[2024-01-25 19:44:50,806] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:50,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:50,807] [INFO] DQC Reference Directory: /var/lib/cwl/stgea8b8ed5-6903-4324-9d35-3e60daa6fd97/dqc_reference
[2024-01-25 19:44:51,945] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:51,945] [INFO] Task started: Prodigal
[2024-01-25 19:44:51,946] [INFO] Running command: gunzip -c /var/lib/cwl/stg18a197a5-00ff-44f2-b31a-941079347080/GCF_003797835.1_ASM379783v1_genomic.fna.gz | prodigal -d GCF_003797835.1_ASM379783v1_genomic.fna/cds.fna -a GCF_003797835.1_ASM379783v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:00,284] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:00,284] [INFO] Task started: HMMsearch
[2024-01-25 19:45:00,284] [INFO] Running command: hmmsearch --tblout GCF_003797835.1_ASM379783v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea8b8ed5-6903-4324-9d35-3e60daa6fd97/dqc_reference/reference_markers.hmm GCF_003797835.1_ASM379783v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:00,500] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:00,501] [INFO] Found 6/6 markers.
[2024-01-25 19:45:00,526] [INFO] Query marker FASTA was written to GCF_003797835.1_ASM379783v1_genomic.fna/markers.fasta
[2024-01-25 19:45:00,526] [INFO] Task started: Blastn
[2024-01-25 19:45:00,526] [INFO] Running command: blastn -query GCF_003797835.1_ASM379783v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea8b8ed5-6903-4324-9d35-3e60daa6fd97/dqc_reference/reference_markers.fasta -out GCF_003797835.1_ASM379783v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:01,592] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:01,594] [INFO] Selected 17 target genomes.
[2024-01-25 19:45:01,595] [INFO] Target genome list was writen to GCF_003797835.1_ASM379783v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:01,609] [INFO] Task started: fastANI
[2024-01-25 19:45:01,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg18a197a5-00ff-44f2-b31a-941079347080/GCF_003797835.1_ASM379783v1_genomic.fna.gz --refList GCF_003797835.1_ASM379783v1_genomic.fna/target_genomes.txt --output GCF_003797835.1_ASM379783v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:13,110] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:13,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea8b8ed5-6903-4324-9d35-3e60daa6fd97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:13,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea8b8ed5-6903-4324-9d35-3e60daa6fd97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:13,121] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:45:13,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:45:13,121] [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
Kocuria soli	strain=M5W7-7	GCA_003797835.1	2485125	2485125	type	True	100.0	961	966	95	conclusive
Kocuria coralli	strain=SCSIO 13007	GCA_008831305.1	1461025	1461025	type	True	81.4092	561	966	95	below_threshold
Kocuria subflava	strain=YIM 13062	GCA_012163155.1	1736139	1736139	type	True	81.0312	535	966	95	below_threshold
Kocuria palustris	strain=TAGA27	GCA_016907795.1	71999	71999	type	True	80.0808	438	966	95	below_threshold
Kocuria varians	strain=NBRC 15358	GCA_006539885.1	1272	1272	type	True	79.3571	329	966	95	below_threshold
Kocuria rhizophila	strain=TA68	GCA_003667225.1	72000	72000	type	True	79.2513	321	966	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	79.104	357	966	95	below_threshold
Kocuria tytonis	strain=442	GCA_003226895.2	2054280	2054280	type	True	79.0786	326	966	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	79.0347	354	966	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	79.0313	351	966	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	78.8302	370	966	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.0058	200	966	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.7587	147	966	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	77.7268	146	966	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.3317	171	966	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	77.2314	181	966	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.1501	122	966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:13,123] [INFO] DFAST Taxonomy check result was written to GCF_003797835.1_ASM379783v1_genomic.fna/tc_result.tsv
[2024-01-25 19:45:13,123] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:13,123] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:13,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea8b8ed5-6903-4324-9d35-3e60daa6fd97/dqc_reference/checkm_data
[2024-01-25 19:45:13,124] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:13,159] [INFO] Task started: CheckM
[2024-01-25 19:45:13,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003797835.1_ASM379783v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003797835.1_ASM379783v1_genomic.fna/checkm_input GCF_003797835.1_ASM379783v1_genomic.fna/checkm_result
[2024-01-25 19:45:49,949] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:49,950] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:49,975] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:49,976] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:49,976] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003797835.1_ASM379783v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:49,976] [INFO] Task started: Blastn
[2024-01-25 19:45:49,976] [INFO] Running command: blastn -query GCF_003797835.1_ASM379783v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea8b8ed5-6903-4324-9d35-3e60daa6fd97/dqc_reference/reference_markers_gtdb.fasta -out GCF_003797835.1_ASM379783v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:51,655] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:51,658] [INFO] Selected 13 target genomes.
[2024-01-25 19:45:51,658] [INFO] Target genome list was writen to GCF_003797835.1_ASM379783v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:51,672] [INFO] Task started: fastANI
[2024-01-25 19:45:51,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg18a197a5-00ff-44f2-b31a-941079347080/GCF_003797835.1_ASM379783v1_genomic.fna.gz --refList GCF_003797835.1_ASM379783v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003797835.1_ASM379783v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:00,612] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:00,621] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:00,621] [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_003797835.1	s__Kocuria soli	100.0	961	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.88	97.88	0.93	0.93	2	conclusive
GCF_008831305.1	s__Kocuria coralli	81.397	562	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012163155.1	s__Kocuria subflava	81.0251	533	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	99.27	98.56	0.95	0.91	3	-
GCF_016907795.1	s__Kocuria palustris	80.0777	439	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.24	97.70	0.90	0.87	15	-
GCF_007666205.1	s__Kocuria palustris_A	80.0061	435	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539885.1	s__Kocuria varians	79.3282	331	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	99.47	99.47	0.94	0.94	2	-
GCF_000010285.1	s__Kocuria rhizophila_A	79.3113	331	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.71	97.98	0.95	0.89	9	-
GCF_001580365.1	s__Kocuria turfanensis	79.1169	356	966	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	78.992	358	966	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	78.8835	373	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.85	97.54	0.92	0.85	16	-
GCF_014636775.1	s__Kocuria dechangensis	78.8423	369	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376105.1	s__Specibacter sp013376105	77.2314	181	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001543895.1	s__Carbonactinospora thermoautotrophica	76.7323	96	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Carbonactinosporaceae;g__Carbonactinospora	95.0	99.44	99.44	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:00,625] [INFO] GTDB search result was written to GCF_003797835.1_ASM379783v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:00,626] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:00,629] [INFO] DFAST_QC result json was written to GCF_003797835.1_ASM379783v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:00,629] [INFO] DFAST_QC completed!
[2024-01-25 19:46:00,629] [INFO] Total running time: 0h1m10s