[2024-01-24 13:17:27,212] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:27,214] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:27,214] [INFO] DQC Reference Directory: /var/lib/cwl/stg29221490-63b7-426e-990e-38d578054081/dqc_reference
[2024-01-24 13:17:28,442] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:28,443] [INFO] Task started: Prodigal
[2024-01-24 13:17:28,444] [INFO] Running command: gunzip -c /var/lib/cwl/stg90f77aa8-093a-47d3-b434-9f6ebd741203/GCF_003112535.1_ASM311253v1_genomic.fna.gz | prodigal -d GCF_003112535.1_ASM311253v1_genomic.fna/cds.fna -a GCF_003112535.1_ASM311253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:56,242] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:56,242] [INFO] Task started: HMMsearch
[2024-01-24 13:17:56,242] [INFO] Running command: hmmsearch --tblout GCF_003112535.1_ASM311253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29221490-63b7-426e-990e-38d578054081/dqc_reference/reference_markers.hmm GCF_003112535.1_ASM311253v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:56,625] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:56,627] [INFO] Found 6/6 markers.
[2024-01-24 13:17:56,700] [INFO] Query marker FASTA was written to GCF_003112535.1_ASM311253v1_genomic.fna/markers.fasta
[2024-01-24 13:17:56,701] [INFO] Task started: Blastn
[2024-01-24 13:17:56,701] [INFO] Running command: blastn -query GCF_003112535.1_ASM311253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29221490-63b7-426e-990e-38d578054081/dqc_reference/reference_markers.fasta -out GCF_003112535.1_ASM311253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:58,028] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:58,035] [INFO] Selected 16 target genomes.
[2024-01-24 13:17:58,036] [INFO] Target genome list was writen to GCF_003112535.1_ASM311253v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:58,046] [INFO] Task started: fastANI
[2024-01-24 13:17:58,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg90f77aa8-093a-47d3-b434-9f6ebd741203/GCF_003112535.1_ASM311253v1_genomic.fna.gz --refList GCF_003112535.1_ASM311253v1_genomic.fna/target_genomes.txt --output GCF_003112535.1_ASM311253v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:38,105] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:38,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29221490-63b7-426e-990e-38d578054081/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:38,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29221490-63b7-426e-990e-38d578054081/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:38,124] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:38,124] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:38,124] [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 rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	100.0	3017	3021	95	conclusive
Streptomyces humidus	strain=JCM 4386	GCA_014649655.1	52259	52259	type	True	92.5328	2220	3021	95	below_threshold
Streptomyces asoensis	strain=JCM 4185	GCA_014649075.1	249586	249586	type	True	88.2943	2138	3021	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	88.2921	2144	3021	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	86.8941	2076	3021	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	86.4883	1712	3021	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.0636	1911	3021	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	84.9685	1855	3021	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.7796	1712	3021	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	84.73	1830	3021	95	below_threshold
Streptomyces swartbergensis	strain=HMC13	GCA_002148965.1	487165	487165	type	True	84.7213	1604	3021	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.5131	1639	3021	95	below_threshold
Streptomyces chromofuscus	strain=JCM 4354	GCA_014649435.1	42881	42881	type	True	84.4205	1656	3021	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	84.2539	1960	3021	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.5509	1854	3021	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	83.1625	1807	3021	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:38,126] [INFO] DFAST Taxonomy check result was written to GCF_003112535.1_ASM311253v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:38,127] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:38,127] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:38,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29221490-63b7-426e-990e-38d578054081/dqc_reference/checkm_data
[2024-01-24 13:18:38,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:38,213] [INFO] Task started: CheckM
[2024-01-24 13:18:38,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003112535.1_ASM311253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003112535.1_ASM311253v1_genomic.fna/checkm_input GCF_003112535.1_ASM311253v1_genomic.fna/checkm_result
[2024-01-24 13:20:48,693] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:48,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:48,721] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:48,722] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:48,722] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003112535.1_ASM311253v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:48,722] [INFO] Task started: Blastn
[2024-01-24 13:20:48,723] [INFO] Running command: blastn -query GCF_003112535.1_ASM311253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29221490-63b7-426e-990e-38d578054081/dqc_reference/reference_markers_gtdb.fasta -out GCF_003112535.1_ASM311253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:50,873] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:50,877] [INFO] Selected 11 target genomes.
[2024-01-24 13:20:50,878] [INFO] Target genome list was writen to GCF_003112535.1_ASM311253v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:50,931] [INFO] Task started: fastANI
[2024-01-24 13:20:50,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg90f77aa8-093a-47d3-b434-9f6ebd741203/GCF_003112535.1_ASM311253v1_genomic.fna.gz --refList GCF_003112535.1_ASM311253v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003112535.1_ASM311253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:18,680] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:18,699] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:18,700] [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_003112535.1	s__Streptomyces rishiriensis	100.0	3017	3021	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_001746365.1	s__Streptomyces sp001746365	94.2517	2419	3021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649655.1	s__Streptomyces humidus	92.5289	2221	3021	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	89.0612	2200	3021	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	88.9643	2109	3021	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	88.9085	2166	3021	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	88.8223	2163	3021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001184025.1	s__Streptomyces sp001184025	88.776	2031	3021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.49	98.49	0.84	0.84	2	-
GCF_900110755.1	s__Streptomyces sp900110755	88.5111	1961	3021	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	88.4068	2131	3021	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	88.2747	2147	3021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.07	98.15	0.93	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:18,703] [INFO] GTDB search result was written to GCF_003112535.1_ASM311253v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:18,703] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:18,707] [INFO] DFAST_QC result json was written to GCF_003112535.1_ASM311253v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:18,707] [INFO] DFAST_QC completed!
[2024-01-24 13:21:18,707] [INFO] Total running time: 0h3m51s