[2024-01-24 13:40:45,868] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:45,871] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:45,871] [INFO] DQC Reference Directory: /var/lib/cwl/stga13643d9-aa47-4a41-aaf1-6635fe6f55f2/dqc_reference
[2024-01-24 13:40:47,167] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,168] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,168] [INFO] Running command: gunzip -c /var/lib/cwl/stg253f2ee5-c256-4010-b301-48456acae264/GCF_024529975.1_ASM2452997v1_genomic.fna.gz | prodigal -d GCF_024529975.1_ASM2452997v1_genomic.fna/cds.fna -a GCF_024529975.1_ASM2452997v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:01,586] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:01,586] [INFO] Task started: HMMsearch
[2024-01-24 13:41:01,587] [INFO] Running command: hmmsearch --tblout GCF_024529975.1_ASM2452997v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga13643d9-aa47-4a41-aaf1-6635fe6f55f2/dqc_reference/reference_markers.hmm GCF_024529975.1_ASM2452997v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:01,910] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:01,912] [INFO] Found 6/6 markers.
[2024-01-24 13:41:01,961] [INFO] Query marker FASTA was written to GCF_024529975.1_ASM2452997v1_genomic.fna/markers.fasta
[2024-01-24 13:41:01,962] [INFO] Task started: Blastn
[2024-01-24 13:41:01,962] [INFO] Running command: blastn -query GCF_024529975.1_ASM2452997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga13643d9-aa47-4a41-aaf1-6635fe6f55f2/dqc_reference/reference_markers.fasta -out GCF_024529975.1_ASM2452997v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:02,692] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:02,696] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:02,697] [INFO] Target genome list was writen to GCF_024529975.1_ASM2452997v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:02,714] [INFO] Task started: fastANI
[2024-01-24 13:41:02,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg253f2ee5-c256-4010-b301-48456acae264/GCF_024529975.1_ASM2452997v1_genomic.fna.gz --refList GCF_024529975.1_ASM2452997v1_genomic.fna/target_genomes.txt --output GCF_024529975.1_ASM2452997v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:15,975] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:15,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga13643d9-aa47-4a41-aaf1-6635fe6f55f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:15,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga13643d9-aa47-4a41-aaf1-6635fe6f55f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:15,989] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:15,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:15,989] [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 quintilis	strain=CECT 7734	GCA_024529975.1	1117707	1117707	type	True	100.0	1946	1949	95	conclusive
Vibrio quintilis		GCA_900143745.1	1117707	1117707	type	True	99.945	1830	1949	95	conclusive
Vibrio aerogenes	strain=LMG 19650	GCA_024346755.1	92172	92172	type	True	83.5554	1339	1949	95	below_threshold
Vibrio aerogenes	strain=CECT 7868	GCA_900130105.1	92172	92172	type	True	83.5076	1307	1949	95	below_threshold
Vibrio zhugei	strain=KCTC 62784	GCA_024347155.1	2479546	2479546	type	True	79.569	139	1949	95	below_threshold
Vibrio spartinae	strain=CECT 9026	GCA_024347135.1	1918945	1918945	type	True	78.715	295	1949	95	below_threshold
Vibrio rhizosphaerae	strain=LMG 23790	GCA_024347095.1	398736	398736	type	True	78.6063	303	1949	95	below_threshold
Vibrio mangrovi	strain=CECT 7927	GCA_024346955.1	474394	474394	type	True	78.4136	377	1949	95	below_threshold
Vibrio spartinae	strain=CECT 9026	GCA_900149295.1	1918945	1918945	type	True	78.1369	292	1949	95	below_threshold
Vibrio ruber	strain=CECT 7878	GCA_900163965.1	184755	184755	type	True	78.0416	307	1949	95	below_threshold
Vibrio mangrovi	strain=CECT 7927	GCA_900184095.1	474394	474394	type	True	78.0384	365	1949	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	78.0318	130	1949	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:15,991] [INFO] DFAST Taxonomy check result was written to GCF_024529975.1_ASM2452997v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:15,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:15,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:15,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga13643d9-aa47-4a41-aaf1-6635fe6f55f2/dqc_reference/checkm_data
[2024-01-24 13:41:15,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:16,056] [INFO] Task started: CheckM
[2024-01-24 13:41:16,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024529975.1_ASM2452997v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024529975.1_ASM2452997v1_genomic.fna/checkm_input GCF_024529975.1_ASM2452997v1_genomic.fna/checkm_result
[2024-01-24 13:42:03,708] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:03,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:03,732] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:03,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:03,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024529975.1_ASM2452997v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:03,733] [INFO] Task started: Blastn
[2024-01-24 13:42:03,733] [INFO] Running command: blastn -query GCF_024529975.1_ASM2452997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga13643d9-aa47-4a41-aaf1-6635fe6f55f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_024529975.1_ASM2452997v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:04,817] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:04,821] [INFO] Selected 17 target genomes.
[2024-01-24 13:42:04,821] [INFO] Target genome list was writen to GCF_024529975.1_ASM2452997v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:04,889] [INFO] Task started: fastANI
[2024-01-24 13:42:04,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg253f2ee5-c256-4010-b301-48456acae264/GCF_024529975.1_ASM2452997v1_genomic.fna.gz --refList GCF_024529975.1_ASM2452997v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024529975.1_ASM2452997v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:20,048] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:20,074] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:20,074] [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_900143745.1	s__Vibrio quintilis	99.945	1830	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900130105.1	s__Vibrio aerogenes	83.5011	1308	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003716875.1	s__Vibrio zhugei	79.4398	134	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772105.1	s__Vibrio tubiashii	79.0836	139	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_011064285.1	s__Vibrio ziniensis	78.8816	174	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002196515.1	s__Vibrio gazogenes_A	78.6077	299	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003144035.1	s__Vibrio sp003144035	78.315	161	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006124995.1	s__Vibrio sp006124995	78.2921	127	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000467125.1	s__Vibrio proteolyticus	78.2887	159	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.93	98.89	0.93	0.91	5	-
GCF_900129185.1	s__Vibrio gazogenes	78.2571	283	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.97	99.97	0.98	0.98	2	-
GCF_001506075.1	s__Vibrio sp001506075	78.2238	301	1949	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	78.1953	285	1949	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	78.1224	293	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.28	99.28	0.90	0.90	2	-
GCF_900184095.1	s__Vibrio mangrovi	78.0387	365	1949	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	77.9964	312	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013114595.1	s__Vibrio sp013114595	77.3357	135	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972145.1	s__Photobacterium halotolerans_A	77.2221	112	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:20,076] [INFO] GTDB search result was written to GCF_024529975.1_ASM2452997v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:20,077] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:20,081] [INFO] DFAST_QC result json was written to GCF_024529975.1_ASM2452997v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:20,081] [INFO] DFAST_QC completed!
[2024-01-24 13:42:20,081] [INFO] Total running time: 0h1m34s