[2024-01-25 18:47:35,553] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:47:35,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:47:35,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg78e1657e-962a-4864-bc32-d103046883b2/dqc_reference
[2024-01-25 18:47:36,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:47:36,685] [INFO] Task started: Prodigal
[2024-01-25 18:47:36,685] [INFO] Running command: gunzip -c /var/lib/cwl/stg387e2aab-b3ff-48e2-9232-9a1aea1fbcc7/GCF_009734705.1_ASM973470v1_genomic.fna.gz | prodigal -d GCF_009734705.1_ASM973470v1_genomic.fna/cds.fna -a GCF_009734705.1_ASM973470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:47:44,660] [INFO] Task succeeded: Prodigal
[2024-01-25 18:47:44,660] [INFO] Task started: HMMsearch
[2024-01-25 18:47:44,660] [INFO] Running command: hmmsearch --tblout GCF_009734705.1_ASM973470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78e1657e-962a-4864-bc32-d103046883b2/dqc_reference/reference_markers.hmm GCF_009734705.1_ASM973470v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:47:44,857] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:47:44,858] [INFO] Found 6/6 markers.
[2024-01-25 18:47:44,883] [INFO] Query marker FASTA was written to GCF_009734705.1_ASM973470v1_genomic.fna/markers.fasta
[2024-01-25 18:47:44,883] [INFO] Task started: Blastn
[2024-01-25 18:47:44,883] [INFO] Running command: blastn -query GCF_009734705.1_ASM973470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78e1657e-962a-4864-bc32-d103046883b2/dqc_reference/reference_markers.fasta -out GCF_009734705.1_ASM973470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:45,778] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:45,781] [INFO] Selected 19 target genomes.
[2024-01-25 18:47:45,781] [INFO] Target genome list was writen to GCF_009734705.1_ASM973470v1_genomic.fna/target_genomes.txt
[2024-01-25 18:47:45,797] [INFO] Task started: fastANI
[2024-01-25 18:47:45,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg387e2aab-b3ff-48e2-9232-9a1aea1fbcc7/GCF_009734705.1_ASM973470v1_genomic.fna.gz --refList GCF_009734705.1_ASM973470v1_genomic.fna/target_genomes.txt --output GCF_009734705.1_ASM973470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:57,260] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:57,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78e1657e-962a-4864-bc32-d103046883b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:57,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78e1657e-962a-4864-bc32-d103046883b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:57,272] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:47:57,272] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:57,272] [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 koreensis	strain=JCM 15915	GCA_009734705.1	592378	592378	type	True	100.0	959	960	95	conclusive
Rothia koreensis	strain=JCM 15915	GCA_004136575.1	592378	592378	type	True	99.9689	932	960	95	conclusive
Rothia kristinae	strain=ATCC 27570	GCA_004136565.1	37923	37923	type	True	78.4876	284	960	95	below_threshold
Rothia kristinae	strain=FDAARGOS_864	GCA_016028855.1	37923	37923	type	True	78.4828	304	960	95	below_threshold
Rothia kristinae	strain=NBRC 15354	GCA_001570865.1	37923	37923	type	True	78.4294	295	960	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	78.101	211	960	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	77.8863	219	960	95	below_threshold
Kocuria tytonicola	strain=DSM 104133	GCA_003687455.1	2055946	2055946	type	True	77.8546	173	960	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	77.724	215	960	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	77.6853	213	960	95	below_threshold
Zhihengliuella halotolerans	strain=DSM 17364	GCA_004217565.1	370736	370736	type	True	77.6518	144	960	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.2187	146	960	95	below_threshold
Tersicoccus solisilvae	strain=CGMCC 1.15480	GCA_014643255.1	1882339	1882339	type	True	77.2132	165	960	95	below_threshold
Arthrobacter crusticola	strain=SLN-3	GCA_004357995.1	2547960	2547960	type	True	77.0239	126	960	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	76.7895	97	960	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	76.507	87	960	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	76.4265	84	960	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	76.3499	100	960	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	76.1786	97	960	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:57,273] [INFO] DFAST Taxonomy check result was written to GCF_009734705.1_ASM973470v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:57,274] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:57,274] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:57,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78e1657e-962a-4864-bc32-d103046883b2/dqc_reference/checkm_data
[2024-01-25 18:47:57,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:57,305] [INFO] Task started: CheckM
[2024-01-25 18:47:57,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009734705.1_ASM973470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009734705.1_ASM973470v1_genomic.fna/checkm_input GCF_009734705.1_ASM973470v1_genomic.fna/checkm_result
[2024-01-25 18:48:26,049] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:26,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:26,066] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:26,066] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:26,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009734705.1_ASM973470v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:26,068] [INFO] Task started: Blastn
[2024-01-25 18:48:26,068] [INFO] Running command: blastn -query GCF_009734705.1_ASM973470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78e1657e-962a-4864-bc32-d103046883b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_009734705.1_ASM973470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:27,457] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:27,460] [INFO] Selected 15 target genomes.
[2024-01-25 18:48:27,460] [INFO] Target genome list was writen to GCF_009734705.1_ASM973470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:27,496] [INFO] Task started: fastANI
[2024-01-25 18:48:27,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg387e2aab-b3ff-48e2-9232-9a1aea1fbcc7/GCF_009734705.1_ASM973470v1_genomic.fna.gz --refList GCF_009734705.1_ASM973470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009734705.1_ASM973470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:37,005] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:37,014] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:37,015] [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_004136575.1	s__Rothia koreensis	99.9689	932	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	99.36	98.73	0.95	0.92	3	conclusive
GCF_004137765.1	s__Rothia sp004137765	80.0541	504	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394385.1	s__Rothia sp004136585	80.0257	532	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	99.70	99.70	0.98	0.98	2	-
GCF_000710345.2	s__Rothia sp000710345	79.7109	428	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900169715.1	s__Rothia massiliensis	79.0947	317	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.67	98.66	0.95	0.94	3	-
GCF_004136635.1	s__Rothia halotolerans	78.9016	365	960	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	77.8869	219	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
GCF_003687455.1	s__Kocuria tytonicola	77.8546	173	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.95	98.95	0.94	0.94	2	-
GCF_014636775.1	s__Kocuria dechangensis	77.7429	213	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482365.1	s__Kocuria flava	77.6663	215	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.78	97.61	0.93	0.87	4	-
GCF_000786655.1	s__Kocuria marina_A	77.6278	181	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.811	96.52	96.52	0.87	0.87	2	-
GCF_012395835.1	s__Arthrobacter_F mobilis	77.2187	146	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643255.1	s__Tersicoccus solisilvae	77.198	166	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Tersicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004357995.1	s__Arthrobacter_D crusticola	77.0431	125	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602285.1	s__Arthrobacter_D sp003602285	77.0163	115	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	95.90	95.90	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:37,016] [INFO] GTDB search result was written to GCF_009734705.1_ASM973470v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:37,016] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:37,020] [INFO] DFAST_QC result json was written to GCF_009734705.1_ASM973470v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:37,020] [INFO] DFAST_QC completed!
[2024-01-25 18:48:37,020] [INFO] Total running time: 0h1m1s