[2024-01-24 13:46:42,844] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:42,845] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:42,845] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d91243b-69c4-46cc-9e21-4b15fcebc2a5/dqc_reference
[2024-01-24 13:46:44,218] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:44,219] [INFO] Task started: Prodigal
[2024-01-24 13:46:44,219] [INFO] Running command: gunzip -c /var/lib/cwl/stg85cf2b55-43b3-4c35-a709-c67f61bb54da/GCF_014650675.1_ASM1465067v1_genomic.fna.gz | prodigal -d GCF_014650675.1_ASM1465067v1_genomic.fna/cds.fna -a GCF_014650675.1_ASM1465067v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:10,433] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:10,434] [INFO] Task started: HMMsearch
[2024-01-24 13:47:10,434] [INFO] Running command: hmmsearch --tblout GCF_014650675.1_ASM1465067v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d91243b-69c4-46cc-9e21-4b15fcebc2a5/dqc_reference/reference_markers.hmm GCF_014650675.1_ASM1465067v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:10,814] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:10,816] [INFO] Found 6/6 markers.
[2024-01-24 13:47:10,889] [INFO] Query marker FASTA was written to GCF_014650675.1_ASM1465067v1_genomic.fna/markers.fasta
[2024-01-24 13:47:10,889] [INFO] Task started: Blastn
[2024-01-24 13:47:10,889] [INFO] Running command: blastn -query GCF_014650675.1_ASM1465067v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d91243b-69c4-46cc-9e21-4b15fcebc2a5/dqc_reference/reference_markers.fasta -out GCF_014650675.1_ASM1465067v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:12,212] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:12,215] [INFO] Selected 15 target genomes.
[2024-01-24 13:47:12,215] [INFO] Target genome list was writen to GCF_014650675.1_ASM1465067v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:12,218] [INFO] Task started: fastANI
[2024-01-24 13:47:12,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg85cf2b55-43b3-4c35-a709-c67f61bb54da/GCF_014650675.1_ASM1465067v1_genomic.fna.gz --refList GCF_014650675.1_ASM1465067v1_genomic.fna/target_genomes.txt --output GCF_014650675.1_ASM1465067v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:43,118] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:43,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d91243b-69c4-46cc-9e21-4b15fcebc2a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:43,120] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d91243b-69c4-46cc-9e21-4b15fcebc2a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:43,134] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:43,135] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:43,135] [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 anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	100.0	2928	2930	95	conclusive
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	93.3377	2304	2930	95	below_threshold
Streptomyces griseus	strain=NCTC13033	GCA_900460065.1	1911	1911	type	True	93.3054	2259	2930	95	below_threshold
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	91.9501	2145	2930	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	91.8861	1925	2930	95	below_threshold
Streptomyces sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	91.7293	2072	2930	95	below_threshold
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	91.6779	2044	2930	95	below_threshold
Streptomyces californicus	strain=NRRL B-2098	GCA_000717645.1	67351	67351	type	True	90.2807	2073	2930	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	90.2394	2122	2930	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	89.6988	2082	2930	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	88.7398	1587	2930	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.6915	1683	2930	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.3243	1400	2930	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.261	1523	2930	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.0365	1278	2930	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:43,136] [INFO] DFAST Taxonomy check result was written to GCF_014650675.1_ASM1465067v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:43,137] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:43,137] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:43,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d91243b-69c4-46cc-9e21-4b15fcebc2a5/dqc_reference/checkm_data
[2024-01-24 13:47:43,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:43,217] [INFO] Task started: CheckM
[2024-01-24 13:47:43,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650675.1_ASM1465067v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650675.1_ASM1465067v1_genomic.fna/checkm_input GCF_014650675.1_ASM1465067v1_genomic.fna/checkm_result
[2024-01-24 13:49:38,833] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:38,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:38,854] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:38,855] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:38,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650675.1_ASM1465067v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:38,856] [INFO] Task started: Blastn
[2024-01-24 13:49:38,856] [INFO] Running command: blastn -query GCF_014650675.1_ASM1465067v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d91243b-69c4-46cc-9e21-4b15fcebc2a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650675.1_ASM1465067v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:40,907] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:40,912] [INFO] Selected 9 target genomes.
[2024-01-24 13:49:40,912] [INFO] Target genome list was writen to GCF_014650675.1_ASM1465067v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:40,945] [INFO] Task started: fastANI
[2024-01-24 13:49:40,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg85cf2b55-43b3-4c35-a709-c67f61bb54da/GCF_014650675.1_ASM1465067v1_genomic.fna.gz --refList GCF_014650675.1_ASM1465067v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650675.1_ASM1465067v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:00,589] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:00,601] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:00,601] [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_014650675.1	s__Streptomyces anulatus	100.0	2928	2930	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.62	96.42	0.89	0.81	27	conclusive
GCF_018619185.1	s__Streptomyces sp018619185	94.4117	2068	2930	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002551245.1	s__Streptomyces sp002551245	94.1933	1963	2930	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377965.1	s__Streptomyces sp000377965	94.1468	2186	2930	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900460065.1	s__Streptomyces griseus	93.3061	2259	2930	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.49	99.03	0.95	0.93	10	-
GCF_002910905.1	s__Streptomyces sp002910905	92.8388	1905	2930	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002551355.1	s__Streptomyces sp002551355	92.6696	2112	2930	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002154345.1	s__Streptomyces fimicarius	92.5274	1846	2930	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.88	95.22	0.89	0.81	11	-
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	92.2116	2163	2930	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:00,603] [INFO] GTDB search result was written to GCF_014650675.1_ASM1465067v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:00,604] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:00,609] [INFO] DFAST_QC result json was written to GCF_014650675.1_ASM1465067v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:00,609] [INFO] DFAST_QC completed!
[2024-01-24 13:50:00,609] [INFO] Total running time: 0h3m18s