[2024-01-24 11:34:38,682] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:38,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:38,686] [INFO] DQC Reference Directory: /var/lib/cwl/stg93205da6-f203-40e4-ab90-f2602e55ca7f/dqc_reference
[2024-01-24 11:34:41,320] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:41,324] [INFO] Task started: Prodigal
[2024-01-24 11:34:41,324] [INFO] Running command: gunzip -c /var/lib/cwl/stgc28d0c92-5974-444b-9fa0-d02e71fc1952/GCF_013416885.1_ASM1341688v1_genomic.fna.gz | prodigal -d GCF_013416885.1_ASM1341688v1_genomic.fna/cds.fna -a GCF_013416885.1_ASM1341688v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:51,962] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:51,963] [INFO] Task started: HMMsearch
[2024-01-24 11:34:51,963] [INFO] Running command: hmmsearch --tblout GCF_013416885.1_ASM1341688v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93205da6-f203-40e4-ab90-f2602e55ca7f/dqc_reference/reference_markers.hmm GCF_013416885.1_ASM1341688v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:52,320] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:52,322] [INFO] Found 6/6 markers.
[2024-01-24 11:34:52,361] [INFO] Query marker FASTA was written to GCF_013416885.1_ASM1341688v1_genomic.fna/markers.fasta
[2024-01-24 11:34:52,362] [INFO] Task started: Blastn
[2024-01-24 11:34:52,362] [INFO] Running command: blastn -query GCF_013416885.1_ASM1341688v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93205da6-f203-40e4-ab90-f2602e55ca7f/dqc_reference/reference_markers.fasta -out GCF_013416885.1_ASM1341688v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:53,243] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:53,245] [INFO] Selected 17 target genomes.
[2024-01-24 11:34:53,246] [INFO] Target genome list was writen to GCF_013416885.1_ASM1341688v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:53,277] [INFO] Task started: fastANI
[2024-01-24 11:34:53,277] [INFO] Running command: fastANI --query /var/lib/cwl/stgc28d0c92-5974-444b-9fa0-d02e71fc1952/GCF_013416885.1_ASM1341688v1_genomic.fna.gz --refList GCF_013416885.1_ASM1341688v1_genomic.fna/target_genomes.txt --output GCF_013416885.1_ASM1341688v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:13,220] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:13,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93205da6-f203-40e4-ab90-f2602e55ca7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:13,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93205da6-f203-40e4-ab90-f2602e55ca7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:13,235] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:35:13,235] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:13,235] [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 gallaecicus	strain=VB 8.9	GCA_013416885.1	552386	552386	type	True	100.0	1638	1640	95	conclusive
Vibrio gallaecicus	strain=DSM 23502	GCA_005281825.1	552386	552386	type	True	100.0	1638	1640	95	conclusive
Vibrio gallaecicus	strain=CECT 7244	GCA_024347495.1	552386	552386	type	True	99.998	1638	1640	95	conclusive
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	83.1315	775	1640	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	83.1286	740	1640	95	below_threshold
Vibrio bathopelagicus	strain=Sal10	GCA_014879975.1	2777577	2777577	type	True	83.0132	777	1640	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	82.9822	779	1640	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	82.9783	773	1640	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	82.9277	767	1640	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_900089765.1	1194427	1194427	type	True	82.811	710	1640	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	82.7577	746	1640	95	below_threshold
Vibrio cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	82.7571	760	1640	95	below_threshold
Vibrio echinoideorum	strain=NFH.MB010	GCA_004764665.1	2100116	2100116	type	True	82.755	771	1640	95	below_threshold
Vibrio kanaloae	strain=LMG 20539	GCA_024347535.1	170673	170673	type	True	82.6778	724	1640	95	below_threshold
Vibrio kanaloae	strain=CCUG 56968	GCA_008801285.1	170673	170673	type	True	82.5976	721	1640	95	below_threshold
Vibrio profundi	strain=TP187	GCA_005281835.1	1774960	1774960	type	True	81.7307	658	1640	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	81.4086	645	1640	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:13,237] [INFO] DFAST Taxonomy check result was written to GCF_013416885.1_ASM1341688v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:13,237] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:13,237] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:13,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93205da6-f203-40e4-ab90-f2602e55ca7f/dqc_reference/checkm_data
[2024-01-24 11:35:13,239] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:13,298] [INFO] Task started: CheckM
[2024-01-24 11:35:13,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013416885.1_ASM1341688v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013416885.1_ASM1341688v1_genomic.fna/checkm_input GCF_013416885.1_ASM1341688v1_genomic.fna/checkm_result
[2024-01-24 11:35:49,536] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:49,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:49,552] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:49,553] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:49,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013416885.1_ASM1341688v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:49,554] [INFO] Task started: Blastn
[2024-01-24 11:35:49,554] [INFO] Running command: blastn -query GCF_013416885.1_ASM1341688v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93205da6-f203-40e4-ab90-f2602e55ca7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013416885.1_ASM1341688v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:50,773] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:50,776] [INFO] Selected 21 target genomes.
[2024-01-24 11:35:50,776] [INFO] Target genome list was writen to GCF_013416885.1_ASM1341688v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:50,790] [INFO] Task started: fastANI
[2024-01-24 11:35:50,790] [INFO] Running command: fastANI --query /var/lib/cwl/stgc28d0c92-5974-444b-9fa0-d02e71fc1952/GCF_013416885.1_ASM1341688v1_genomic.fna.gz --refList GCF_013416885.1_ASM1341688v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013416885.1_ASM1341688v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:11,970] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:11,990] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:11,990] [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_005281825.1	s__Vibrio gallaecicus	100.0	1638	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_013114625.1	s__Vibrio sp013114625	91.3722	1382	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557875.1	s__Vibrio splendidus_F	83.1047	747	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_014878155.1	s__Vibrio lentus	83.0752	763	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.56	0.86	0.83	91	-
GCF_006333845.1	s__Vibrio tasmaniensis	83.0728	715	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	-
GCF_002875945.1	s__Vibrio lentus_A	83.0466	755	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014879975.1	s__Vibrio bathopelagicus	83.0136	777	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858795.1	s__Vibrio sp007858795	82.9622	752	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156525.1	s__Vibrio celticus	82.9104	749	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	99.99	99.99	1.00	1.00	2	-
GCF_013394185.1	s__Vibrio sp013394185	82.8782	758	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000272105.2	s__Vibrio splendidus_I	82.8708	734	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316985.1	s__Vibrio sp000316985	82.825	689	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272405.2	s__Vibrio tasmaniensis_A	82.7981	747	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
GCF_002156475.1	s__Vibrio gigantis	82.7688	745	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	-
GCF_002875705.1	s__Vibrio sp002875705	82.7668	725	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_004764665.1	s__Vibrio echinoideorum	82.7604	770	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.83	0.88	0.82	5	-
GCF_000272045.2	s__Vibrio crassostreae_C	82.6771	778	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_008801285.1	s__Vibrio kanaloae	82.6094	721	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.50	98.26	0.91	0.88	16	-
GCF_002954585.1	s__Vibrio chagasii_A	82.4406	691	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.42	95.44	0.90	0.87	4	-
GCF_001635455.1	s__Vibrio sp001635455	81.9663	688	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281835.1	s__Vibrio profundi	81.7377	657	1640	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 11:36:11,992] [INFO] GTDB search result was written to GCF_013416885.1_ASM1341688v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:11,992] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:11,997] [INFO] DFAST_QC result json was written to GCF_013416885.1_ASM1341688v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:11,998] [INFO] DFAST_QC completed!
[2024-01-24 11:36:11,998] [INFO] Total running time: 0h1m33s