[2024-01-24 12:31:57,237] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:57,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:57,241] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3638667-6592-4885-8af2-f66be7220640/dqc_reference
[2024-01-24 12:31:58,723] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:58,724] [INFO] Task started: Prodigal
[2024-01-24 12:31:58,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f5e137d-21a2-4db7-96cc-56234675953c/GCF_000967545.1_S2757_genomic.fna.gz | prodigal -d GCF_000967545.1_S2757_genomic.fna/cds.fna -a GCF_000967545.1_S2757_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:08,633] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:08,634] [INFO] Task started: HMMsearch
[2024-01-24 12:32:08,634] [INFO] Running command: hmmsearch --tblout GCF_000967545.1_S2757_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3638667-6592-4885-8af2-f66be7220640/dqc_reference/reference_markers.hmm GCF_000967545.1_S2757_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:08,947] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:08,949] [INFO] Found 6/6 markers.
[2024-01-24 12:32:09,000] [INFO] Query marker FASTA was written to GCF_000967545.1_S2757_genomic.fna/markers.fasta
[2024-01-24 12:32:09,001] [INFO] Task started: Blastn
[2024-01-24 12:32:09,001] [INFO] Running command: blastn -query GCF_000967545.1_S2757_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3638667-6592-4885-8af2-f66be7220640/dqc_reference/reference_markers.fasta -out GCF_000967545.1_S2757_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:09,850] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:09,854] [INFO] Selected 14 target genomes.
[2024-01-24 12:32:09,854] [INFO] Target genome list was writen to GCF_000967545.1_S2757_genomic.fna/target_genomes.txt
[2024-01-24 12:32:09,860] [INFO] Task started: fastANI
[2024-01-24 12:32:09,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f5e137d-21a2-4db7-96cc-56234675953c/GCF_000967545.1_S2757_genomic.fna.gz --refList GCF_000967545.1_S2757_genomic.fna/target_genomes.txt --output GCF_000967545.1_S2757_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:22,444] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:22,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3638667-6592-4885-8af2-f66be7220640/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:22,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3638667-6592-4885-8af2-f66be7220640/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:22,456] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:32:22,456] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:32:22,457] [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 tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	82.4783	834	1325	95	below_threshold
Vibrio bivalvicida	strain=605	GCA_001399455.2	1276888	1276888	type	True	82.4361	785	1325	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	82.3977	807	1325	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	82.3817	831	1325	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	81.6112	641	1325	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	81.5249	643	1325	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	81.2625	635	1325	95	below_threshold
Vibrio pacinii	strain=DSM 19139	GCA_000711795.1	170674	170674	type	True	80.85	597	1325	95	below_threshold
Vibrio salilacus	strain=DSG-S6	GCA_002811245.1	1323749	1323749	type	True	80.7491	544	1325	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.1997	400	1325	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.049	389	1325	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.0316	390	1325	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.9521	379	1325	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	79.9202	366	1325	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:22,458] [INFO] DFAST Taxonomy check result was written to GCF_000967545.1_S2757_genomic.fna/tc_result.tsv
[2024-01-24 12:32:22,459] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:22,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:22,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3638667-6592-4885-8af2-f66be7220640/dqc_reference/checkm_data
[2024-01-24 12:32:22,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:22,501] [INFO] Task started: CheckM
[2024-01-24 12:32:22,502] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000967545.1_S2757_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000967545.1_S2757_genomic.fna/checkm_input GCF_000967545.1_S2757_genomic.fna/checkm_result
[2024-01-24 12:32:57,792] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:57,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:57,818] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:57,819] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:57,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000967545.1_S2757_genomic.fna/markers.fasta)
[2024-01-24 12:32:57,820] [INFO] Task started: Blastn
[2024-01-24 12:32:57,820] [INFO] Running command: blastn -query GCF_000967545.1_S2757_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3638667-6592-4885-8af2-f66be7220640/dqc_reference/reference_markers_gtdb.fasta -out GCF_000967545.1_S2757_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:59,047] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:59,053] [INFO] Selected 12 target genomes.
[2024-01-24 12:32:59,054] [INFO] Target genome list was writen to GCF_000967545.1_S2757_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:59,064] [INFO] Task started: fastANI
[2024-01-24 12:32:59,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f5e137d-21a2-4db7-96cc-56234675953c/GCF_000967545.1_S2757_genomic.fna.gz --refList GCF_000967545.1_S2757_genomic.fna/target_genomes_gtdb.txt --output GCF_000967545.1_S2757_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:09,738] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:09,748] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:09,749] [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_000967545.1	s__Vibrio galatheae	100.0	1322	1325	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_000772105.1	s__Vibrio tubiashii	82.4781	834	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_001399455.2	s__Vibrio bivalvicida	82.4361	785	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.39	98.39	0.93	0.93	2	-
GCF_001695575.1	s__Vibrio europaeus	82.3889	830	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_000775715.1	s__Vibrio tubiashii_A	81.8692	710	1325	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	81.6003	642	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004551525.1	s__Vibrio ouci	81.5444	648	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013369335.1	s__Vibrio sp013369335	81.319	595	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970385.1	s__Vibrio aquaticus	81.2667	635	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000808535.1	s__Vibrio sinaloensis	81.1955	560	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_000711795.1	s__Vibrio pacinii	80.85	597	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.5386	N/A	N/A	N/A	N/A	1	-
GCF_002811245.1	s__Vibrio salilacus	80.7671	542	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.5386	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:09,751] [INFO] GTDB search result was written to GCF_000967545.1_S2757_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:09,752] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:09,758] [INFO] DFAST_QC result json was written to GCF_000967545.1_S2757_genomic.fna/dqc_result.json
[2024-01-24 12:33:09,758] [INFO] DFAST_QC completed!
[2024-01-24 12:33:09,759] [INFO] Total running time: 0h1m13s