[2024-01-24 13:48:59,830] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,832] [INFO] DQC Reference Directory: /var/lib/cwl/stgc930928f-8ae3-4e22-acc7-caa09a64bb0d/dqc_reference
[2024-01-24 13:49:01,185] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,186] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,186] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ba11afb-15cd-40a9-ba1d-8a06e0c1a25a/GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna.gz | prodigal -d GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/cds.fna -a GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:14,096] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:14,096] [INFO] Task started: HMMsearch
[2024-01-24 13:49:14,097] [INFO] Running command: hmmsearch --tblout GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc930928f-8ae3-4e22-acc7-caa09a64bb0d/dqc_reference/reference_markers.hmm GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:14,361] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:14,362] [INFO] Found 6/6 markers.
[2024-01-24 13:49:14,418] [INFO] Query marker FASTA was written to GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/markers.fasta
[2024-01-24 13:49:14,419] [INFO] Task started: Blastn
[2024-01-24 13:49:14,419] [INFO] Running command: blastn -query GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc930928f-8ae3-4e22-acc7-caa09a64bb0d/dqc_reference/reference_markers.fasta -out GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:15,292] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:15,296] [INFO] Selected 25 target genomes.
[2024-01-24 13:49:15,296] [INFO] Target genome list was writen to GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:15,302] [INFO] Task started: fastANI
[2024-01-24 13:49:15,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ba11afb-15cd-40a9-ba1d-8a06e0c1a25a/GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna.gz --refList GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/target_genomes.txt --output GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:33,320] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:33,321] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc930928f-8ae3-4e22-acc7-caa09a64bb0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:33,321] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc930928f-8ae3-4e22-acc7-caa09a64bb0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:33,342] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:33,342] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:33,342] [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
Cobetia crustatorum	strain=JO1	GCA_000591415.1	553385	553385	type	True	100.0	1273	1275	95	conclusive
Cobetia marina	strain=JCM 21022	GCA_001720485.1	28258	28258	type	True	83.9516	939	1275	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	78.0851	203	1275	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	78.0643	209	1275	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	78.0277	228	1275	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	77.999	280	1275	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.9853	232	1275	95	below_threshold
Halomonas borealis	strain=ATF 5.2	GCA_004798905.1	2508710	2508710	type	True	77.8822	229	1275	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	77.8793	231	1275	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	77.8745	205	1275	95	below_threshold
Chromohalobacter nigrandesensis	strain=DSM 14323	GCA_023061285.1	119863	119863	type	True	77.8011	187	1275	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.769	237	1275	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	77.7646	242	1275	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	77.7571	275	1275	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	77.7551	232	1275	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	77.727	237	1275	95	below_threshold
Halomonas cupida	strain=DSM 4740	GCA_900142755.1	44933	44933	type	True	77.6403	220	1275	95	below_threshold
Halomonas xianhensis	strain=CGMCC 1.6848	GCA_900113605.1	442341	442341	type	True	77.5978	234	1275	95	below_threshold
Chromohalobacter beijerinckii	strain=DSM 7218	GCA_023061185.1	86179	86179	type	True	77.5597	189	1275	95	below_threshold
Halomonas pellis	strain=L5	GCA_008297955.1	2606936	2606936	type	True	77.5417	205	1275	95	below_threshold
Chromohalobacter japonicus	strain=CECT 7219	GCA_023061175.1	223900	223900	type	True	77.5406	184	1275	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	77.4167	219	1275	95	below_threshold
Halomonas lutea	strain=DSM 23508	GCA_000378505.1	453962	453962	type	True	77.394	198	1275	95	below_threshold
Halomonas songnenensis	strain=CGMCC 1.12152	GCA_003002925.1	1176243	1176243	type	True	77.3773	167	1275	95	below_threshold
Halomonas xinjiangensis	strain=TRM 0175	GCA_000759345.1	1166948	1166948	type	True	77.2625	198	1275	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:33,344] [INFO] DFAST Taxonomy check result was written to GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:33,345] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:33,345] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:33,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc930928f-8ae3-4e22-acc7-caa09a64bb0d/dqc_reference/checkm_data
[2024-01-24 13:49:33,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:33,388] [INFO] Task started: CheckM
[2024-01-24 13:49:33,388] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/checkm_input GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/checkm_result
[2024-01-24 13:50:16,131] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:16,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:16,160] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:16,160] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:16,161] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/markers.fasta)
[2024-01-24 13:50:16,161] [INFO] Task started: Blastn
[2024-01-24 13:50:16,161] [INFO] Running command: blastn -query GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc930928f-8ae3-4e22-acc7-caa09a64bb0d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:17,495] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:17,499] [INFO] Selected 11 target genomes.
[2024-01-24 13:50:17,500] [INFO] Target genome list was writen to GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:17,510] [INFO] Task started: fastANI
[2024-01-24 13:50:17,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ba11afb-15cd-40a9-ba1d-8a06e0c1a25a/GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna.gz --refList GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/target_genomes_gtdb.txt --output GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:26,178] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:26,193] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:26,193] [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_000591415.1	s__Cobetia crustatorum	100.0	1273	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	98.71	98.71	0.93	0.93	2	conclusive
GCF_009796845.1	s__Cobetia sp009796845	87.5046	1068	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000754225.1	s__Cobetia amphilecti	84.0065	894	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	96.77	95.09	0.91	0.86	19	-
GCF_001720485.1	s__Cobetia marina	83.9516	939	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	98.51	98.31	0.95	0.93	9	-
GCF_009363755.1	s__Halomonas sp009363755	78.1545	246	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	78.0851	203	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971685.1	s__Halomonas_B sp001971685	77.8818	249	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246875.1	s__Halomonas sp000246875	77.8549	218	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182195.1	s__Halomonas sp003182195	77.8522	205	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
GCA_003552795.1	s__Halomonas sp003552795	77.4011	160	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378505.1	s__Halomonas_C lutea	77.3776	200	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:26,195] [INFO] GTDB search result was written to GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:26,195] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:26,199] [INFO] DFAST_QC result json was written to GCF_000591415.1_Draft_genome_of_Cobetia_crustatorum_JO1_genomic.fna/dqc_result.json
[2024-01-24 13:50:26,200] [INFO] DFAST_QC completed!
[2024-01-24 13:50:26,200] [INFO] Total running time: 0h1m26s