[2024-01-25 18:06:35,619] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:35,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:35,620] [INFO] DQC Reference Directory: /var/lib/cwl/stga07981d0-d0d7-46af-8fc7-e7590a452dc8/dqc_reference
[2024-01-25 18:06:36,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:36,750] [INFO] Task started: Prodigal
[2024-01-25 18:06:36,750] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4a863e6-0e39-4f35-a1b1-a257f0e4d32a/GCF_003640665.1_ASM364066v1_genomic.fna.gz | prodigal -d GCF_003640665.1_ASM364066v1_genomic.fna/cds.fna -a GCF_003640665.1_ASM364066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:45,446] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:45,447] [INFO] Task started: HMMsearch
[2024-01-25 18:06:45,447] [INFO] Running command: hmmsearch --tblout GCF_003640665.1_ASM364066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga07981d0-d0d7-46af-8fc7-e7590a452dc8/dqc_reference/reference_markers.hmm GCF_003640665.1_ASM364066v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:45,679] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:45,680] [INFO] Found 6/6 markers.
[2024-01-25 18:06:45,705] [INFO] Query marker FASTA was written to GCF_003640665.1_ASM364066v1_genomic.fna/markers.fasta
[2024-01-25 18:06:45,705] [INFO] Task started: Blastn
[2024-01-25 18:06:45,705] [INFO] Running command: blastn -query GCF_003640665.1_ASM364066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga07981d0-d0d7-46af-8fc7-e7590a452dc8/dqc_reference/reference_markers.fasta -out GCF_003640665.1_ASM364066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:46,662] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:46,664] [INFO] Selected 22 target genomes.
[2024-01-25 18:06:46,665] [INFO] Target genome list was writen to GCF_003640665.1_ASM364066v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:46,680] [INFO] Task started: fastANI
[2024-01-25 18:06:46,680] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a863e6-0e39-4f35-a1b1-a257f0e4d32a/GCF_003640665.1_ASM364066v1_genomic.fna.gz --refList GCF_003640665.1_ASM364066v1_genomic.fna/target_genomes.txt --output GCF_003640665.1_ASM364066v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:01,125] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:01,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga07981d0-d0d7-46af-8fc7-e7590a452dc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:01,125] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga07981d0-d0d7-46af-8fc7-e7590a452dc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:01,138] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:07:01,138] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:07:01,138] [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
Galactobacter caseinivorans	strain=JZ R-183	GCA_003640665.1	2676123	2676123	type	True	100.0	976	977	95	conclusive
Galactobacter valiniphilus	strain=JZ R-35	GCA_003575975.1	2676122	2676122	type	True	80.3036	532	977	95	below_threshold
Micrococcus endophyticus	strain=DSM 17945	GCA_014205115.1	455343	455343	type	True	78.0464	247	977	95	below_threshold
Micrococcus lylae	strain=NBRC 15355	GCA_001570885.1	1273	1273	type	True	78.0102	218	977	95	below_threshold
Zhihengliuella salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	77.8913	208	977	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	77.8726	230	977	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	77.6993	175	977	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	77.6738	139	977	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.6705	156	977	95	below_threshold
Glutamicibacter uratoxydans	strain=NBRC 15515	GCA_006539925.1	43667	43667	type	True	77.656	189	977	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	77.6294	184	977	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.6227	176	977	95	below_threshold
Rothia kristinae	strain=NBRC 15354	GCA_001570865.1	37923	37923	type	True	77.6068	181	977	95	below_threshold
Citricoccus zhacaiensis	strain=CGMCC 1.7064	GCA_014645315.1	489142	489142	type	True	77.5836	203	977	95	below_threshold
Rothia kristinae	strain=FDAARGOS_864	GCA_016028855.1	37923	37923	type	True	77.5709	181	977	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.5681	207	977	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	77.5025	218	977	95	below_threshold
Kocuria tytonis	strain=442	GCA_003226895.2	2054280	2054280	type	True	77.4784	190	977	95	below_threshold
Nesterenkonia jeotgali	strain=DSM 19081	GCA_014138825.1	317018	317018	type	True	77.2596	151	977	95	below_threshold
Zhihengliuella flava	strain=DSM 26152	GCA_015751895.1	1285193	1285193	type	True	77.1664	175	977	95	below_threshold
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	75.9801	111	977	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	75.8201	108	977	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:01,140] [INFO] DFAST Taxonomy check result was written to GCF_003640665.1_ASM364066v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:01,140] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:01,140] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:01,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga07981d0-d0d7-46af-8fc7-e7590a452dc8/dqc_reference/checkm_data
[2024-01-25 18:07:01,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:01,171] [INFO] Task started: CheckM
[2024-01-25 18:07:01,171] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003640665.1_ASM364066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003640665.1_ASM364066v1_genomic.fna/checkm_input GCF_003640665.1_ASM364066v1_genomic.fna/checkm_result
[2024-01-25 18:07:30,427] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:30,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:30,444] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:30,444] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:30,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003640665.1_ASM364066v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:30,444] [INFO] Task started: Blastn
[2024-01-25 18:07:30,445] [INFO] Running command: blastn -query GCF_003640665.1_ASM364066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga07981d0-d0d7-46af-8fc7-e7590a452dc8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003640665.1_ASM364066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:31,855] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:31,858] [INFO] Selected 28 target genomes.
[2024-01-25 18:07:31,858] [INFO] Target genome list was writen to GCF_003640665.1_ASM364066v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:31,873] [INFO] Task started: fastANI
[2024-01-25 18:07:31,873] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a863e6-0e39-4f35-a1b1-a257f0e4d32a/GCF_003640665.1_ASM364066v1_genomic.fna.gz --refList GCF_003640665.1_ASM364066v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003640665.1_ASM364066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:48,960] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:48,974] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:48,974] [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_003640665.1	s__Galactobacter caseinivorans	100.0	976	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Galactobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003575975.1	s__Galactobacter valiniphilus	80.3042	532	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Galactobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008580665.1	s__Zafaria cholistanensis	78.2729	256	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zafaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116905.1	s__Citricoccus terreus	78.1546	215	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005877055.1	s__Citricoccus sp005877055	78.1469	232	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482545.1	s__Specibacter sp000482545	78.0352	231	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205115.1	s__Micrococcus endophyticus	78.0321	248	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.47	97.28	0.90	0.88	4	-
GCF_001570885.1	s__Micrococcus lylae	78.0102	218	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	98.72	97.35	0.93	0.90	6	-
GCF_015355785.1	s__Arthrobacter_B gandavensis_A	77.9743	156	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651715.1	s__Zhihengliuella salsuginis	77.8913	208	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876535.1	s__Paeniglutamicibacter kerguelensis	77.872	230	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084045.1	s__Paeniglutamicibacter sp019084045	77.856	247	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006094275.1	s__Glutamicibacter creatinolyticus	77.8273	223	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.17	97.78	0.92	0.89	4	-
GCF_017876575.1	s__Paeniglutamicibacter psychrophenolicus	77.7392	246	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	77.6937	235	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539925.1	s__Glutamicibacter uratoxydans	77.656	189	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010285.1	s__Kocuria rhizophila_A	77.6354	212	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.71	97.98	0.95	0.89	9	-
GCF_014645315.1	s__Citricoccus zhacaiensis	77.614	201	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570865.1	s__Rothia kristinae	77.5905	182	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.74	96.46	0.96	0.92	16	-
GCF_012395835.1	s__Arthrobacter_F mobilis	77.565	208	977	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_013376105.1	s__Specibacter sp013376105	77.5025	218	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715295.1	s__Pseudarthrobacter sp006715295	77.4947	180	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751895.1	s__Zhihengliuella flava	77.137	177	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230195.1	s__Streptomyces zhaozhouensis	75.9801	111	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:48,976] [INFO] GTDB search result was written to GCF_003640665.1_ASM364066v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:48,976] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:48,979] [INFO] DFAST_QC result json was written to GCF_003640665.1_ASM364066v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:48,980] [INFO] DFAST_QC completed!
[2024-01-25 18:07:48,980] [INFO] Total running time: 0h1m13s