[2024-01-24 13:22:02,266] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:02,268] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:02,269] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d108b94-6bcd-477b-8d94-d68b2970c8b2/dqc_reference
[2024-01-24 13:22:03,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,635] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg8dc97d62-7e58-4fad-a3a6-ada0741fdf8d/GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/cds.fna -a GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:15,790] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:15,791] [INFO] Task started: HMMsearch
[2024-01-24 13:22:15,791] [INFO] Running command: hmmsearch --tblout GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d108b94-6bcd-477b-8d94-d68b2970c8b2/dqc_reference/reference_markers.hmm GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:16,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:16,123] [INFO] Found 6/6 markers.
[2024-01-24 13:22:16,162] [INFO] Query marker FASTA was written to GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:22:16,162] [INFO] Task started: Blastn
[2024-01-24 13:22:16,162] [INFO] Running command: blastn -query GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d108b94-6bcd-477b-8d94-d68b2970c8b2/dqc_reference/reference_markers.fasta -out GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:16,931] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:16,934] [INFO] Selected 10 target genomes.
[2024-01-24 13:22:16,935] [INFO] Target genome list was writen to GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:22:16,953] [INFO] Task started: fastANI
[2024-01-24 13:22:16,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dc97d62-7e58-4fad-a3a6-ada0741fdf8d/GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna.gz --refList GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:29,659] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:29,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d108b94-6bcd-477b-8d94-d68b2970c8b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:29,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d108b94-6bcd-477b-8d94-d68b2970c8b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:29,670] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:22:29,671] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:29,671] [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
Vibrio gazogenes	strain=DSM 21264	GCA_900129185.1	687	687	type	True	100.0	1518	1524	95	conclusive
Vibrio gazogenes	strain=PB1	GCA_023920225.1	687	687	type	True	99.9911	1519	1524	95	conclusive
Vibrio gazogenes	strain=ATCC 29988	GCA_024346915.1	687	687	type	True	99.9863	1521	1524	95	conclusive
Vibrio gazogenes	strain=type strain: CECT 5068	GCA_900163915.1	687	687	type	True	99.8907	1207	1524	95	conclusive
Vibrio spartinae	strain=CECT 9026	GCA_900149295.1	1918945	1918945	type	True	91.9305	1324	1524	95	below_threshold
Vibrio spartinae	strain=CECT 9026	GCA_024347135.1	1918945	1918945	type	True	91.9082	1317	1524	95	below_threshold
Vibrio rhizosphaerae	strain=LMG 23790	GCA_024347095.1	398736	398736	type	True	85.768	1177	1524	95	below_threshold
Vibrio mangrovi	strain=CECT 7927	GCA_024346955.1	474394	474394	type	True	81.3274	878	1524	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	78.2133	182	1524	95	below_threshold
Vibrio plantisponsor	strain=LMG 24470	GCA_013041605.1	664643	664643	type	True	78.1765	192	1524	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:29,672] [INFO] DFAST Taxonomy check result was written to GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:22:29,673] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:29,673] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:29,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d108b94-6bcd-477b-8d94-d68b2970c8b2/dqc_reference/checkm_data
[2024-01-24 13:22:29,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:29,725] [INFO] Task started: CheckM
[2024-01-24 13:22:29,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/checkm_input GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:23:12,466] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:12,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:12,488] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:12,488] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:12,489] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:23:12,489] [INFO] Task started: Blastn
[2024-01-24 13:23:12,489] [INFO] Running command: blastn -query GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d108b94-6bcd-477b-8d94-d68b2970c8b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:13,443] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:13,447] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:13,447] [INFO] Target genome list was writen to GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:13,460] [INFO] Task started: fastANI
[2024-01-24 13:23:13,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dc97d62-7e58-4fad-a3a6-ada0741fdf8d/GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna.gz --refList GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:24,243] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:24,257] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:24,257] [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_900129185.1	s__Vibrio gazogenes	100.0	1518	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.97	99.97	0.98	0.98	2	conclusive
GCF_002196515.1	s__Vibrio gazogenes_A	94.171	1343	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900149295.1	s__Vibrio spartinae	91.9341	1323	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.28	99.28	0.90	0.90	2	-
GCF_001506075.1	s__Vibrio sp001506075	88.2499	1211	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163965.1	s__Vibrio ruber	86.419	1206	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711805.1	s__Vibrio rhizosphaerae	85.7483	1149	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000740015.1	s__Vibrio diazotrophicus	78.2133	182	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
GCF_011064285.1	s__Vibrio ziniensis	78.1957	181	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013041605.1	s__Vibrio plantisponsor	78.1956	191	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.35	98.35	0.93	0.93	2	-
GCF_014596725.1	s__Vibrio sp014596725	78.0465	187	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.52	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:24,259] [INFO] GTDB search result was written to GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:24,259] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:24,262] [INFO] DFAST_QC result json was written to GCF_900129185.1_IMG-taxon_2582581274_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:23:24,262] [INFO] DFAST_QC completed!
[2024-01-24 13:23:24,262] [INFO] Total running time: 0h1m22s