[2024-01-24 14:07:30,430] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:30,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:30,434] [INFO] DQC Reference Directory: /var/lib/cwl/stg926990a5-2943-41f1-860c-764e89689ef1/dqc_reference
[2024-01-24 14:07:31,710] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:31,711] [INFO] Task started: Prodigal
[2024-01-24 14:07:31,711] [INFO] Running command: gunzip -c /var/lib/cwl/stge540722f-b924-442a-9b2f-19088fef9f39/GCF_016028855.1_ASM1602885v1_genomic.fna.gz | prodigal -d GCF_016028855.1_ASM1602885v1_genomic.fna/cds.fna -a GCF_016028855.1_ASM1602885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:38,543] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:38,544] [INFO] Task started: HMMsearch
[2024-01-24 14:07:38,544] [INFO] Running command: hmmsearch --tblout GCF_016028855.1_ASM1602885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg926990a5-2943-41f1-860c-764e89689ef1/dqc_reference/reference_markers.hmm GCF_016028855.1_ASM1602885v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:38,781] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:38,783] [INFO] Found 6/6 markers.
[2024-01-24 14:07:38,810] [INFO] Query marker FASTA was written to GCF_016028855.1_ASM1602885v1_genomic.fna/markers.fasta
[2024-01-24 14:07:38,811] [INFO] Task started: Blastn
[2024-01-24 14:07:38,811] [INFO] Running command: blastn -query GCF_016028855.1_ASM1602885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg926990a5-2943-41f1-860c-764e89689ef1/dqc_reference/reference_markers.fasta -out GCF_016028855.1_ASM1602885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:40,069] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:40,074] [INFO] Selected 15 target genomes.
[2024-01-24 14:07:40,074] [INFO] Target genome list was writen to GCF_016028855.1_ASM1602885v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:40,079] [INFO] Task started: fastANI
[2024-01-24 14:07:40,079] [INFO] Running command: fastANI --query /var/lib/cwl/stge540722f-b924-442a-9b2f-19088fef9f39/GCF_016028855.1_ASM1602885v1_genomic.fna.gz --refList GCF_016028855.1_ASM1602885v1_genomic.fna/target_genomes.txt --output GCF_016028855.1_ASM1602885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:49,331] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:49,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg926990a5-2943-41f1-860c-764e89689ef1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:49,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg926990a5-2943-41f1-860c-764e89689ef1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:49,344] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:07:49,344] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:49,344] [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
Rothia kristinae	strain=FDAARGOS_864	GCA_016028855.1	37923	37923	type	True	100.0	792	792	95	conclusive
Rothia kristinae	strain=ATCC 27570	GCA_004136565.1	37923	37923	type	True	99.996	777	792	95	conclusive
Rothia kristinae	strain=NBRC 15354	GCA_001570865.1	37923	37923	type	True	99.1624	750	792	95	conclusive
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	79.9483	380	792	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	79.6179	416	792	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	79.3299	407	792	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	79.215	392	792	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_003124035.1	1275	1275	suspected-type	True	79.1698	387	792	95	below_threshold
Rothia koreensis	strain=JCM 15915	GCA_009734705.1	592378	592378	type	True	78.6417	292	792	95	below_threshold
Rothia koreensis	strain=JCM 15915	GCA_004136575.1	592378	592378	type	True	78.5942	284	792	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	78.5919	268	792	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.2041	276	792	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	77.8909	142	792	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.6959	227	792	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.5803	216	792	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:49,346] [INFO] DFAST Taxonomy check result was written to GCF_016028855.1_ASM1602885v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:49,347] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:49,347] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:49,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg926990a5-2943-41f1-860c-764e89689ef1/dqc_reference/checkm_data
[2024-01-24 14:07:49,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:49,374] [INFO] Task started: CheckM
[2024-01-24 14:07:49,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016028855.1_ASM1602885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016028855.1_ASM1602885v1_genomic.fna/checkm_input GCF_016028855.1_ASM1602885v1_genomic.fna/checkm_result
[2024-01-24 14:08:28,545] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:28,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:28,561] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:28,561] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:28,561] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016028855.1_ASM1602885v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:28,562] [INFO] Task started: Blastn
[2024-01-24 14:08:28,562] [INFO] Running command: blastn -query GCF_016028855.1_ASM1602885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg926990a5-2943-41f1-860c-764e89689ef1/dqc_reference/reference_markers_gtdb.fasta -out GCF_016028855.1_ASM1602885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:30,773] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:30,777] [INFO] Selected 12 target genomes.
[2024-01-24 14:08:30,777] [INFO] Target genome list was writen to GCF_016028855.1_ASM1602885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:30,783] [INFO] Task started: fastANI
[2024-01-24 14:08:30,783] [INFO] Running command: fastANI --query /var/lib/cwl/stge540722f-b924-442a-9b2f-19088fef9f39/GCF_016028855.1_ASM1602885v1_genomic.fna.gz --refList GCF_016028855.1_ASM1602885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016028855.1_ASM1602885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:38,946] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:38,961] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:38,961] [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_001570865.1	s__Rothia kristinae	99.1777	749	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.74	96.46	0.96	0.92	16	conclusive
GCF_004136635.1	s__Rothia halotolerans	81.4088	477	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580365.1	s__Kocuria turfanensis	79.9508	381	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
GCF_001482365.1	s__Kocuria flava	79.6249	416	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.78	97.61	0.93	0.87	4	-
GCF_006094695.1	s__Kocuria rosea	79.3291	387	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.85	97.54	0.92	0.85	16	-
GCF_001483755.1	s__Kocuria polaris_A	79.2745	380	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636775.1	s__Kocuria dechangensis	79.2274	391	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007666205.1	s__Kocuria palustris_A	78.9939	330	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007681555.1	s__Kocuria salsicia	78.9129	333	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.09	95.42	0.92	0.89	8	-
GCF_000710345.2	s__Rothia sp000710345	78.6894	315	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004136575.1	s__Rothia koreensis	78.5811	286	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	99.36	98.73	0.95	0.92	3	-
GCF_001766675.1	s__Arthrobacter_G sp001766675	77.7613	214	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:38,996] [INFO] GTDB search result was written to GCF_016028855.1_ASM1602885v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:38,997] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:39,002] [INFO] DFAST_QC result json was written to GCF_016028855.1_ASM1602885v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:39,002] [INFO] DFAST_QC completed!
[2024-01-24 14:08:39,002] [INFO] Total running time: 0h1m9s