[2024-01-25 18:56:05,454] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:05,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:05,465] [INFO] DQC Reference Directory: /var/lib/cwl/stgbed218a5-d62a-4935-8852-68b9b2ac8c9c/dqc_reference
[2024-01-25 18:56:06,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:06,645] [INFO] Task started: Prodigal
[2024-01-25 18:56:06,645] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a7a19ac-8353-441c-919c-f50a79604574/GCF_000718135.1_ASM71813v1_genomic.fna.gz | prodigal -d GCF_000718135.1_ASM71813v1_genomic.fna/cds.fna -a GCF_000718135.1_ASM71813v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:27,106] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:27,106] [INFO] Task started: HMMsearch
[2024-01-25 18:56:27,106] [INFO] Running command: hmmsearch --tblout GCF_000718135.1_ASM71813v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbed218a5-d62a-4935-8852-68b9b2ac8c9c/dqc_reference/reference_markers.hmm GCF_000718135.1_ASM71813v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:27,444] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:27,445] [INFO] Found 6/6 markers.
[2024-01-25 18:56:27,505] [INFO] Query marker FASTA was written to GCF_000718135.1_ASM71813v1_genomic.fna/markers.fasta
[2024-01-25 18:56:27,506] [INFO] Task started: Blastn
[2024-01-25 18:56:27,506] [INFO] Running command: blastn -query GCF_000718135.1_ASM71813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbed218a5-d62a-4935-8852-68b9b2ac8c9c/dqc_reference/reference_markers.fasta -out GCF_000718135.1_ASM71813v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:28,689] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:28,693] [INFO] Selected 15 target genomes.
[2024-01-25 18:56:28,693] [INFO] Target genome list was writen to GCF_000718135.1_ASM71813v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:28,707] [INFO] Task started: fastANI
[2024-01-25 18:56:28,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a7a19ac-8353-441c-919c-f50a79604574/GCF_000718135.1_ASM71813v1_genomic.fna.gz --refList GCF_000718135.1_ASM71813v1_genomic.fna/target_genomes.txt --output GCF_000718135.1_ASM71813v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:58,749] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:58,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbed218a5-d62a-4935-8852-68b9b2ac8c9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:58,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbed218a5-d62a-4935-8852-68b9b2ac8c9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:58,760] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:56:58,760] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:56:58,761] [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 microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	93.3268	2167	2597	95	below_threshold
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	92.0008	2060	2597	95	below_threshold
Streptomyces cavourensis	strain=DSM 41795	GCA_006788935.1	67258	67258	type	True	91.9917	2076	2597	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	91.6122	1689	2597	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	89.5578	2049	2597	95	below_threshold
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	89.4043	2011	2597	95	below_threshold
Streptomyces sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	89.3756	1908	2597	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	89.3669	1805	2597	95	below_threshold
Streptomyces griseus	strain=NCTC13033	GCA_900460065.1	1911	1911	type	True	89.1217	1992	2597	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.8576	1617	2597	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.7016	1422	2597	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.4658	1474	2597	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	82.3402	1032	2597	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	81.8268	1469	2597	95	below_threshold
Streptomyces zagrosensis	strain=CECT 8305	GCA_014203645.1	1042984	1042984	type	True	79.5733	1086	2597	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:58,762] [INFO] DFAST Taxonomy check result was written to GCF_000718135.1_ASM71813v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:58,762] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:58,762] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:58,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbed218a5-d62a-4935-8852-68b9b2ac8c9c/dqc_reference/checkm_data
[2024-01-25 18:56:58,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:58,838] [INFO] Task started: CheckM
[2024-01-25 18:56:58,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000718135.1_ASM71813v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000718135.1_ASM71813v1_genomic.fna/checkm_input GCF_000718135.1_ASM71813v1_genomic.fna/checkm_result
[2024-01-25 18:58:15,206] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:15,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:15,241] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:15,241] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:15,243] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000718135.1_ASM71813v1_genomic.fna/markers.fasta)
[2024-01-25 18:58:15,244] [INFO] Task started: Blastn
[2024-01-25 18:58:15,244] [INFO] Running command: blastn -query GCF_000718135.1_ASM71813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbed218a5-d62a-4935-8852-68b9b2ac8c9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000718135.1_ASM71813v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:17,278] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:17,280] [INFO] Selected 9 target genomes.
[2024-01-25 18:58:17,281] [INFO] Target genome list was writen to GCF_000718135.1_ASM71813v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:17,290] [INFO] Task started: fastANI
[2024-01-25 18:58:17,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a7a19ac-8353-441c-919c-f50a79604574/GCF_000718135.1_ASM71813v1_genomic.fna.gz --refList GCF_000718135.1_ASM71813v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000718135.1_ASM71813v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:37,096] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:37,103] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:37,103] [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_000718135.1	s__Streptomyces cyaneofuscatus	100.0	2590	2597	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	95.81	0.91	0.85	12	conclusive
GCF_001905595.1	s__Streptomyces sp001905595	94.6443	1953	2597	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.40	99.32	0.92	0.90	4	-
GCF_003610995.1	s__Streptomyces sp003116725	93.5675	2011	2597	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.40	95.27	0.92	0.85	7	-
GCF_014650075.1	s__Streptomyces microflavus	93.3248	2167	2597	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.25	97.27	0.91	0.85	13	-
GCF_002082585.1	s__Streptomyces albolongus	92.173	1997	2597	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003268675.1	s__Streptomyces bacillaris	91.9104	2068	2597	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.84	95.80	0.88	0.83	37	-
GCF_016901035.1	s__Streptomyces sp016901035	89.5806	1789	2597	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018619185.1	s__Streptomyces sp018619185	89.3189	1826	2597	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002941025.1	s__Streptomyces sp002941025	84.7601	1687	2597	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:37,105] [INFO] GTDB search result was written to GCF_000718135.1_ASM71813v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:37,105] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:37,108] [INFO] DFAST_QC result json was written to GCF_000718135.1_ASM71813v1_genomic.fna/dqc_result.json
[2024-01-25 18:58:37,108] [INFO] DFAST_QC completed!
[2024-01-25 18:58:37,108] [INFO] Total running time: 0h2m32s