[2024-01-24 11:20:03,887] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:03,888] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:03,889] [INFO] DQC Reference Directory: /var/lib/cwl/stg5989ff3c-6437-4cb7-be9b-1942c3e4749f/dqc_reference
[2024-01-24 11:20:05,071] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:05,072] [INFO] Task started: Prodigal
[2024-01-24 11:20:05,072] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd440b1c-8a99-452e-b51c-f5a53b61836e/GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/cds.fna -a GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:14,913] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:14,914] [INFO] Task started: HMMsearch
[2024-01-24 11:20:14,914] [INFO] Running command: hmmsearch --tblout GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5989ff3c-6437-4cb7-be9b-1942c3e4749f/dqc_reference/reference_markers.hmm GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:15,117] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:15,118] [INFO] Found 6/6 markers.
[2024-01-24 11:20:15,148] [INFO] Query marker FASTA was written to GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:20:15,149] [INFO] Task started: Blastn
[2024-01-24 11:20:15,149] [INFO] Running command: blastn -query GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5989ff3c-6437-4cb7-be9b-1942c3e4749f/dqc_reference/reference_markers.fasta -out GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:16,131] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:16,134] [INFO] Selected 10 target genomes.
[2024-01-24 11:20:16,134] [INFO] Target genome list was writen to GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:20:16,138] [INFO] Task started: fastANI
[2024-01-24 11:20:16,138] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd440b1c-8a99-452e-b51c-f5a53b61836e/GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna.gz --refList GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:25,685] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:25,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5989ff3c-6437-4cb7-be9b-1942c3e4749f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:25,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5989ff3c-6437-4cb7-be9b-1942c3e4749f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:25,695] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:25,695] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:25,695] [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
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	100.0	1179	1182	95	conclusive
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	92.1526	992	1182	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	92.1028	954	1182	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	89.0077	879	1182	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	87.3081	894	1182	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	84.7987	822	1182	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	83.545	777	1182	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	83.0278	728	1182	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	82.1793	706	1182	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	81.723	683	1182	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:25,697] [INFO] DFAST Taxonomy check result was written to GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:20:25,698] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:25,698] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:25,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5989ff3c-6437-4cb7-be9b-1942c3e4749f/dqc_reference/checkm_data
[2024-01-24 11:20:25,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:25,734] [INFO] Task started: CheckM
[2024-01-24 11:20:25,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/checkm_input GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:20:56,893] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:56,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:56,910] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:56,910] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:56,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:20:56,911] [INFO] Task started: Blastn
[2024-01-24 11:20:56,911] [INFO] Running command: blastn -query GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5989ff3c-6437-4cb7-be9b-1942c3e4749f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:58,775] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:58,778] [INFO] Selected 6 target genomes.
[2024-01-24 11:20:58,778] [INFO] Target genome list was writen to GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:58,783] [INFO] Task started: fastANI
[2024-01-24 11:20:58,783] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd440b1c-8a99-452e-b51c-f5a53b61836e/GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna.gz --refList GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:04,452] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:04,459] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:04,459] [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_900116405.1	s__Halomonas saccharevitans	100.0	1179	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003056305.1	s__Halomonas denitrificans	92.1526	992	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005780185.1	s__Halomonas urmiana	92.1028	954	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	91.0387	936	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886615.1	s__Halomonas aestuarii	89.0281	877	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363555.1	s__Halomonas ventosae	87.3225	893	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:04,460] [INFO] GTDB search result was written to GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:04,461] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:04,464] [INFO] DFAST_QC result json was written to GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:21:04,464] [INFO] DFAST_QC completed!
[2024-01-24 11:21:04,464] [INFO] Total running time: 0h1m1s