[2024-01-24 13:18:41,598] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,602] [INFO] DQC Reference Directory: /var/lib/cwl/stge2372180-d767-41d3-857b-1050d75e6144/dqc_reference
[2024-01-24 13:18:43,099] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:43,100] [INFO] Task started: Prodigal
[2024-01-24 13:18:43,101] [INFO] Running command: gunzip -c /var/lib/cwl/stg09e3e5b2-9c2b-4e36-9558-c0591b459498/GCF_014649655.1_ASM1464965v1_genomic.fna.gz | prodigal -d GCF_014649655.1_ASM1464965v1_genomic.fna/cds.fna -a GCF_014649655.1_ASM1464965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:11,008] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:11,009] [INFO] Task started: HMMsearch
[2024-01-24 13:19:11,009] [INFO] Running command: hmmsearch --tblout GCF_014649655.1_ASM1464965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2372180-d767-41d3-857b-1050d75e6144/dqc_reference/reference_markers.hmm GCF_014649655.1_ASM1464965v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:11,369] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:11,371] [INFO] Found 6/6 markers.
[2024-01-24 13:19:11,441] [INFO] Query marker FASTA was written to GCF_014649655.1_ASM1464965v1_genomic.fna/markers.fasta
[2024-01-24 13:19:11,442] [INFO] Task started: Blastn
[2024-01-24 13:19:11,442] [INFO] Running command: blastn -query GCF_014649655.1_ASM1464965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2372180-d767-41d3-857b-1050d75e6144/dqc_reference/reference_markers.fasta -out GCF_014649655.1_ASM1464965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:12,715] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:12,719] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:12,720] [INFO] Target genome list was writen to GCF_014649655.1_ASM1464965v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:12,730] [INFO] Task started: fastANI
[2024-01-24 13:19:12,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg09e3e5b2-9c2b-4e36-9558-c0591b459498/GCF_014649655.1_ASM1464965v1_genomic.fna.gz --refList GCF_014649655.1_ASM1464965v1_genomic.fna/target_genomes.txt --output GCF_014649655.1_ASM1464965v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:55,974] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:55,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2372180-d767-41d3-857b-1050d75e6144/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:55,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2372180-d767-41d3-857b-1050d75e6144/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:55,994] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:55,995] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:55,995] [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 humidus	strain=JCM 4386	GCA_014649655.1	52259	52259	type	True	100.0	3150	3155	95	conclusive
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	92.5536	2207	3155	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	88.0196	2004	3155	95	below_threshold
Streptomyces asoensis	strain=JCM 4185	GCA_014649075.1	249586	249586	type	True	87.8721	2017	3155	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	86.6787	2057	3155	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	86.6758	1705	3155	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	86.5702	1957	3155	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	84.8275	1816	3155	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.5658	1844	3155	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	84.537	1843	3155	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.4987	1643	3155	95	below_threshold
Streptomyces swartbergensis	strain=HMC13	GCA_002148965.1	487165	487165	type	True	84.4287	1559	3155	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	84.4133	1827	3155	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	84.256	1747	3155	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	83.9571	1812	3155	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	83.5096	1530	3155	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.3617	1827	3155	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	83.0884	1778	3155	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:55,997] [INFO] DFAST Taxonomy check result was written to GCF_014649655.1_ASM1464965v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:55,997] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:55,997] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:55,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2372180-d767-41d3-857b-1050d75e6144/dqc_reference/checkm_data
[2024-01-24 13:19:55,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:56,094] [INFO] Task started: CheckM
[2024-01-24 13:19:56,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649655.1_ASM1464965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649655.1_ASM1464965v1_genomic.fna/checkm_input GCF_014649655.1_ASM1464965v1_genomic.fna/checkm_result
[2024-01-24 13:22:15,452] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:15,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:15,477] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:15,477] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:15,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649655.1_ASM1464965v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:15,478] [INFO] Task started: Blastn
[2024-01-24 13:22:15,478] [INFO] Running command: blastn -query GCF_014649655.1_ASM1464965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2372180-d767-41d3-857b-1050d75e6144/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649655.1_ASM1464965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:17,672] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:17,675] [INFO] Selected 11 target genomes.
[2024-01-24 13:22:17,675] [INFO] Target genome list was writen to GCF_014649655.1_ASM1464965v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:17,682] [INFO] Task started: fastANI
[2024-01-24 13:22:17,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg09e3e5b2-9c2b-4e36-9558-c0591b459498/GCF_014649655.1_ASM1464965v1_genomic.fna.gz --refList GCF_014649655.1_ASM1464965v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649655.1_ASM1464965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:46,935] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:46,945] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:46,945] [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_014649655.1	s__Streptomyces humidus	100.0	3150	3155	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_003112535.1	s__Streptomyces rishiriensis	92.5645	2206	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746365.1	s__Streptomyces sp001746365	92.4375	2140	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013085465.1	s__Streptomyces cacaoi_A	88.6492	2034	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129855.1	s__Streptomyces sp900129855	88.6173	1988	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.68	99.68	0.97	0.97	2	-
GCA_001298545.1	s__Streptomyces sp001298545	88.4383	2042	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.23	95.13	0.87	0.84	4	-
GCF_001428885.1	s__Streptomyces sp001428885	88.2957	2039	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016860545.1	s__Streptomyces asoensis	87.9747	2011	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.07	98.15	0.93	0.87	3	-
GCF_900110755.1	s__Streptomyces sp900110755	87.9006	1943	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003032475.1	s__Streptomyces sp003032475	87.8657	2112	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001896135.2	s__Streptomyces phaeoluteigriseus	86.0453	1829	3155	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 13:22:46,947] [INFO] GTDB search result was written to GCF_014649655.1_ASM1464965v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:46,947] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:46,951] [INFO] DFAST_QC result json was written to GCF_014649655.1_ASM1464965v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:46,951] [INFO] DFAST_QC completed!
[2024-01-24 13:22:46,951] [INFO] Total running time: 0h4m5s