[2024-01-24 14:46:57,412] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:57,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:57,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg4693ab09-a88e-4259-ac66-9f28b2f7843f/dqc_reference
[2024-01-24 14:46:58,746] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,748] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,748] [INFO] Running command: gunzip -c /var/lib/cwl/stgc507cb49-97c4-4031-8a74-01a4020cd503/GCF_014200305.1_ASM1420030v1_genomic.fna.gz | prodigal -d GCF_014200305.1_ASM1420030v1_genomic.fna/cds.fna -a GCF_014200305.1_ASM1420030v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:08,082] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:08,083] [INFO] Task started: HMMsearch
[2024-01-24 14:47:08,083] [INFO] Running command: hmmsearch --tblout GCF_014200305.1_ASM1420030v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4693ab09-a88e-4259-ac66-9f28b2f7843f/dqc_reference/reference_markers.hmm GCF_014200305.1_ASM1420030v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:08,355] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:08,357] [INFO] Found 6/6 markers.
[2024-01-24 14:47:08,383] [INFO] Query marker FASTA was written to GCF_014200305.1_ASM1420030v1_genomic.fna/markers.fasta
[2024-01-24 14:47:08,383] [INFO] Task started: Blastn
[2024-01-24 14:47:08,384] [INFO] Running command: blastn -query GCF_014200305.1_ASM1420030v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4693ab09-a88e-4259-ac66-9f28b2f7843f/dqc_reference/reference_markers.fasta -out GCF_014200305.1_ASM1420030v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:09,204] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:09,207] [INFO] Selected 22 target genomes.
[2024-01-24 14:47:09,207] [INFO] Target genome list was writen to GCF_014200305.1_ASM1420030v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:09,219] [INFO] Task started: fastANI
[2024-01-24 14:47:09,219] [INFO] Running command: fastANI --query /var/lib/cwl/stgc507cb49-97c4-4031-8a74-01a4020cd503/GCF_014200305.1_ASM1420030v1_genomic.fna.gz --refList GCF_014200305.1_ASM1420030v1_genomic.fna/target_genomes.txt --output GCF_014200305.1_ASM1420030v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:24,717] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:24,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4693ab09-a88e-4259-ac66-9f28b2f7843f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:24,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4693ab09-a88e-4259-ac66-9f28b2f7843f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:24,735] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:24,736] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:24,736] [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
Neomicrococcus lactis	strain=DSM 23694	GCA_014200305.1	732241	732241	type	True	100.0	899	900	95	conclusive
Neomicrococcus aestuarii	strain=DSM 105783	GCA_014201135.1	556325	556325	type	True	83.4914	600	900	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	78.1751	133	900	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	78.0889	120	900	95	below_threshold
Glutamicibacter arilaitensis	strain=Re117	GCA_000197735.1	256701	256701	type	True	78.0763	139	900	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.9763	124	900	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	77.9435	181	900	95	below_threshold
Paeniglutamicibacter psychrophenolicus	strain=DSM 15454	GCA_017876575.1	257454	257454	type	True	77.8962	169	900	95	below_threshold
Glutamicibacter mishrai	strain=S5-52	GCA_012221945.1	1775880	1775880	type	True	77.7899	146	900	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	77.7439	117	900	95	below_threshold
Paeniglutamicibacter terrestris	strain=ANT13_2	GCA_012271785.1	2723403	2723403	type	True	77.6332	138	900	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.4819	129	900	95	below_threshold
Arthrobacter luteolus	strain=DSM 13067	GCA_008973725.1	98672	98672	type	True	77.4604	130	900	95	below_threshold
Galactobacter valiniphilus	strain=JZ R-35	GCA_003575975.1	2676122	2676122	type	True	77.4167	142	900	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.3657	117	900	95	below_threshold
Arthrobacter psychrolactophilus	strain=B7	GCA_003219795.1	92442	92442	type	True	77.3605	116	900	95	below_threshold
Glutamicibacter uratoxydans	strain=NBRC 15515	GCA_006539925.1	43667	43667	type	True	77.3244	143	900	95	below_threshold
Arthrobacter koreensis	strain=DSM 16760	GCA_009193255.1	199136	199136	type	True	77.2403	134	900	95	below_threshold
Arthrobacter luteolus	strain=NBRC 107841	GCA_001552075.1	98672	98672	type	True	77.178	131	900	95	below_threshold
Galactobacter caseinivorans	strain=JZ R-183	GCA_003640665.1	2676123	2676123	type	True	77.1688	127	900	95	below_threshold
Arthrobacter gandavensis	strain=JCM 13316	GCA_009192735.1	169960	169960	type	True	77.1465	119	900	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	76.9101	106	900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:24,738] [INFO] DFAST Taxonomy check result was written to GCF_014200305.1_ASM1420030v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:24,738] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:24,739] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:24,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4693ab09-a88e-4259-ac66-9f28b2f7843f/dqc_reference/checkm_data
[2024-01-24 14:47:24,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:24,769] [INFO] Task started: CheckM
[2024-01-24 14:47:24,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014200305.1_ASM1420030v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014200305.1_ASM1420030v1_genomic.fna/checkm_input GCF_014200305.1_ASM1420030v1_genomic.fna/checkm_result
[2024-01-24 14:47:57,653] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:57,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:57,673] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:57,673] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:57,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014200305.1_ASM1420030v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:57,674] [INFO] Task started: Blastn
[2024-01-24 14:47:57,674] [INFO] Running command: blastn -query GCF_014200305.1_ASM1420030v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4693ab09-a88e-4259-ac66-9f28b2f7843f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014200305.1_ASM1420030v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:58,801] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:58,807] [INFO] Selected 24 target genomes.
[2024-01-24 14:47:58,807] [INFO] Target genome list was writen to GCF_014200305.1_ASM1420030v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:58,826] [INFO] Task started: fastANI
[2024-01-24 14:47:58,826] [INFO] Running command: fastANI --query /var/lib/cwl/stgc507cb49-97c4-4031-8a74-01a4020cd503/GCF_014200305.1_ASM1420030v1_genomic.fna.gz --refList GCF_014200305.1_ASM1420030v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014200305.1_ASM1420030v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:14,571] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:14,594] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:14,594] [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_014200305.1	s__Neomicrococcus lactis	100.0	899	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Neomicrococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014201135.1	s__Neomicrococcus aestuarii	83.4914	600	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Neomicrococcus	95.0	97.24	97.24	0.93	0.93	2	-
GCF_000197735.1	s__Glutamicibacter arilaitensis	78.0763	139	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.79	97.54	0.91	0.83	7	-
GCF_017876535.1	s__Paeniglutamicibacter kerguelensis	77.9939	183	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001766675.1	s__Arthrobacter_G sp001766675	77.9903	148	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018622995.1	s__Arthrobacter_B sp018622995	77.9763	124	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.13	98.27	0.96	0.92	3	-
GCF_900094805.1	s__Glutamicibacter sp900094805	77.9687	118	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001863355.1	s__Paeniglutamicibacter sp001863355	77.8867	172	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979865.1	s__Glutamicibacter sp002979865	77.8319	130	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.88	98.56	0.94	0.92	3	-
GCF_005796225.1	s__Pseudarthrobacter sp005796225	77.6761	115	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002975435.1	s__Paeniglutamicibacter sp002975435	77.5547	120	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005796185.1	s__Pseudarthrobacter sp005796185	77.5271	112	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307035.1	s__Arthrobacter_B sp001307035	77.5265	123	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	98.39	98.39	0.92	0.92	2	-
GCF_003575975.1	s__Galactobacter valiniphilus	77.4167	142	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Galactobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017368795.1	s__PO-11 sp017368795	77.388	150	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__PO-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157505.1	s__Arthrobacter_D agilis_D	77.3788	120	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003219795.1	s__Specibacter psychrolactophilus	77.3436	114	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008580665.1	s__Zafaria cholistanensis	77.3311	160	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zafaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539925.1	s__Glutamicibacter uratoxydans	77.3244	143	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428365.1	s__Arthrobacter_I sp001428365	77.2832	143	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369445.1	s__Arthrobacter_G silvisoli	77.2414	140	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193255.1	s__Arthrobacter_B koreensis	77.2403	134	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.08	99.08	0.97	0.97	2	-
GCF_001552075.1	s__Arthrobacter_B luteolus	77.178	131	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003640665.1	s__Galactobacter caseinivorans	77.1688	127	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Galactobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:14,596] [INFO] GTDB search result was written to GCF_014200305.1_ASM1420030v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:14,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:14,603] [INFO] DFAST_QC result json was written to GCF_014200305.1_ASM1420030v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:14,603] [INFO] DFAST_QC completed!
[2024-01-24 14:48:14,604] [INFO] Total running time: 0h1m17s