[2024-01-24 13:48:59,752] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg85dbdec5-1fec-4174-be30-830c4bd1f4d3/dqc_reference
[2024-01-24 13:49:01,108] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,109] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,110] [INFO] Running command: gunzip -c /var/lib/cwl/stg839bb028-5105-4410-87de-a2a71abda830/GCF_900452855.1_51765_A01_genomic.fna.gz | prodigal -d GCF_900452855.1_51765_A01_genomic.fna/cds.fna -a GCF_900452855.1_51765_A01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:13,639] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:13,639] [INFO] Task started: HMMsearch
[2024-01-24 13:49:13,639] [INFO] Running command: hmmsearch --tblout GCF_900452855.1_51765_A01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85dbdec5-1fec-4174-be30-830c4bd1f4d3/dqc_reference/reference_markers.hmm GCF_900452855.1_51765_A01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:13,972] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:13,973] [INFO] Found 6/6 markers.
[2024-01-24 13:49:14,020] [INFO] Query marker FASTA was written to GCF_900452855.1_51765_A01_genomic.fna/markers.fasta
[2024-01-24 13:49:14,020] [INFO] Task started: Blastn
[2024-01-24 13:49:14,020] [INFO] Running command: blastn -query GCF_900452855.1_51765_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stg85dbdec5-1fec-4174-be30-830c4bd1f4d3/dqc_reference/reference_markers.fasta -out GCF_900452855.1_51765_A01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:14,876] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:14,880] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:14,881] [INFO] Target genome list was writen to GCF_900452855.1_51765_A01_genomic.fna/target_genomes.txt
[2024-01-24 13:49:14,886] [INFO] Task started: fastANI
[2024-01-24 13:49:14,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg839bb028-5105-4410-87de-a2a71abda830/GCF_900452855.1_51765_A01_genomic.fna.gz --refList GCF_900452855.1_51765_A01_genomic.fna/target_genomes.txt --output GCF_900452855.1_51765_A01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:32,761] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:32,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85dbdec5-1fec-4174-be30-830c4bd1f4d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:32,762] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85dbdec5-1fec-4174-be30-830c4bd1f4d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:32,776] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:49:32,776] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:49:32,777] [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 anguillarum	strain=NCTC12159	GCA_900452855.1	55601	55601	type	True	100.0	1465	1468	95	inconclusive
Vibrio anguillarum	strain=DSM 21597	GCA_001989995.2	55601	55601	type	True	99.9001	1272	1468	95	inconclusive
Vibrio qinghaiensis	strain=Q67	GCA_002257545.1	2025808	2025808	type	True	95.9655	1120	1468	95	inconclusive
Vibrio aestuarianus subsp. francensis	strain=02/041	GCA_012395215.1	1443279	28171	type	True	82.3851	780	1468	95	below_threshold
Vibrio aestuarianus subsp. cardii	strain=12/122 3T3	GCA_011090275.1	2807650	28171	type	True	82.3287	744	1468	95	below_threshold
Vibrio aestuarianus	strain=LMG 7909	GCA_012395185.1	28171	28171	type	True	81.8922	733	1468	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.6879	319	1468	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	79.6466	371	1468	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	79.574	460	1468	95	below_threshold
Vibrio cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	79.5494	340	1468	95	below_threshold
Vibrio cidicii	strain=2756-81	GCA_009763805.1	1763883	1763883	type	True	79.5287	378	1468	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	79.4695	472	1468	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	79.463	375	1468	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	79.3257	343	1468	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	79.1568	385	1468	95	below_threshold
Vibrio cholerae	strain=ATCC 14035	GCA_000621645.1	666	666	type	True	79.0331	468	1468	95	below_threshold
Vibrio paracholerae	strain=EDC-792	GCA_017169525.1	650003	650003	type	True	78.8597	439	1468	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:32,778] [INFO] DFAST Taxonomy check result was written to GCF_900452855.1_51765_A01_genomic.fna/tc_result.tsv
[2024-01-24 13:49:32,779] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:32,779] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:32,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85dbdec5-1fec-4174-be30-830c4bd1f4d3/dqc_reference/checkm_data
[2024-01-24 13:49:32,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:32,825] [INFO] Task started: CheckM
[2024-01-24 13:49:32,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900452855.1_51765_A01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900452855.1_51765_A01_genomic.fna/checkm_input GCF_900452855.1_51765_A01_genomic.fna/checkm_result
[2024-01-24 13:50:14,539] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:14,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:14,566] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:14,567] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:14,567] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900452855.1_51765_A01_genomic.fna/markers.fasta)
[2024-01-24 13:50:14,568] [INFO] Task started: Blastn
[2024-01-24 13:50:14,568] [INFO] Running command: blastn -query GCF_900452855.1_51765_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stg85dbdec5-1fec-4174-be30-830c4bd1f4d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900452855.1_51765_A01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:15,781] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:15,785] [INFO] Selected 18 target genomes.
[2024-01-24 13:50:15,785] [INFO] Target genome list was writen to GCF_900452855.1_51765_A01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:15,799] [INFO] Task started: fastANI
[2024-01-24 13:50:15,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg839bb028-5105-4410-87de-a2a71abda830/GCF_900452855.1_51765_A01_genomic.fna.gz --refList GCF_900452855.1_51765_A01_genomic.fna/target_genomes_gtdb.txt --output GCF_900452855.1_51765_A01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:32,354] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:32,371] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:32,371] [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_001989995.2	s__Vibrio anguillarum	99.9001	1272	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.39	98.01	0.89	0.80	121	conclusive
GCA_000257205.1	s__Vibrio ordalii	96.1525	942	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.90	98.90	0.96	0.96	2	-
GCF_012395185.1	s__Vibrio aestuarianus	81.883	734	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.70	96.75	0.86	0.80	14	-
GCA_015767675.1	s__Vibrio sp000960595	80.3077	402	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.38	0.94	0.90	8	-
GCF_001471585.2	s__Vibrio cholerae	79.781	484	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.72	95.09	0.90	0.82	1544	-
GCF_900460245.1	s__Vibrio fluvialis	79.6705	431	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
GCF_011064285.1	s__Vibrio ziniensis	79.6118	373	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363415.1	s__Vibrio aquimaris	79.57	230	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009763805.1	s__Vibrio cidicii	79.5408	380	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.20	97.77	0.90	0.87	8	-
GCF_000354175.2	s__Vibrio alginolyticus	79.5392	362	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_000740015.1	s__Vibrio diazotrophicus	79.4591	377	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
GCF_009938225.1	s__Vibrio ponticus	79.348	323	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.69	97.39	0.92	0.85	3	-
GCF_000764325.1	s__Vibrio navarrensis	79.2887	380	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.19	97.06	0.93	0.87	22	-
GCF_004551525.1	s__Vibrio ouci	79.0739	356	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596725.1	s__Vibrio sp014596725	78.893	382	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.52	0.94	0.94	2	-
GCF_003350295.1	s__Vibrio tetraodonis	78.6543	232	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.28	95.28	0.88	0.88	2	-
GCF_007990935.1	s__Vibrio sagamiensis	78.524	235	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.95	99.91	0.97	0.96	3	-
GCF_900233005.1	s__Vibrio tapetis	78.4502	289	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:32,373] [INFO] GTDB search result was written to GCF_900452855.1_51765_A01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:32,374] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:32,380] [INFO] DFAST_QC result json was written to GCF_900452855.1_51765_A01_genomic.fna/dqc_result.json
[2024-01-24 13:50:32,380] [INFO] DFAST_QC completed!
[2024-01-24 13:50:32,381] [INFO] Total running time: 0h1m33s