[2024-01-24 12:42:03,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:03,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:03,172] [INFO] DQC Reference Directory: /var/lib/cwl/stge2cf1fc5-cdf4-46bc-9700-3836030b9eb2/dqc_reference
[2024-01-24 12:42:04,346] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:04,347] [INFO] Task started: Prodigal
[2024-01-24 12:42:04,347] [INFO] Running command: gunzip -c /var/lib/cwl/stg28e59d84-189f-4a35-9591-19f188c6dab5/GCF_024199905.1_ASM2419990v1_genomic.fna.gz | prodigal -d GCF_024199905.1_ASM2419990v1_genomic.fna/cds.fna -a GCF_024199905.1_ASM2419990v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:12,512] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:12,512] [INFO] Task started: HMMsearch
[2024-01-24 12:42:12,513] [INFO] Running command: hmmsearch --tblout GCF_024199905.1_ASM2419990v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2cf1fc5-cdf4-46bc-9700-3836030b9eb2/dqc_reference/reference_markers.hmm GCF_024199905.1_ASM2419990v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:12,791] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:12,792] [INFO] Found 6/6 markers.
[2024-01-24 12:42:12,823] [INFO] Query marker FASTA was written to GCF_024199905.1_ASM2419990v1_genomic.fna/markers.fasta
[2024-01-24 12:42:12,823] [INFO] Task started: Blastn
[2024-01-24 12:42:12,824] [INFO] Running command: blastn -query GCF_024199905.1_ASM2419990v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2cf1fc5-cdf4-46bc-9700-3836030b9eb2/dqc_reference/reference_markers.fasta -out GCF_024199905.1_ASM2419990v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:14,089] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:14,093] [INFO] Selected 18 target genomes.
[2024-01-24 12:42:14,094] [INFO] Target genome list was writen to GCF_024199905.1_ASM2419990v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:18,602] [INFO] Task started: fastANI
[2024-01-24 12:42:18,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg28e59d84-189f-4a35-9591-19f188c6dab5/GCF_024199905.1_ASM2419990v1_genomic.fna.gz --refList GCF_024199905.1_ASM2419990v1_genomic.fna/target_genomes.txt --output GCF_024199905.1_ASM2419990v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:29,255] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:29,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2cf1fc5-cdf4-46bc-9700-3836030b9eb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:29,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2cf1fc5-cdf4-46bc-9700-3836030b9eb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:29,274] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:42:29,275] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:42:29,275] [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	81.2808	474	1060	95	below_threshold
Rothia kristinae	strain=NBRC 15354	GCA_001570865.1	37923	37923	type	True	81.2351	462	1060	95	below_threshold
Rothia kristinae	strain=ATCC 27570	GCA_004136565.1	37923	37923	type	True	81.1606	462	1060	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	79.7569	454	1060	95	below_threshold
Kocuria rosea	strain=DSM 20447	GCA_006717035.1	1275	1275	suspected-type	True	79.6105	424	1060	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	79.5717	449	1060	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	79.5468	456	1060	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	79.5393	446	1060	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_006094695.1	1275	1275	suspected-type	True	79.5283	430	1060	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_003124035.1	1275	1275	suspected-type	True	79.4447	435	1060	95	below_threshold
Rothia koreensis	strain=JCM 15915	GCA_004136575.1	592378	592378	type	True	78.9677	370	1060	95	below_threshold
Rothia koreensis	strain=JCM 15915	GCA_009734705.1	592378	592378	type	True	78.9582	378	1060	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	78.8148	249	1060	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.1692	301	1060	95	below_threshold
Zhihengliuella salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	78.0436	305	1060	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	77.2476	203	1060	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.1835	220	1060	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	77.0366	248	1060	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:29,277] [INFO] DFAST Taxonomy check result was written to GCF_024199905.1_ASM2419990v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:29,278] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:29,278] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:29,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2cf1fc5-cdf4-46bc-9700-3836030b9eb2/dqc_reference/checkm_data
[2024-01-24 12:42:29,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:29,318] [INFO] Task started: CheckM
[2024-01-24 12:42:29,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024199905.1_ASM2419990v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024199905.1_ASM2419990v1_genomic.fna/checkm_input GCF_024199905.1_ASM2419990v1_genomic.fna/checkm_result
[2024-01-24 12:42:57,713] [INFO] Task succeeded: CheckM
[2024-01-24 12:42:57,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:42:57,745] [INFO] ===== Completeness check finished =====
[2024-01-24 12:42:57,746] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:42:57,747] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024199905.1_ASM2419990v1_genomic.fna/markers.fasta)
[2024-01-24 12:42:57,747] [INFO] Task started: Blastn
[2024-01-24 12:42:57,747] [INFO] Running command: blastn -query GCF_024199905.1_ASM2419990v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2cf1fc5-cdf4-46bc-9700-3836030b9eb2/dqc_reference/reference_markers_gtdb.fasta -out GCF_024199905.1_ASM2419990v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:59,879] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:59,883] [INFO] Selected 12 target genomes.
[2024-01-24 12:42:59,883] [INFO] Target genome list was writen to GCF_024199905.1_ASM2419990v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:59,894] [INFO] Task started: fastANI
[2024-01-24 12:42:59,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg28e59d84-189f-4a35-9591-19f188c6dab5/GCF_024199905.1_ASM2419990v1_genomic.fna.gz --refList GCF_024199905.1_ASM2419990v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024199905.1_ASM2419990v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:07,983] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:08,000] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:43:08,000] [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_004136635.1	s__Rothia halotolerans	87.4863	769	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570865.1	s__Rothia kristinae	81.2263	463	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.74	96.46	0.96	0.92	16	-
GCF_001482365.1	s__Kocuria flava	79.7895	459	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.78	97.61	0.93	0.87	4	-
GCF_001580365.1	s__Kocuria turfanensis	79.569	453	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
GCF_014636775.1	s__Kocuria dechangensis	79.5496	451	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006094695.1	s__Kocuria rosea	79.5243	430	1060	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	79.4957	408	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000710345.2	s__Rothia sp000710345	79.1989	358	1060	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	78.955	371	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	99.36	98.73	0.95	0.92	3	-
GCF_013394385.1	s__Rothia sp004136585	78.6429	239	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	99.70	99.70	0.98	0.98	2	-
GCF_012395835.1	s__Arthrobacter_F mobilis	78.1724	300	1060	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_000328305.2	s__Arthrobacter_F crystallopoietes_A	78.0356	245	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:08,003] [INFO] GTDB search result was written to GCF_024199905.1_ASM2419990v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:08,003] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:08,007] [INFO] DFAST_QC result json was written to GCF_024199905.1_ASM2419990v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:08,007] [INFO] DFAST_QC completed!
[2024-01-24 12:43:08,008] [INFO] Total running time: 0h1m5s