[2024-01-24 14:14:20,153] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:20,157] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:20,157] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f1921a2-9b7b-465a-8f2e-c234a38e5c80/dqc_reference
[2024-01-24 14:14:21,476] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,477] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,477] [INFO] Running command: gunzip -c /var/lib/cwl/stg00fd7a3c-1d1e-4738-a7c2-03368e7757d6/GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna.gz | prodigal -d GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/cds.fna -a GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:35,546] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:35,546] [INFO] Task started: HMMsearch
[2024-01-24 14:14:35,547] [INFO] Running command: hmmsearch --tblout GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f1921a2-9b7b-465a-8f2e-c234a38e5c80/dqc_reference/reference_markers.hmm GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:35,905] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:35,906] [INFO] Found 6/6 markers.
[2024-01-24 14:14:35,957] [INFO] Query marker FASTA was written to GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/markers.fasta
[2024-01-24 14:14:35,958] [INFO] Task started: Blastn
[2024-01-24 14:14:35,958] [INFO] Running command: blastn -query GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f1921a2-9b7b-465a-8f2e-c234a38e5c80/dqc_reference/reference_markers.fasta -out GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:36,736] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:36,739] [INFO] Selected 12 target genomes.
[2024-01-24 14:14:36,739] [INFO] Target genome list was writen to GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 14:14:36,746] [INFO] Task started: fastANI
[2024-01-24 14:14:36,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg00fd7a3c-1d1e-4738-a7c2-03368e7757d6/GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna.gz --refList GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/target_genomes.txt --output GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:51,141] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:51,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f1921a2-9b7b-465a-8f2e-c234a38e5c80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:51,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f1921a2-9b7b-465a-8f2e-c234a38e5c80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:51,159] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:14:51,159] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:14:51,160] [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 mediterranei		GCA_900088415.1	689	689	type	True	100.0	1869	1871	95	inconclusive
Vibrio mediterranei	strain=NBRC 15635	GCA_001591125.1	689	689	type	True	99.9845	1837	1871	95	inconclusive
Vibrio barjaei	strain=3062	GCA_001639065.2	1676683	1676683	type	True	95.1694	1628	1871	95	inconclusive
Vibrio thalassae	strain=CECT8203	GCA_900089835.1	1243014	1243014	type	True	88.1522	1203	1871	95	below_threshold
Vibrio hangzhouensis	strain=CGMCC 1.7062	GCA_900107935.1	462991	462991	type	True	82.3586	824	1871	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	79.8698	355	1871	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.514	299	1871	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	79.4747	367	1871	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.4745	303	1871	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	79.4627	349	1871	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	79.2622	360	1871	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	78.8531	311	1871	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:51,162] [INFO] DFAST Taxonomy check result was written to GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 14:14:51,163] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:51,163] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:51,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f1921a2-9b7b-465a-8f2e-c234a38e5c80/dqc_reference/checkm_data
[2024-01-24 14:14:51,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:51,227] [INFO] Task started: CheckM
[2024-01-24 14:14:51,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/checkm_input GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/checkm_result
[2024-01-24 14:15:33,841] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:33,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:33,861] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:33,861] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:33,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/markers.fasta)
[2024-01-24 14:15:33,862] [INFO] Task started: Blastn
[2024-01-24 14:15:33,862] [INFO] Running command: blastn -query GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f1921a2-9b7b-465a-8f2e-c234a38e5c80/dqc_reference/reference_markers_gtdb.fasta -out GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:35,033] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:35,038] [INFO] Selected 11 target genomes.
[2024-01-24 14:15:35,039] [INFO] Target genome list was writen to GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:35,047] [INFO] Task started: fastANI
[2024-01-24 14:15:35,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg00fd7a3c-1d1e-4738-a7c2-03368e7757d6/GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna.gz --refList GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:46,892] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:46,901] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:46,901] [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_900088415.1	s__Vibrio mediterranei	100.0	1869	1871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.1582	98.19	97.23	0.91	0.86	13	conclusive
GCF_001639065.2	s__Vibrio barjaei	95.1582	1629	1871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.1582	N/A	N/A	N/A	N/A	1	conclusive
GCF_900089835.1	s__Vibrio thalassae	88.1387	1204	1871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.8081	N/A	N/A	N/A	N/A	1	-
GCA_000695745.1	s__Vibrio madracius	87.4248	560	1871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.8081	N/A	N/A	N/A	N/A	1	-
GCF_900107935.1	s__Vibrio hangzhouensis	82.3573	825	1871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000755385.1	s__Vibrio maritimus_B	82.03	777	1871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.88	95.88	0.85	0.85	2	-
GCA_000755425.1	s__Vibrio maritimus_A	81.9683	762	1871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003263775.1	s__Vibrio maritimus	81.9319	768	1871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003263785.1	s__Vibrio variabilis	81.6897	720	1871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176235.1	s__Vibrio orientalis	79.5101	354	1871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001695575.1	s__Vibrio europaeus	79.4842	364	1871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:46,903] [INFO] GTDB search result was written to GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:46,903] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:46,907] [INFO] DFAST_QC result json was written to GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka_genomic.fna/dqc_result.json
[2024-01-24 14:15:46,907] [INFO] DFAST_QC completed!
[2024-01-24 14:15:46,907] [INFO] Total running time: 0h1m27s