[2024-01-24 14:06:07,174] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:07,179] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:07,180] [INFO] DQC Reference Directory: /var/lib/cwl/stg69ee8286-635c-4972-a6a2-ff47dafdc8c3/dqc_reference
[2024-01-24 14:06:08,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,571] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,571] [INFO] Running command: gunzip -c /var/lib/cwl/stgd64408e2-d673-4a42-944b-d6ad06e07aee/GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/cds.fna -a GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:43,439] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:43,440] [INFO] Task started: HMMsearch
[2024-01-24 14:06:43,440] [INFO] Running command: hmmsearch --tblout GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69ee8286-635c-4972-a6a2-ff47dafdc8c3/dqc_reference/reference_markers.hmm GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:43,836] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:43,838] [INFO] Found 6/6 markers.
[2024-01-24 14:06:43,916] [INFO] Query marker FASTA was written to GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:06:43,917] [INFO] Task started: Blastn
[2024-01-24 14:06:43,917] [INFO] Running command: blastn -query GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg69ee8286-635c-4972-a6a2-ff47dafdc8c3/dqc_reference/reference_markers.fasta -out GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:45,314] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:45,318] [INFO] Selected 10 target genomes.
[2024-01-24 14:06:45,318] [INFO] Target genome list was writen to GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:06:45,324] [INFO] Task started: fastANI
[2024-01-24 14:06:45,324] [INFO] Running command: fastANI --query /var/lib/cwl/stgd64408e2-d673-4a42-944b-d6ad06e07aee/GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna.gz --refList GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:07,275] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:07,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69ee8286-635c-4972-a6a2-ff47dafdc8c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:07,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69ee8286-635c-4972-a6a2-ff47dafdc8c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:07,285] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:07:07,286] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:07:07,286] [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
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	100.0	2511	2512	95	inconclusive
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	95.5995	2230	2512	95	inconclusive
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	89.8665	2031	2512	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	86.8785	1915	2512	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	86.7429	1879	2512	95	below_threshold
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	83.2382	1561	2512	95	below_threshold
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	82.2189	1155	2512	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.7943	833	2512	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.3706	806	2512	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	78.2433	762	2512	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:07,288] [INFO] DFAST Taxonomy check result was written to GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:07:07,288] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:07,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:07,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69ee8286-635c-4972-a6a2-ff47dafdc8c3/dqc_reference/checkm_data
[2024-01-24 14:07:07,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:07,362] [INFO] Task started: CheckM
[2024-01-24 14:07:07,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/checkm_input GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:08:48,200] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:48,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:48,225] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:48,226] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:48,226] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:08:48,227] [INFO] Task started: Blastn
[2024-01-24 14:08:48,227] [INFO] Running command: blastn -query GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg69ee8286-635c-4972-a6a2-ff47dafdc8c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:50,341] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:50,344] [INFO] Selected 11 target genomes.
[2024-01-24 14:08:50,344] [INFO] Target genome list was writen to GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:50,356] [INFO] Task started: fastANI
[2024-01-24 14:08:50,356] [INFO] Running command: fastANI --query /var/lib/cwl/stgd64408e2-d673-4a42-944b-d6ad06e07aee/GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna.gz --refList GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:13,667] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:13,677] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:13,678] [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_900111175.1	s__Actinokineospora terrae	100.0	2511	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	conclusive
GCF_016907695.1	s__Actinokineospora baliensis	86.735	1880	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482865.1	s__Actinokineospora inagensis	84.4964	1586	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	83.2822	1553	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	82.9605	1481	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101685.1	s__Actinokineospora iranica	82.2316	1153	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182415.1	s__Actinokineospora mzabensis	81.8736	1240	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_001940455.1	s__Actinokineospora bangkokensis	81.3968	1199	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323725.1	s__Actinokineospora xionganensis	81.0793	1060	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379765.1	s__Actinophytocola sp009379765	78.8402	878	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000194155.1	s__Saccharopolyspora spinosa	78.2998	660	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	99.78	99.78	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:13,679] [INFO] GTDB search result was written to GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:13,680] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:13,683] [INFO] DFAST_QC result json was written to GCF_900111175.1_IMG-taxon_2616644847_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:09:13,683] [INFO] DFAST_QC completed!
[2024-01-24 14:09:13,683] [INFO] Total running time: 0h3m7s