1967	2879	95	below_threshold
Streptomyces nojiriensis	strain=NBRC 13794	GCA_016755855.1	66374	66374	type	True	88.1593	1992	2879	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	88.1535	2000	2879	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	88.0591	1981	2879	95	below_threshold
Streptomyces avidinii	strain=DSM 40526	GCA_017874515.1	1895	1895	type	True	88.0481	1989	2879	95	below_threshold
Streptomyces avidinii	strain=JCM 4726	GCA_014650695.1	1895	1895	type	True	88.0331	1974	2879	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	87.8145	1959	2879	95	below_threshold
Streptomyces subrutilus	strain=JCM 4834	GCA_014650935.1	36818	36818	type	True	87.7581	1788	2879	95	below_threshold
Streptomyces subrutilus	strain=ATCC 27467	GCA_008704535.1	36818	36818	type	True	87.734	1824	2879	95	below_threshold
Streptomyces yangpuensis	strain=fd2-tb	GCA_001005295.1	1648182	1648182	type	True	87.4942	1850	2879	95	below_threshold
Streptomyces goshikiensis	strain=JCM 4640	GCA_014650555.1	1942	1942	type	True	87.2145	1850	2879	95	below_threshold
Streptomyces vinaceus	strain=JCM 4849	GCA_014656155.1	1960	1960	type	True	87.1243	1883	2879	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	81.97	1400	2879	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.6288	1340	2879	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.2629	1262	2879	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.0857	1169	2879	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	80.9366	1339	2879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:32,330] [INFO] DFAST Taxonomy check result was written to GCF_016755895.1_ASM1675589v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:32,330] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:32,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:32,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34dd8f8b-eca9-4142-95e0-410e94a927f9/dqc_reference/checkm_data
[2024-01-24 14:31:32,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:32,415] [INFO] Task started: CheckM
[2024-01-24 14:31:32,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016755895.1_ASM1675589v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016755895.1_ASM1675589v1_genomic.fna/checkm_input GCF_016755895.1_ASM1675589v1_genomic.fna/checkm_result
[2024-01-24 14:33:30,406] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:30,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:30,437] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:30,438] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:30,438] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016755895.1_ASM1675589v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:30,439] [INFO] Task started: Blastn
[2024-01-24 14:33:30,439] [INFO] Running command: blastn -query GCF_016755895.1_ASM1675589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34dd8f8b-eca9-4142-95e0-410e94a927f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_016755895.1_ASM1675589v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:32,535] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:32,540] [INFO] Selected 15 target genomes.
[2024-01-24 14:33:32,540] [INFO] Target genome list was writen to GCF_016755895.1_ASM1675589v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:32,554] [INFO] Task started: fastANI
[2024-01-24 14:33:32,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg705929f6-6505-4849-87dd-37614a063e14/GCF_016755895.1_ASM1675589v1_genomic.fna.gz --refList GCF_016755895.1_ASM1675589v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016755895.1_ASM1675589v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:34:06,185] [INFO] Task succeeded: fastANI
[2024-01-24 14:34:06,201] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:34:06,201] [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_000725805.1	s__Streptomyces xanthophaeus	99.9602	2786	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.79	99.60	0.97	0.96	3	conclusive
GCF_018614155.1	s__Streptomyces sp018614155	88.7294	1830	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614075.1	s__Streptomyces sp018614075	88.7122	1658	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720115.1	s__Streptomyces sp000720115	88.2943	1929	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016755875.1	s__Streptomyces spororaveus	88.205	1964	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002080455.1	s__Streptomyces sp002080455	88.1948	1990	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.34	98.21	0.92	0.90	7	-
GCF_017639205.1	s__Streptomyces nojiriensis	88.1155	2005	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014650695.1	s__Streptomyces avidinii	88.0104	1977	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000716685.1	s__Streptomyces virginiae_A	87.9627	1984	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.46	95.91	0.89	0.84	3	-
GCF_000717915.1	s__Streptomyces sp000717915	87.8253	1773	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.47	0.90	0.89	4	-
GCF_001905445.1	s__Streptomyces sp001905445	87.8125	1764	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704535.1	s__Streptomyces subrutilus	87.7269	1825	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.97	0.97	2	-
GCF_001005295.1	s__Streptomyces yangpuensis	87.5362	1844	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.28	0.86	0.84	3	-
GCF_002803845.1	s__Streptomyces lavendulae_C	86.9611	1950	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.97	0.99	0.99	3	-
GCF_003950035.1	s__Streptomyces sp000158895	86.8453	1885	2879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.52	95.50	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:34:06,203] [INFO] GTDB search result was written to GCF_016755895.1_ASM1675589v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:34:06,204] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:34:06,209] [INFO] DFAST_QC result json was written to GCF_016755895.1_ASM1675589v1_genomic.fna/dqc_result.json
[2024-01-24 14:34:06,210] [INFO] DFAST_QC completed!
[2024-01-24 14:34:06,210] [INFO] Total running time: 0h3m49s