[2024-01-24 14:11:51,174] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:51,176] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:51,177] [INFO] DQC Reference Directory: /var/lib/cwl/stgb90d7b6b-c704-4d47-9c08-8d4a7073362c/dqc_reference
[2024-01-24 14:11:52,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:52,679] [INFO] Task started: Prodigal
[2024-01-24 14:11:52,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg1838854c-641c-455f-b8c4-eaf36f13f2e5/GCF_004136635.1_ASM413663v1_genomic.fna.gz | prodigal -d GCF_004136635.1_ASM413663v1_genomic.fna/cds.fna -a GCF_004136635.1_ASM413663v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:01,167] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:01,168] [INFO] Task started: HMMsearch
[2024-01-24 14:12:01,168] [INFO] Running command: hmmsearch --tblout GCF_004136635.1_ASM413663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb90d7b6b-c704-4d47-9c08-8d4a7073362c/dqc_reference/reference_markers.hmm GCF_004136635.1_ASM413663v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:01,512] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:01,514] [INFO] Found 6/6 markers.
[2024-01-24 14:12:01,546] [INFO] Query marker FASTA was written to GCF_004136635.1_ASM413663v1_genomic.fna/markers.fasta
[2024-01-24 14:12:01,547] [INFO] Task started: Blastn
[2024-01-24 14:12:01,547] [INFO] Running command: blastn -query GCF_004136635.1_ASM413663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb90d7b6b-c704-4d47-9c08-8d4a7073362c/dqc_reference/reference_markers.fasta -out GCF_004136635.1_ASM413663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:03,989] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:04,002] [INFO] Selected 15 target genomes.
[2024-01-24 14:12:04,003] [INFO] Target genome list was writen to GCF_004136635.1_ASM413663v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:04,027] [INFO] Task started: fastANI
[2024-01-24 14:12:04,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg1838854c-641c-455f-b8c4-eaf36f13f2e5/GCF_004136635.1_ASM413663v1_genomic.fna.gz --refList GCF_004136635.1_ASM413663v1_genomic.fna/target_genomes.txt --output GCF_004136635.1_ASM413663v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:13,734] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:13,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb90d7b6b-c704-4d47-9c08-8d4a7073362c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:13,735] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb90d7b6b-c704-4d47-9c08-8d4a7073362c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:14,045] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:12:14,045] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:12:14,046] [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=NBRC 15354	GCA_001570865.1	37923	37923	type	True	81.3449	470	1008	95	below_threshold
Rothia kristinae	strain=FDAARGOS_864	GCA_016028855.1	37923	37923	type	True	81.3156	480	1008	95	below_threshold
Rothia kristinae	strain=ATCC 27570	GCA_004136565.1	37923	37923	type	True	81.2604	491	1008	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	79.6118	443	1008	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	79.507	437	1008	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	79.5011	432	1008	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_006094695.1	1275	1275	suspected-type	True	79.4533	428	1008	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_003124035.1	1275	1275	suspected-type	True	79.4235	436	1008	95	below_threshold
Rothia koreensis	strain=JCM 15915	GCA_004136575.1	592378	592378	type	True	79.1211	362	1008	95	below_threshold
Rothia koreensis	strain=JCM 15915	GCA_009734705.1	592378	592378	type	True	79.0711	366	1008	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	78.7224	235	1008	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.1799	315	1008	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	77.7012	232	1008	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	77.0759	219	1008	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	76.5643	125	1008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:14,049] [INFO] DFAST Taxonomy check result was written to GCF_004136635.1_ASM413663v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:14,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:14,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:14,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb90d7b6b-c704-4d47-9c08-8d4a7073362c/dqc_reference/checkm_data
[2024-01-24 14:12:14,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:14,265] [INFO] Task started: CheckM
[2024-01-24 14:12:14,266] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004136635.1_ASM413663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004136635.1_ASM413663v1_genomic.fna/checkm_input GCF_004136635.1_ASM413663v1_genomic.fna/checkm_result
[2024-01-24 14:12:44,918] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:44,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:44,951] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:44,951] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:44,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004136635.1_ASM413663v1_genomic.fna/markers.fasta)
[2024-01-24 14:12:44,952] [INFO] Task started: Blastn
[2024-01-24 14:12:44,952] [INFO] Running command: blastn -query GCF_004136635.1_ASM413663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb90d7b6b-c704-4d47-9c08-8d4a7073362c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004136635.1_ASM413663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:47,840] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:47,844] [INFO] Selected 12 target genomes.
[2024-01-24 14:12:47,845] [INFO] Target genome list was writen to GCF_004136635.1_ASM413663v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:47,855] [INFO] Task started: fastANI
[2024-01-24 14:12:47,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg1838854c-641c-455f-b8c4-eaf36f13f2e5/GCF_004136635.1_ASM413663v1_genomic.fna.gz --refList GCF_004136635.1_ASM413663v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004136635.1_ASM413663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:12:56,265] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:56,319] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:12:56,319] [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	100.0	1008	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001570865.1	s__Rothia kristinae	81.3703	468	1008	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	79.6005	444	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.78	97.61	0.93	0.87	4	-
GCF_014636775.1	s__Kocuria dechangensis	79.5867	424	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001483755.1	s__Kocuria polaris_A	79.5119	414	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580365.1	s__Kocuria turfanensis	79.5017	432	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
GCF_006094695.1	s__Kocuria rosea	79.4417	429	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.85	97.54	0.92	0.85	16	-
GCF_000710345.2	s__Rothia sp000710345	79.2261	364	1008	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	79.1081	363	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	99.36	98.73	0.95	0.92	3	-
GCF_004137765.1	s__Rothia sp004137765	78.4817	245	1008	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	78.2563	254	1008	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	78.1677	316	1008	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 14:12:56,321] [INFO] GTDB search result was written to GCF_004136635.1_ASM413663v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:12:56,322] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:12:56,328] [INFO] DFAST_QC result json was written to GCF_004136635.1_ASM413663v1_genomic.fna/dqc_result.json
[2024-01-24 14:12:56,329] [INFO] DFAST_QC completed!
[2024-01-24 14:12:56,329] [INFO] Total running time: 0h1m5s