[2024-01-25 19:24:45,021] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:45,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:45,023] [INFO] DQC Reference Directory: /var/lib/cwl/stg361d2077-6add-4302-b8d8-daf13f059512/dqc_reference
[2024-01-25 19:24:48,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:48,895] [INFO] Task started: Prodigal
[2024-01-25 19:24:48,896] [INFO] Running command: gunzip -c /var/lib/cwl/stgb22f5f1b-6933-4a5c-817d-da7696f82e14/GCF_003716875.1_ASM371687v1_genomic.fna.gz | prodigal -d GCF_003716875.1_ASM371687v1_genomic.fna/cds.fna -a GCF_003716875.1_ASM371687v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:24:58,108] [INFO] Task succeeded: Prodigal
[2024-01-25 19:24:58,108] [INFO] Task started: HMMsearch
[2024-01-25 19:24:58,109] [INFO] Running command: hmmsearch --tblout GCF_003716875.1_ASM371687v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg361d2077-6add-4302-b8d8-daf13f059512/dqc_reference/reference_markers.hmm GCF_003716875.1_ASM371687v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:24:58,408] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:24:58,410] [INFO] Found 6/6 markers.
[2024-01-25 19:24:58,443] [INFO] Query marker FASTA was written to GCF_003716875.1_ASM371687v1_genomic.fna/markers.fasta
[2024-01-25 19:24:58,444] [INFO] Task started: Blastn
[2024-01-25 19:24:58,444] [INFO] Running command: blastn -query GCF_003716875.1_ASM371687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg361d2077-6add-4302-b8d8-daf13f059512/dqc_reference/reference_markers.fasta -out GCF_003716875.1_ASM371687v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:24:59,293] [INFO] Task succeeded: Blastn
[2024-01-25 19:24:59,295] [INFO] Selected 11 target genomes.
[2024-01-25 19:24:59,296] [INFO] Target genome list was writen to GCF_003716875.1_ASM371687v1_genomic.fna/target_genomes.txt
[2024-01-25 19:24:59,552] [INFO] Task started: fastANI
[2024-01-25 19:24:59,552] [INFO] Running command: fastANI --query /var/lib/cwl/stgb22f5f1b-6933-4a5c-817d-da7696f82e14/GCF_003716875.1_ASM371687v1_genomic.fna.gz --refList GCF_003716875.1_ASM371687v1_genomic.fna/target_genomes.txt --output GCF_003716875.1_ASM371687v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:10,927] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:10,927] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg361d2077-6add-4302-b8d8-daf13f059512/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:10,928] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg361d2077-6add-4302-b8d8-daf13f059512/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:10,935] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:25:10,936] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:25:10,936] [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 zhugei	strain=HBUAS61001	GCA_003716875.1	2479546	2479546	type	True	100.0	1335	1336	95	conclusive
Vibrio zhugei	strain=KCTC 62784	GCA_024347155.1	2479546	2479546	type	True	99.9963	1334	1336	95	conclusive
Vibrio palustris	strain=CECT 9027	GCA_024346995.1	1918946	1918946	type	True	82.6296	787	1336	95	below_threshold
Vibrio palustris	strain=CECT 9027	GCA_900162645.1	1918946	1918946	type	True	82.3746	769	1336	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	80.0142	349	1336	95	below_threshold
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	79.8306	138	1336	95	below_threshold
Vibrio tritonius	strain=JCM 16456	GCA_001547935.1	1435069	1435069	type	True	79.7763	332	1336	95	below_threshold
Vibrio hippocampi	strain=CECT 8226	GCA_921292975.1	654686	654686	type	True	79.4925	179	1336	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	79.2785	148	1336	95	below_threshold
Vibrio hangzhouensis	strain=CGMCC 1.7062	GCA_900107935.1	462991	462991	type	True	78.6272	153	1336	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	78.5668	182	1336	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:10,937] [INFO] DFAST Taxonomy check result was written to GCF_003716875.1_ASM371687v1_genomic.fna/tc_result.tsv
[2024-01-25 19:25:10,938] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:10,938] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:10,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg361d2077-6add-4302-b8d8-daf13f059512/dqc_reference/checkm_data
[2024-01-25 19:25:10,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:10,981] [INFO] Task started: CheckM
[2024-01-25 19:25:10,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003716875.1_ASM371687v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003716875.1_ASM371687v1_genomic.fna/checkm_input GCF_003716875.1_ASM371687v1_genomic.fna/checkm_result
[2024-01-25 19:25:41,530] [INFO] Task succeeded: CheckM
[2024-01-25 19:25:41,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:25:41,551] [INFO] ===== Completeness check finished =====
[2024-01-25 19:25:41,551] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:25:41,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003716875.1_ASM371687v1_genomic.fna/markers.fasta)
[2024-01-25 19:25:41,552] [INFO] Task started: Blastn
[2024-01-25 19:25:41,552] [INFO] Running command: blastn -query GCF_003716875.1_ASM371687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg361d2077-6add-4302-b8d8-daf13f059512/dqc_reference/reference_markers_gtdb.fasta -out GCF_003716875.1_ASM371687v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:42,722] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:42,727] [INFO] Selected 19 target genomes.
[2024-01-25 19:25:42,727] [INFO] Target genome list was writen to GCF_003716875.1_ASM371687v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:25:42,836] [INFO] Task started: fastANI
[2024-01-25 19:25:42,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgb22f5f1b-6933-4a5c-817d-da7696f82e14/GCF_003716875.1_ASM371687v1_genomic.fna.gz --refList GCF_003716875.1_ASM371687v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003716875.1_ASM371687v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:26:00,023] [INFO] Task succeeded: fastANI
[2024-01-25 19:26:00,039] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:26:00,040] [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_003716875.1	s__Vibrio zhugei	100.0	1335	1336	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_900162645.1	s__Vibrio palustris	82.3675	770	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015686695.1	s__Vibrio nitrifigilis	79.9985	340	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.79	98.79	0.95	0.95	2	-
GCF_002563795.1	s__Vibrio sp002563795	79.9629	198	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001547935.1	s__Vibrio tritonius	79.7588	335	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019226825.1	s__Vibrio sp004804295	79.6962	232	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.23	99.23	0.93	0.93	2	-
GCF_000354175.2	s__Vibrio alginolyticus	79.5747	192	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_000176155.1	s__Vibrio metschnikovii	79.4809	206	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.65	97.32	0.91	0.86	50	-
GCF_002163755.1	s__Vibrio campbellii	79.4431	177	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_009665255.1	s__Vibrio metoecus_B	79.2904	234	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.11	98.11	0.94	0.94	2	-
GCF_013041605.1	s__Vibrio plantisponsor	78.934	222	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.35	98.35	0.93	0.93	2	-
GCF_000189275.1	s__Vibrio sinaloensis_B	78.9201	165	1336	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	78.8484	228	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
GCA_001048675.1	s__Vibrio diabolicus	78.8095	185	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_000467125.1	s__Vibrio proteolyticus	78.7658	188	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.93	98.89	0.93	0.91	5	-
GCF_002741985.1	s__Vibrio rotiferianus	78.6283	177	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_900107935.1	s__Vibrio hangzhouensis	78.6267	152	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827885.1	s__Vibrio renipiscarius	78.533	181	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001591145.1	s__Vibrio harveyi	78.4388	156	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
--------------------------------------------------------------------------------
[2024-01-25 19:26:00,041] [INFO] GTDB search result was written to GCF_003716875.1_ASM371687v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:26:00,041] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:26:00,045] [INFO] DFAST_QC result json was written to GCF_003716875.1_ASM371687v1_genomic.fna/dqc_result.json
[2024-01-25 19:26:00,046] [INFO] DFAST_QC completed!
[2024-01-25 19:26:00,046] [INFO] Total running time: 0h1m15s