[2024-01-24 13:43:26,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:43:26,997] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:43:26,997] [INFO] DQC Reference Directory: /var/lib/cwl/stg4845a1db-72bc-442b-9d32-eec63ff7e686/dqc_reference
[2024-01-24 13:43:28,199] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:43:28,200] [INFO] Task started: Prodigal
[2024-01-24 13:43:28,200] [INFO] Running command: gunzip -c /var/lib/cwl/stg02d891dd-ef2f-4f6d-b70f-925523465323/GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/cds.fna -a GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:57,941] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:57,942] [INFO] Task started: HMMsearch
[2024-01-24 13:43:57,942] [INFO] Running command: hmmsearch --tblout GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4845a1db-72bc-442b-9d32-eec63ff7e686/dqc_reference/reference_markers.hmm GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:58,288] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:58,289] [INFO] Found 6/6 markers.
[2024-01-24 13:43:58,361] [INFO] Query marker FASTA was written to GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:43:58,362] [INFO] Task started: Blastn
[2024-01-24 13:43:58,362] [INFO] Running command: blastn -query GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4845a1db-72bc-442b-9d32-eec63ff7e686/dqc_reference/reference_markers.fasta -out GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:59,556] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:59,559] [INFO] Selected 15 target genomes.
[2024-01-24 13:43:59,560] [INFO] Target genome list was writen to GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:43:59,565] [INFO] Task started: fastANI
[2024-01-24 13:43:59,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg02d891dd-ef2f-4f6d-b70f-925523465323/GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna.gz --refList GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:44:38,292] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:38,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4845a1db-72bc-442b-9d32-eec63ff7e686/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:44:38,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4845a1db-72bc-442b-9d32-eec63ff7e686/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:44:38,304] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:44:38,304] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:44:38,305] [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
Actinoplanes philippinensis	strain=DSM 43019	GCA_900113015.1	35752	35752	type	True	100.0	3424	3428	95	conclusive
Actinoplanes philippinensis	strain=NBRC 13878	GCA_016862335.1	35752	35752	type	True	99.9787	3345	3428	95	conclusive
Actinoplanes xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	89.0055	2648	3428	95	below_threshold
Actinoplanes italicus	strain=NBRC 13911	GCA_016862235.1	113567	113567	type	True	86.2217	2384	3428	95	below_threshold
Actinoplanes italicus	strain=DSM 43146	GCA_003001815.1	113567	113567	type	True	86.1837	2452	3428	95	below_threshold
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	85.1098	2045	3428	95	below_threshold
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	85.034	2111	3428	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	84.9942	2115	3428	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	84.953	2082	3428	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	82.5689	1979	3428	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	82.543	1955	3428	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.4717	996	3428	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.38	1501	3428	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.3185	1294	3428	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.3156	1216	3428	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:44:38,306] [INFO] DFAST Taxonomy check result was written to GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:44:38,306] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:44:38,306] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:44:38,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4845a1db-72bc-442b-9d32-eec63ff7e686/dqc_reference/checkm_data
[2024-01-24 13:44:38,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:44:38,396] [INFO] Task started: CheckM
[2024-01-24 13:44:38,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/checkm_input GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:46:30,870] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:30,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:30,893] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:30,894] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:30,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:46:30,894] [INFO] Task started: Blastn
[2024-01-24 13:46:30,894] [INFO] Running command: blastn -query GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4845a1db-72bc-442b-9d32-eec63ff7e686/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:32,912] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:32,915] [INFO] Selected 13 target genomes.
[2024-01-24 13:46:32,916] [INFO] Target genome list was writen to GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:32,926] [INFO] Task started: fastANI
[2024-01-24 13:46:32,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg02d891dd-ef2f-4f6d-b70f-925523465323/GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna.gz --refList GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:10,841] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:10,854] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:10,855] [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_900113015.1	s__Actinoplanes philippinensis	100.0	3424	3428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003148685.1	s__Actinoplanes xinjiangensis	89.0079	2648	3428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003001815.1	s__Actinoplanes italicus	86.1705	2454	3428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016862455.1	s__Actinoplanes utahensis	85.0324	2067	3428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014205215.1	s__Actinoplanes lobatus	85.0181	2167	3428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
GCF_014647795.1	s__Actinoplanes campanulatus	85.0142	2111	3428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	-
GCF_017592555.1	s__Actinoplanes sp017592555	84.9472	2082	3428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862075.1	s__Actinoplanes couchii	84.2205	2215	3428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284295.1	s__Actinoplanes missouriensis	83.1154	1849	3428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205225.1	s__Actinoplanes octamycinicus	82.6079	1971	3428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862395.1	s__Actinoplanes siamensis	82.5146	1683	3428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	82.3733	1941	3428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900119315.1	s__Actinoplanes sp900119315	82.1264	1751	3428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:10,856] [INFO] GTDB search result was written to GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:10,857] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:10,861] [INFO] DFAST_QC result json was written to GCF_900113015.1_IMG-taxon_2675903218_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:47:10,861] [INFO] DFAST_QC completed!
[2024-01-24 13:47:10,861] [INFO] Total running time: 0h3m44s