[2024-01-24 11:26:20,897] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,899] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,899] [INFO] DQC Reference Directory: /var/lib/cwl/stg91ce178b-6544-4899-a734-42d575891c79/dqc_reference
[2024-01-24 11:26:22,118] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:22,120] [INFO] Task started: Prodigal
[2024-01-24 11:26:22,120] [INFO] Running command: gunzip -c /var/lib/cwl/stg08452068-c612-45a3-af5b-fb514f935af0/GCF_016598615.1_ASM1659861v1_genomic.fna.gz | prodigal -d GCF_016598615.1_ASM1659861v1_genomic.fna/cds.fna -a GCF_016598615.1_ASM1659861v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:57,077] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:57,077] [INFO] Task started: HMMsearch
[2024-01-24 11:26:57,078] [INFO] Running command: hmmsearch --tblout GCF_016598615.1_ASM1659861v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91ce178b-6544-4899-a734-42d575891c79/dqc_reference/reference_markers.hmm GCF_016598615.1_ASM1659861v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:57,605] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:57,607] [INFO] Found 6/6 markers.
[2024-01-24 11:26:57,689] [INFO] Query marker FASTA was written to GCF_016598615.1_ASM1659861v1_genomic.fna/markers.fasta
[2024-01-24 11:26:57,690] [INFO] Task started: Blastn
[2024-01-24 11:26:57,690] [INFO] Running command: blastn -query GCF_016598615.1_ASM1659861v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91ce178b-6544-4899-a734-42d575891c79/dqc_reference/reference_markers.fasta -out GCF_016598615.1_ASM1659861v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:59,157] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:59,161] [INFO] Selected 28 target genomes.
[2024-01-24 11:26:59,162] [INFO] Target genome list was writen to GCF_016598615.1_ASM1659861v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:59,178] [INFO] Task started: fastANI
[2024-01-24 11:26:59,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg08452068-c612-45a3-af5b-fb514f935af0/GCF_016598615.1_ASM1659861v1_genomic.fna.gz --refList GCF_016598615.1_ASM1659861v1_genomic.fna/target_genomes.txt --output GCF_016598615.1_ASM1659861v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:28:08,491] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:08,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91ce178b-6544-4899-a734-42d575891c79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:28:08,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91ce178b-6544-4899-a734-42d575891c79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:28:08,516] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:28:08,516] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:28:08,516] [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 phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	94.5199	2707	3781	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	94.5156	3129	3781	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	88.035	1927	3781	95	below_threshold
Streptomyces fructofermentans	strain=JCM 4956	GCA_014651055.1	152141	152141	type	True	86.6466	2117	3781	95	below_threshold
Streptomyces scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	86.2458	2188	3781	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_003568675.1	2315329	2315329	type	True	85.8785	2164	3781	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_005768555.2	2315329	2315329	type	True	85.8597	2169	3781	95	below_threshold
Streptomyces mirabilis	strain=JCM 4551	GCA_014650275.1	68239	68239	suspected-type	True	85.075	2259	3781	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	85.0718	1980	3781	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	85.0009	2201	3781	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.9824	2104	3781	95	below_threshold
Streptomyces lacrimifluminis	strain=CGMCC 4.7272	GCA_014646095.1	1500077	1500077	type	True	84.2863	1939	3781	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.986	2162	3781	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.9771	1786	3781	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.9367	2088	3781	95	below_threshold
Streptomyces geranii	strain=A301	GCA_002954775.1	2058923	2058923	type	True	83.828	1981	3781	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	83.5436	1851	3781	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	83.2953	1752	3781	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	83.2871	1614	3781	95	below_threshold
Streptomyces tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	83.2369	1800	3781	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	83.0691	1532	3781	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	82.7587	1894	3781	95	below_threshold
Streptomyces lasiicapitis	strain=CGMCC 4.7349	GCA_014646335.1	1923961	1923961	type	True	82.4399	1805	3781	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	81.2141	1521	3781	95	below_threshold
Streptomyces kanasensis	strain=ZX01	GCA_001484625.1	936756	936756	type	True	81.0758	1261	3781	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	80.844	1505	3781	95	below_threshold
Streptomyces zagrosensis	strain=CECT 8305	GCA_014203645.1	1042984	1042984	type	True	79.3002	1091	3781	95	below_threshold
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	79.2688	1261	3781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:28:08,518] [INFO] DFAST Taxonomy check result was written to GCF_016598615.1_ASM1659861v1_genomic.fna/tc_result.tsv
[2024-01-24 11:28:08,518] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:28:08,519] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:28:08,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91ce178b-6544-4899-a734-42d575891c79/dqc_reference/checkm_data
[2024-01-24 11:28:08,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:28:08,618] [INFO] Task started: CheckM
[2024-01-24 11:28:08,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016598615.1_ASM1659861v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016598615.1_ASM1659861v1_genomic.fna/checkm_input GCF_016598615.1_ASM1659861v1_genomic.fna/checkm_result
[2024-01-24 11:30:54,372] [INFO] Task succeeded: CheckM
[2024-01-24 11:30:54,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.29%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 11:30:54,405] [INFO] ===== Completeness check finished =====
[2024-01-24 11:30:54,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:30:54,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016598615.1_ASM1659861v1_genomic.fna/markers.fasta)
[2024-01-24 11:30:54,406] [INFO] Task started: Blastn
[2024-01-24 11:30:54,406] [INFO] Running command: blastn -query GCF_016598615.1_ASM1659861v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91ce178b-6544-4899-a734-42d575891c79/dqc_reference/reference_markers_gtdb.fasta -out GCF_016598615.1_ASM1659861v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:30:56,691] [INFO] Task succeeded: Blastn
[2024-01-24 11:30:56,695] [INFO] Selected 16 target genomes.
[2024-01-24 11:30:56,696] [INFO] Target genome list was writen to GCF_016598615.1_ASM1659861v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:30:56,748] [INFO] Task started: fastANI
[2024-01-24 11:30:56,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg08452068-c612-45a3-af5b-fb514f935af0/GCF_016598615.1_ASM1659861v1_genomic.fna.gz --refList GCF_016598615.1_ASM1659861v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016598615.1_ASM1659861v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:31:36,240] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:36,261] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:31:36,261] [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_016598615.1	s__Streptomyces sp016598615	100.0	3779	3781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001418655.1	s__Streptomyces phaeochromogenes	94.5273	2706	3781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.97	95.89	0.88	0.87	3	-
GCF_007050945.1	s__Streptomyces sp007050945	94.5005	3053	3781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008905045.1	s__Streptomyces albicerus	89.6395	2595	3781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019090165.1	s__Streptomyces sp019090165	89.021	2437	3781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650955.1	s__Streptomyces tauricus	88.2425	2361	3781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418335.1	s__Streptomyces aurantiacus	88.0667	1923	3781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.25	99.25	0.97	0.97	2	-
GCF_018070025.1	s__Streptomyces sp018070025	88.0602	2443	3781	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	87.4083	2078	3781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651055.1	s__Streptomyces fructofermentans	86.6435	2117	3781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045015.1	s__Streptomyces scabichelini	86.2106	2194	3781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112595.1	s__Streptomyces rubrogriseus	83.2148	1806	3781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCF_000931445.1	s__Streptomyces cyaneogriseus	83.131	1671	3781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
GCF_009769735.1	s__Streptomyces sp009769735	82.8054	1853	3781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009862265.1	s__Streptomyces sp009862265	81.8224	1406	3781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103455.1	s__Streptomyces wuyuanensis	81.2272	1477	3781	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 11:31:36,265] [INFO] GTDB search result was written to GCF_016598615.1_ASM1659861v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:31:36,270] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:31:36,278] [INFO] DFAST_QC result json was written to GCF_016598615.1_ASM1659861v1_genomic.fna/dqc_result.json
[2024-01-24 11:31:36,279] [INFO] DFAST_QC completed!
[2024-01-24 11:31:36,279] [INFO] Total running time: 0h5m15s