[2024-01-25 18:20:20,683] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:20:20,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:20:20,685] [INFO] DQC Reference Directory: /var/lib/cwl/stg05b8382f-0346-41ce-b031-ef2255729f68/dqc_reference
[2024-01-25 18:20:21,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:20:21,836] [INFO] Task started: Prodigal
[2024-01-25 18:20:21,837] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f4d2765-5dbc-4acc-9f82-50a97aa51626/GCF_011064285.1_ASM1106428v1_genomic.fna.gz | prodigal -d GCF_011064285.1_ASM1106428v1_genomic.fna/cds.fna -a GCF_011064285.1_ASM1106428v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:20:31,308] [INFO] Task succeeded: Prodigal
[2024-01-25 18:20:31,309] [INFO] Task started: HMMsearch
[2024-01-25 18:20:31,309] [INFO] Running command: hmmsearch --tblout GCF_011064285.1_ASM1106428v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05b8382f-0346-41ce-b031-ef2255729f68/dqc_reference/reference_markers.hmm GCF_011064285.1_ASM1106428v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:20:31,557] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:20:31,559] [INFO] Found 6/6 markers.
[2024-01-25 18:20:31,597] [INFO] Query marker FASTA was written to GCF_011064285.1_ASM1106428v1_genomic.fna/markers.fasta
[2024-01-25 18:20:31,598] [INFO] Task started: Blastn
[2024-01-25 18:20:31,598] [INFO] Running command: blastn -query GCF_011064285.1_ASM1106428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05b8382f-0346-41ce-b031-ef2255729f68/dqc_reference/reference_markers.fasta -out GCF_011064285.1_ASM1106428v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:20:32,374] [INFO] Task succeeded: Blastn
[2024-01-25 18:20:32,378] [INFO] Selected 18 target genomes.
[2024-01-25 18:20:32,378] [INFO] Target genome list was writen to GCF_011064285.1_ASM1106428v1_genomic.fna/target_genomes.txt
[2024-01-25 18:20:32,384] [INFO] Task started: fastANI
[2024-01-25 18:20:32,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f4d2765-5dbc-4acc-9f82-50a97aa51626/GCF_011064285.1_ASM1106428v1_genomic.fna.gz --refList GCF_011064285.1_ASM1106428v1_genomic.fna/target_genomes.txt --output GCF_011064285.1_ASM1106428v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:20:50,614] [INFO] Task succeeded: fastANI
[2024-01-25 18:20:50,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05b8382f-0346-41ce-b031-ef2255729f68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:20:50,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05b8382f-0346-41ce-b031-ef2255729f68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:20:50,626] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:20:50,626] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:20:50,626] [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 ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	100.0	1550	1550	95	conclusive
Vibrio plantisponsor	strain=LMG 24470	GCA_013041605.1	664643	664643	type	True	86.3337	1070	1550	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	85.4259	1076	1550	95	below_threshold
Vibrio fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	80.0813	500	1550	95	below_threshold
Vibrio fluvialis	strain=NCTC11327	GCA_900460245.1	676	676	type	True	79.9334	505	1550	95	below_threshold
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	79.9216	395	1550	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	79.8485	335	1550	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.7792	310	1550	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	79.7752	394	1550	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.7606	352	1550	95	below_threshold
Vibrio furnissii	strain=FDAARGOS_777	GCA_006364355.1	29494	29494	type	True	79.7098	492	1550	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	79.4806	367	1550	95	below_threshold
Vibrio furnissii	strain=CIP 102972	GCA_000176175.1	29494	29494	type	True	79.4471	472	1550	95	below_threshold
Vibrio rotiferianus	strain=CAIM 577	GCA_002741985.1	190895	190895	type	True	79.3827	364	1550	95	below_threshold
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001011015.1	670	670	type	True	79.2109	388	1550	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	79.1951	384	1550	95	below_threshold
Vibrio owensii	strain=DY05	GCA_000817815.1	696485	696485	type	True	79.1359	390	1550	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	78.9833	323	1550	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:20:50,628] [INFO] DFAST Taxonomy check result was written to GCF_011064285.1_ASM1106428v1_genomic.fna/tc_result.tsv
[2024-01-25 18:20:50,629] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:20:50,630] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:20:50,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05b8382f-0346-41ce-b031-ef2255729f68/dqc_reference/checkm_data
[2024-01-25 18:20:50,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:20:50,692] [INFO] Task started: CheckM
[2024-01-25 18:20:50,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011064285.1_ASM1106428v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011064285.1_ASM1106428v1_genomic.fna/checkm_input GCF_011064285.1_ASM1106428v1_genomic.fna/checkm_result
[2024-01-25 18:21:22,667] [INFO] Task succeeded: CheckM
[2024-01-25 18:21:22,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:21:22,689] [INFO] ===== Completeness check finished =====
[2024-01-25 18:21:22,689] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:21:22,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011064285.1_ASM1106428v1_genomic.fna/markers.fasta)
[2024-01-25 18:21:22,690] [INFO] Task started: Blastn
[2024-01-25 18:21:22,690] [INFO] Running command: blastn -query GCF_011064285.1_ASM1106428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05b8382f-0346-41ce-b031-ef2255729f68/dqc_reference/reference_markers_gtdb.fasta -out GCF_011064285.1_ASM1106428v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:21:23,908] [INFO] Task succeeded: Blastn
[2024-01-25 18:21:23,912] [INFO] Selected 9 target genomes.
[2024-01-25 18:21:23,912] [INFO] Target genome list was writen to GCF_011064285.1_ASM1106428v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:21:23,917] [INFO] Task started: fastANI
[2024-01-25 18:21:23,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f4d2765-5dbc-4acc-9f82-50a97aa51626/GCF_011064285.1_ASM1106428v1_genomic.fna.gz --refList GCF_011064285.1_ASM1106428v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011064285.1_ASM1106428v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:21:34,101] [INFO] Task succeeded: fastANI
[2024-01-25 18:21:34,108] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:21:34,108] [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_011064285.1	s__Vibrio ziniensis	100.0	1550	1550	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_013041605.1	s__Vibrio plantisponsor	86.3422	1069	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.35	98.35	0.93	0.93	2	-
GCF_000740015.1	s__Vibrio diazotrophicus	85.417	1077	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
GCF_014596725.1	s__Vibrio sp014596725	84.687	1058	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.52	0.94	0.94	2	-
GCF_900460245.1	s__Vibrio fluvialis	79.997	505	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
GCF_009938165.1	s__Vibrio taketomensis	79.8414	342	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_001274785.1	s__Vibrio hepatarius	79.4651	356	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
GCF_000176175.1	s__Vibrio furnissii	79.422	474	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.58	97.97	0.95	0.91	12	-
GCF_000817815.1	s__Vibrio owensii	79.1474	389	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
--------------------------------------------------------------------------------
[2024-01-25 18:21:34,109] [INFO] GTDB search result was written to GCF_011064285.1_ASM1106428v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:21:34,110] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:21:34,112] [INFO] DFAST_QC result json was written to GCF_011064285.1_ASM1106428v1_genomic.fna/dqc_result.json
[2024-01-25 18:21:34,113] [INFO] DFAST_QC completed!
[2024-01-25 18:21:34,113] [INFO] Total running time: 0h1m13s