[2024-01-24 13:01:12,524] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b22dd84-27bc-48f7-a278-744af8d46244/dqc_reference
[2024-01-24 13:01:13,779] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,780] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,780] [INFO] Running command: gunzip -c /var/lib/cwl/stg696db3d2-c129-4495-91d6-8933e88cbf88/GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/cds.fna -a GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:21,201] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:21,201] [INFO] Task started: HMMsearch
[2024-01-24 13:01:21,201] [INFO] Running command: hmmsearch --tblout GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b22dd84-27bc-48f7-a278-744af8d46244/dqc_reference/reference_markers.hmm GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:21,540] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:21,541] [INFO] Found 6/6 markers.
[2024-01-24 13:01:21,571] [INFO] Query marker FASTA was written to GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:01:21,571] [INFO] Task started: Blastn
[2024-01-24 13:01:21,572] [INFO] Running command: blastn -query GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b22dd84-27bc-48f7-a278-744af8d46244/dqc_reference/reference_markers.fasta -out GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:22,322] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:22,332] [INFO] Selected 16 target genomes.
[2024-01-24 13:01:22,332] [INFO] Target genome list was writen to GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:01:22,345] [INFO] Task started: fastANI
[2024-01-24 13:01:22,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg696db3d2-c129-4495-91d6-8933e88cbf88/GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna.gz --refList GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:34,730] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:34,731] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b22dd84-27bc-48f7-a278-744af8d46244/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:34,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b22dd84-27bc-48f7-a278-744af8d46244/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:34,742] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:34,742] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:34,742] [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
Rosenbergiella nectarea	strain=8N4	GCA_900111105.1	988801	988801	type	True	100.0	1082	1084	95	conclusive
Rosenbergiella epipactidis	strain=2.1A	GCA_018494055.1	1544694	1544694	type	True	87.7605	896	1084	95	below_threshold
Rosenbergiella collisarenosi	strain=8.8A	GCA_018494085.1	1544695	1544695	type	True	82.6507	633	1084	95	below_threshold
Rosenbergiella australiborealis	strain=CdVSA20.1	GCA_018494035.1	1544696	1544696	type	True	81.3836	533	1084	95	below_threshold
Tatumella citrea	strain=DSM 13699	GCA_002163585.1	53336	53336	type	True	78.6261	165	1084	95	below_threshold
Tatumella morbirosei	strain=LMG 23360	GCA_000757425.2	642227	642227	type	True	78.5093	165	1084	95	below_threshold
Escherichia fergusonii	strain=FDAARGOS_1499	GCA_020097475.1	564	564	type	True	78.4526	92	1084	95	below_threshold
Mangrovibacter plantisponsor	strain=DSM 19579	GCA_003182475.1	451513	451513	type	True	78.2657	98	1084	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	78.2222	141	1084	95	below_threshold
Tatumella ptyseos	strain=ATCC 33301	GCA_000439895.1	82987	82987	type	True	78.2177	165	1084	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	78.0924	134	1084	95	below_threshold
Brenneria roseae subsp. roseae	strain=LMG 27714	GCA_003115845.1	1508506	1509241	type	True	77.9779	84	1084	95	below_threshold
Brenneria roseae subsp. americana	strain=LMG 27715	GCA_003115815.1	1508507	1509241	type	True	77.9538	84	1084	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	77.8706	140	1084	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:34,744] [INFO] DFAST Taxonomy check result was written to GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:01:34,745] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:34,745] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:34,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b22dd84-27bc-48f7-a278-744af8d46244/dqc_reference/checkm_data
[2024-01-24 13:01:34,746] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:34,778] [INFO] Task started: CheckM
[2024-01-24 13:01:34,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/checkm_input GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:02:02,686] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:02,687] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:02,718] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:02,719] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:02,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:02:02,719] [INFO] Task started: Blastn
[2024-01-24 13:02:02,720] [INFO] Running command: blastn -query GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b22dd84-27bc-48f7-a278-744af8d46244/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:03,744] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:03,750] [INFO] Selected 12 target genomes.
[2024-01-24 13:02:03,751] [INFO] Target genome list was writen to GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:03,774] [INFO] Task started: fastANI
[2024-01-24 13:02:03,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg696db3d2-c129-4495-91d6-8933e88cbf88/GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna.gz --refList GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:12,956] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:12,966] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:12,966] [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_900111105.1	s__Rosenbergiella nectarea	100.0	1082	1084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.23	96.23	0.89	0.89	2	conclusive
GCF_018494055.1	s__Rosenbergiella epipactidis	87.769	895	1084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.28	95.56	0.88	0.85	5	-
GCF_018494065.1	s__Rosenbergiella sp018494065	86.0571	782	1084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018494085.1	s__Rosenbergiella collisarenosi	82.6538	634	1084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	99.00	99.00	0.87	0.87	2	-
GCF_018494035.1	s__Rosenbergiella australiborealis	81.3892	534	1084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002042885.1	s__Citrobacter portucalensis	79.4796	93	1084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.01	95.95	0.89	0.83	128	-
GCF_005843885.1	s__Escherichia sp005843885	79.1576	92	1084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	96.83	95.39	0.87	0.80	37	-
GCA_902706205.1	s__Scandinavium sp902706205	79.0009	97	1084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598695.1	s__Klebsiella oxytoca	78.8037	105	1084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.31	98.97	0.94	0.89	181	-
GCA_901456055.1	s__Phytobacter ursingii	78.317	112	1084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	97.10	96.01	0.86	0.80	7	-
GCF_002095535.1	s__Pantoea cypripedii	78.2222	141	1084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	0.99	0.99	2	-
GCF_015672735.1	s__Citrobacter sp015672735	78.114	102	1084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:12,968] [INFO] GTDB search result was written to GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:12,969] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:12,972] [INFO] DFAST_QC result json was written to GCF_900111105.1_IMG-taxon_2651870171_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:02:12,973] [INFO] DFAST_QC completed!
[2024-01-24 13:02:12,973] [INFO] Total running time: 0h1m0s