[2024-01-25 17:48:20,753] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:20,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:20,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg8575ec6b-538a-495e-959b-c92d8ba5bfc1/dqc_reference
[2024-01-25 17:48:21,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:21,935] [INFO] Task started: Prodigal
[2024-01-25 17:48:21,936] [INFO] Running command: gunzip -c /var/lib/cwl/stga37ae023-b0c0-47d3-8929-66590514eb29/GCF_014137865.1_ASM1413786v1_genomic.fna.gz | prodigal -d GCF_014137865.1_ASM1413786v1_genomic.fna/cds.fna -a GCF_014137865.1_ASM1413786v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:28,305] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:28,305] [INFO] Task started: HMMsearch
[2024-01-25 17:48:28,306] [INFO] Running command: hmmsearch --tblout GCF_014137865.1_ASM1413786v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8575ec6b-538a-495e-959b-c92d8ba5bfc1/dqc_reference/reference_markers.hmm GCF_014137865.1_ASM1413786v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:28,511] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:28,512] [INFO] Found 6/6 markers.
[2024-01-25 17:48:28,534] [INFO] Query marker FASTA was written to GCF_014137865.1_ASM1413786v1_genomic.fna/markers.fasta
[2024-01-25 17:48:28,535] [INFO] Task started: Blastn
[2024-01-25 17:48:28,535] [INFO] Running command: blastn -query GCF_014137865.1_ASM1413786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8575ec6b-538a-495e-959b-c92d8ba5bfc1/dqc_reference/reference_markers.fasta -out GCF_014137865.1_ASM1413786v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:29,219] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:29,222] [INFO] Selected 28 target genomes.
[2024-01-25 17:48:29,222] [INFO] Target genome list was writen to GCF_014137865.1_ASM1413786v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:29,277] [INFO] Task started: fastANI
[2024-01-25 17:48:29,277] [INFO] Running command: fastANI --query /var/lib/cwl/stga37ae023-b0c0-47d3-8929-66590514eb29/GCF_014137865.1_ASM1413786v1_genomic.fna.gz --refList GCF_014137865.1_ASM1413786v1_genomic.fna/target_genomes.txt --output GCF_014137865.1_ASM1413786v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:46,524] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:46,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8575ec6b-538a-495e-959b-c92d8ba5bfc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:46,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8575ec6b-538a-495e-959b-c92d8ba5bfc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:46,537] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:48:46,537] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:48:46,538] [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
Alpinimonas psychrophila	strain=DSM 23737	GCA_014137865.1	748908	748908	type	True	100.0	736	739	95	conclusive
Aurantimicrobium minutum	strain=KNC	GCA_002355535.1	708131	708131	type	True	78.4764	92	739	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	78.2605	95	739	95	below_threshold
Aurantimicrobium photophilum	strain=MWH-Mo1	GCA_003194085.1	1987356	1987356	type	True	78.0151	128	739	95	below_threshold
Mycetocola zhujimingii	strain=449 = CGMCC 1.16372	GCA_003065425.1	2079792	2079792	type	True	77.9124	74	739	95	below_threshold
Glaciihabitans tibetensis	strain=CGMCC 1.12484	GCA_003003265.1	1266600	1266600	type	True	77.7334	57	739	95	below_threshold
Microterricola gilva	strain=DSM 18319	GCA_004217495.1	393267	393267	type	True	77.7288	91	739	95	below_threshold
Subtercola frigoramans	strain=DSM 13057	GCA_016907385.1	120298	120298	type	True	77.6263	73	739	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	77.4626	103	739	95	below_threshold
Microcella putealis	strain=DSM 19627	GCA_006716545.1	337005	337005	type	True	77.4515	69	739	95	below_threshold
Rathayibacter caricis	strain=DSM 15933	GCA_003044275.1	110936	110936	type	True	77.3344	71	739	95	below_threshold
Agromyces atrinae	strain=DSM 23870	GCA_013407835.1	592376	592376	type	True	77.295	79	739	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	77.23	82	739	95	below_threshold
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	77.1341	67	739	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	77.0638	68	739	95	below_threshold
Mycetocola manganoxydans	strain=KCTC 19753	GCA_014651755.1	699879	699879	type	True	77.051	66	739	95	below_threshold
Cryobacterium melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	77.041	106	739	95	below_threshold
Agromyces atrinae	strain=DSM 23870	GCA_004134805.1	592376	592376	type	True	76.954	78	739	95	below_threshold
Lacisediminihabitans changchengi	strain=G11-30	GCA_016634425.1	2787634	2787634	type	True	76.8356	63	739	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	76.8075	73	739	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	76.5852	86	739	95	below_threshold
Rathayibacter tritici	strain=DSM 7486	GCA_002932875.1	33888	33888	type	True	76.572	58	739	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:46,540] [INFO] DFAST Taxonomy check result was written to GCF_014137865.1_ASM1413786v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:46,540] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:46,540] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:46,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8575ec6b-538a-495e-959b-c92d8ba5bfc1/dqc_reference/checkm_data
[2024-01-25 17:48:46,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:46,567] [INFO] Task started: CheckM
[2024-01-25 17:48:46,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014137865.1_ASM1413786v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014137865.1_ASM1413786v1_genomic.fna/checkm_input GCF_014137865.1_ASM1413786v1_genomic.fna/checkm_result
[2024-01-25 17:49:09,871] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:09,872] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.25%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:09,887] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:09,888] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:09,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014137865.1_ASM1413786v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:09,888] [INFO] Task started: Blastn
[2024-01-25 17:49:09,888] [INFO] Running command: blastn -query GCF_014137865.1_ASM1413786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8575ec6b-538a-495e-959b-c92d8ba5bfc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014137865.1_ASM1413786v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:11,012] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:11,014] [INFO] Selected 24 target genomes.
[2024-01-25 17:49:11,015] [INFO] Target genome list was writen to GCF_014137865.1_ASM1413786v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:11,034] [INFO] Task started: fastANI
[2024-01-25 17:49:11,035] [INFO] Running command: fastANI --query /var/lib/cwl/stga37ae023-b0c0-47d3-8929-66590514eb29/GCF_014137865.1_ASM1413786v1_genomic.fna.gz --refList GCF_014137865.1_ASM1413786v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014137865.1_ASM1413786v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:24,961] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:24,975] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:24,975] [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_014137865.1	s__Alpinimonas psychrophila	100.0	736	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Alpinimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003611035.1	s__Cryobacterium soli	78.2215	96	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003194085.1	s__Aurantimicrobium sp003194085	78.0151	128	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aurantimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542775.1	s__Microterricola viridarii_A	78.0093	100	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410665.1	s__Leifsonia_B psychrotolerans	77.9395	89	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200405.1	s__Cryobacterium roopkundense	77.7326	101	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004217495.1	s__Microterricola gilva	77.7153	91	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425085.1	s__Microterricola sp001425085	77.6492	94	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403305.1	s__Cryobacterium sp004403305	77.5861	97	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907385.1	s__Subtercola frigoramans	77.563	72	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907615.1	s__UBA963 sp903907615	77.4415	61	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__UBA963	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104895.1	s__Microterricola viridarii	77.4343	104	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	96.4039	N/A	N/A	N/A	N/A	1	-
GCA_903859205.1	s__CAIOLM01 sp903859205	77.4202	97	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__CAIOLM01	95.0	99.95	99.95	0.98	0.98	2	-
GCF_004402375.1	s__Cryobacterium breve	77.267	88	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013409865.1	s__Herbiconiux flava	77.206	88	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	95.35	95.35	0.90	0.90	2	-
GCF_017565305.1	s__Leifsonia sp017565305	77.1202	66	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	97.25	97.25	0.89	0.89	2	-
GCF_013113715.1	s__Herbiconiux sp013113715	77.1146	90	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836535.1	s__Microbacterium sp014836535	77.0638	68	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003602235.1	s__Cryobacterium sp003602235	77.041	106	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929805.1	s__Cryobacterium sp002929805	77.0275	87	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.19	99.19	0.89	0.89	2	-
GCF_001421485.1	s__Agreia sp001421485	76.8918	80	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agreia	95.0	97.75	97.58	0.92	0.91	3	-
GCA_009699665.1	s__UBA963 sp009699665	76.8847	59	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__UBA963	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292955.1	s__UBA963 sp002292955	76.816	59	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__UBA963	95.0	99.76	99.76	0.78	0.78	2	-
GCF_018613895.1	s__Curtobacterium sp018613895	76.605	51	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:24,976] [INFO] GTDB search result was written to GCF_014137865.1_ASM1413786v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:24,977] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:24,980] [INFO] DFAST_QC result json was written to GCF_014137865.1_ASM1413786v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:24,981] [INFO] DFAST_QC completed!
[2024-01-25 17:49:24,981] [INFO] Total running time: 0h1m4s