[2024-01-24 14:14:47,175] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:47,182] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:47,182] [INFO] DQC Reference Directory: /var/lib/cwl/stga8d26e16-039d-4815-82db-1f2596376947/dqc_reference
[2024-01-24 14:14:49,421] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:49,422] [INFO] Task started: Prodigal
[2024-01-24 14:14:49,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b78cb2a-217d-4d9f-9247-77539129d6c4/GCF_011758565.1_ASM1175856v1_genomic.fna.gz | prodigal -d GCF_011758565.1_ASM1175856v1_genomic.fna/cds.fna -a GCF_011758565.1_ASM1175856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:02,972] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:02,973] [INFO] Task started: HMMsearch
[2024-01-24 14:15:02,973] [INFO] Running command: hmmsearch --tblout GCF_011758565.1_ASM1175856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8d26e16-039d-4815-82db-1f2596376947/dqc_reference/reference_markers.hmm GCF_011758565.1_ASM1175856v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:03,275] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:03,276] [INFO] Found 6/6 markers.
[2024-01-24 14:15:03,312] [INFO] Query marker FASTA was written to GCF_011758565.1_ASM1175856v1_genomic.fna/markers.fasta
[2024-01-24 14:15:03,313] [INFO] Task started: Blastn
[2024-01-24 14:15:03,313] [INFO] Running command: blastn -query GCF_011758565.1_ASM1175856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8d26e16-039d-4815-82db-1f2596376947/dqc_reference/reference_markers.fasta -out GCF_011758565.1_ASM1175856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:04,149] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:04,153] [INFO] Selected 26 target genomes.
[2024-01-24 14:15:04,154] [INFO] Target genome list was writen to GCF_011758565.1_ASM1175856v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:04,164] [INFO] Task started: fastANI
[2024-01-24 14:15:04,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b78cb2a-217d-4d9f-9247-77539129d6c4/GCF_011758565.1_ASM1175856v1_genomic.fna.gz --refList GCF_011758565.1_ASM1175856v1_genomic.fna/target_genomes.txt --output GCF_011758565.1_ASM1175856v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:19,871] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:19,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8d26e16-039d-4815-82db-1f2596376947/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:19,873] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8d26e16-039d-4815-82db-1f2596376947/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:19,893] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:19,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:19,893] [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
Lysinibacter cavernae	strain=DSM 27960	GCA_011758565.1	1640652	1640652	type	True	100.0	1246	1248	95	conclusive
Klugiella xanthotipulae	strain=DSM 18031	GCA_006716695.1	244735	244735	type	True	78.2141	205	1248	95	below_threshold
Leucobacter aridicollis	strain=DSM 17380	GCA_013409595.1	283878	283878	type	True	77.7098	107	1248	95	below_threshold
Leucobacter exalbidus	strain=DSM 22850	GCA_017834145.1	662960	662960	type	True	77.6075	96	1248	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	77.479	142	1248	95	below_threshold
Herbiconiux ginsengi	strain=CGMCC 4.3491	GCA_900107435.1	381665	381665	type	True	77.4513	119	1248	95	below_threshold
Salinibacterium amurskyense	strain=JCM 12362	GCA_003668745.1	205941	205941	type	True	77.4031	100	1248	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	77.4022	157	1248	95	below_threshold
Leucobacter aridicollis	strain=L-9	GCA_016758215.1	283878	283878	type	True	77.2732	104	1248	95	below_threshold
Salinibacterium amurskyense	strain=DSM 16400	GCA_002797685.1	205941	205941	type	True	77.26	98	1248	95	below_threshold
Leucobacter komagatae	strain=DSM 8803	GCA_006716085.1	55969	55969	type	True	77.2474	117	1248	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	77.2055	132	1248	95	below_threshold
Agreia pratensis	strain=VKM Ac-2510	GCA_900177685.1	150121	150121	type	True	77.1221	105	1248	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG 3645	GCA_013359815.1	2035	2035	suspected-type	True	77.0494	92	1248	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	76.9197	130	1248	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	76.8868	68	1248	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	76.8829	90	1248	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	76.859	120	1248	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	76.8575	91	1248	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	76.8139	130	1248	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	76.7685	108	1248	95	below_threshold
Gulosibacter hominis	strain=401352-2018	GCA_904842695.1	2770504	2770504	type	True	76.3284	52	1248	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	75.4564	59	1248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:19,895] [INFO] DFAST Taxonomy check result was written to GCF_011758565.1_ASM1175856v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:19,895] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:19,895] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:19,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8d26e16-039d-4815-82db-1f2596376947/dqc_reference/checkm_data
[2024-01-24 14:15:19,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:19,935] [INFO] Task started: CheckM
[2024-01-24 14:15:19,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011758565.1_ASM1175856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011758565.1_ASM1175856v1_genomic.fna/checkm_input GCF_011758565.1_ASM1175856v1_genomic.fna/checkm_result
[2024-01-24 14:16:00,772] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:00,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:00,794] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:00,794] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:00,795] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011758565.1_ASM1175856v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:00,795] [INFO] Task started: Blastn
[2024-01-24 14:16:00,795] [INFO] Running command: blastn -query GCF_011758565.1_ASM1175856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8d26e16-039d-4815-82db-1f2596376947/dqc_reference/reference_markers_gtdb.fasta -out GCF_011758565.1_ASM1175856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:01,887] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:01,891] [INFO] Selected 30 target genomes.
[2024-01-24 14:16:01,892] [INFO] Target genome list was writen to GCF_011758565.1_ASM1175856v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:01,946] [INFO] Task started: fastANI
[2024-01-24 14:16:01,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b78cb2a-217d-4d9f-9247-77539129d6c4/GCF_011758565.1_ASM1175856v1_genomic.fna.gz --refList GCF_011758565.1_ASM1175856v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011758565.1_ASM1175856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:17,563] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:17,582] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:17,583] [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_011758565.1	s__Lysinibacter cavernae	100.0	1244	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lysinibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006716695.1	s__Klugiella xanthotipulae	78.3	203	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Klugiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409595.1	s__Leucobacter aridicollis	77.7098	107	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.50	96.99	0.93	0.86	3	-
GCF_017834145.1	s__Leucobacter exalbidus	77.701	96	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542775.1	s__Microterricola viridarii_A	77.4813	151	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167575.1	s__Okibacterium fritillariae	77.479	142	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Okibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107435.1	s__Herbiconiux ginsengi	77.4513	119	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002812805.1	s__Microbacterium lacus	77.3273	85	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.80	97.80	0.90	0.90	2	-
GCF_900104895.1	s__Microterricola viridarii	77.2715	157	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	96.4039	N/A	N/A	N/A	N/A	1	-
GCF_900102005.1	s__Microbacterium sp900102005	77.261	96	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.39	98.39	0.95	0.95	2	-
GCF_015864665.1	s__Rhodoglobus sp015864665	77.2584	86	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	98.48	98.48	0.93	0.93	2	-
GCF_006716085.1	s__Leucobacter komagatae	77.2474	117	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421485.1	s__Agreia sp001421485	77.2248	116	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agreia	95.0	97.75	97.58	0.92	0.91	3	-
GCF_001422485.1	s__Agreia sp001422485	77.2206	118	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agreia	95.0	96.67	96.67	0.90	0.90	2	-
GCF_015864945.1	s__Rhodoglobus sp015864945	77.1605	86	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929845.1	s__Cryobacterium sp002929845	77.1523	98	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.90	95.88	0.91	0.88	15	-
GCF_004570845.1	s__Leifsonia_A flava	77.1358	129	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	95.29	95.29	0.90	0.90	2	-
GCF_001425085.1	s__Microterricola sp001425085	77.1356	154	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003367665.1	s__Leifsonia sp003367665	76.9596	105	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383475.1	s__Microbacterium sp000383475	76.9168	100	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.27	98.25	0.96	0.95	4	-
GCA_016771945.1	s__Leucobacter sulfamidivorax	76.8102	115	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729855.1	s__Agromyces luteolus	76.7792	123	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801885.1	s__Naasia lichenicola	76.7404	103	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Naasia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017990305.1	s__Leucobacter sp017990305	76.5382	64	1248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:17,584] [INFO] GTDB search result was written to GCF_011758565.1_ASM1175856v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:17,585] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:17,590] [INFO] DFAST_QC result json was written to GCF_011758565.1_ASM1175856v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:17,590] [INFO] DFAST_QC completed!
[2024-01-24 14:16:17,590] [INFO] Total running time: 0h1m30s