[2024-01-25 17:48:05,708] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:05,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:05,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e74153e-2d26-4699-aa98-8b9603accc6e/dqc_reference
[2024-01-25 17:48:06,820] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:06,820] [INFO] Task started: Prodigal
[2024-01-25 17:48:06,821] [INFO] Running command: gunzip -c /var/lib/cwl/stg96a3e661-6e28-431f-a233-36296107d6cb/GCF_016900875.1_ASM1690087v1_genomic.fna.gz | prodigal -d GCF_016900875.1_ASM1690087v1_genomic.fna/cds.fna -a GCF_016900875.1_ASM1690087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:16,359] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:16,359] [INFO] Task started: HMMsearch
[2024-01-25 17:48:16,359] [INFO] Running command: hmmsearch --tblout GCF_016900875.1_ASM1690087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e74153e-2d26-4699-aa98-8b9603accc6e/dqc_reference/reference_markers.hmm GCF_016900875.1_ASM1690087v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:16,596] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:16,597] [INFO] Found 6/6 markers.
[2024-01-25 17:48:16,633] [INFO] Query marker FASTA was written to GCF_016900875.1_ASM1690087v1_genomic.fna/markers.fasta
[2024-01-25 17:48:16,633] [INFO] Task started: Blastn
[2024-01-25 17:48:16,633] [INFO] Running command: blastn -query GCF_016900875.1_ASM1690087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e74153e-2d26-4699-aa98-8b9603accc6e/dqc_reference/reference_markers.fasta -out GCF_016900875.1_ASM1690087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:17,374] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:17,377] [INFO] Selected 27 target genomes.
[2024-01-25 17:48:17,377] [INFO] Target genome list was writen to GCF_016900875.1_ASM1690087v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:17,414] [INFO] Task started: fastANI
[2024-01-25 17:48:17,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg96a3e661-6e28-431f-a233-36296107d6cb/GCF_016900875.1_ASM1690087v1_genomic.fna.gz --refList GCF_016900875.1_ASM1690087v1_genomic.fna/target_genomes.txt --output GCF_016900875.1_ASM1690087v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:38,269] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:38,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e74153e-2d26-4699-aa98-8b9603accc6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:38,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e74153e-2d26-4699-aa98-8b9603accc6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:38,284] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:48:38,284] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:48:38,285] [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 ulleungensis	strain=188UL20-2	GCA_016900875.1	2807619	2807619	type	True	100.0	1447	1447	95	conclusive
Vibrio ezurae	strain=NBRC 102218	GCA_000467185.1	252583	252583	type	True	79.4322	189	1447	95	below_threshold
Vibrio ishigakensis	strain=JCM 19231	GCA_024347675.1	1481914	1481914	type	True	79.2821	198	1447	95	below_threshold
Vibrio comitans	strain=LMG 23416	GCA_024346835.1	413401	413401	type	True	79.2462	194	1447	95	below_threshold
Vibrio ezurae	strain=HDS1-1	GCA_003568985.1	252583	252583	type	True	79.2207	201	1447	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	79.2137	195	1447	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	79.1831	196	1447	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	79.1459	181	1447	95	below_threshold
Vibrio coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	79.1363	184	1447	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	79.1039	200	1447	95	below_threshold
Vibrio comitans	strain=NBRC 102076	GCA_006538565.1	413401	413401	type	True	79.0536	188	1447	95	below_threshold
Vibrio hippocampi	strain=CECT 8226	GCA_921292975.1	654686	654686	type	True	78.9878	197	1447	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	78.9728	193	1447	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	78.9718	207	1447	95	below_threshold
Vibrio halioticoli	strain=IAM 14596	GCA_003568965.1	71388	71388	type	True	78.9418	204	1447	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	78.938	195	1447	95	below_threshold
Vibrio halioticoli	strain=NBRC 102217	GCA_000496695.1	71388	71388	type	True	78.9312	192	1447	95	below_threshold
Vibrio natriegens	strain=ATCC 14048	GCA_000417905.1	691	691	type	True	78.7948	175	1447	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	78.7657	188	1447	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	78.7497	183	1447	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	78.7438	199	1447	95	below_threshold
Vibrio ichthyoenteri	strain=ATCC 700023	GCA_000222605.2	142461	142461	type	True	78.6175	185	1447	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	78.6092	167	1447	95	below_threshold
Vibrio harveyi	strain=NBRC 15634	GCA_001591145.1	669	669	type	True	78.5533	183	1447	95	below_threshold
Vibrio cidicii	strain=2756-81	GCA_009763805.1	1763883	1763883	type	True	78.3809	167	1447	95	below_threshold
Vibrio navarrensis	strain=ATCC 51183	GCA_000764325.1	29495	29495	type	True	78.3157	168	1447	95	below_threshold
Vibrio metoecus	strain=OP3H	GCA_000696385.1	1481663	1481663	type	True	77.9849	151	1447	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:38,289] [INFO] DFAST Taxonomy check result was written to GCF_016900875.1_ASM1690087v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:38,290] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:38,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:38,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e74153e-2d26-4699-aa98-8b9603accc6e/dqc_reference/checkm_data
[2024-01-25 17:48:38,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:38,336] [INFO] Task started: CheckM
[2024-01-25 17:48:38,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016900875.1_ASM1690087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016900875.1_ASM1690087v1_genomic.fna/checkm_input GCF_016900875.1_ASM1690087v1_genomic.fna/checkm_result
[2024-01-25 17:49:10,715] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:10,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:10,739] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:10,740] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:10,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016900875.1_ASM1690087v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:10,740] [INFO] Task started: Blastn
[2024-01-25 17:49:10,740] [INFO] Running command: blastn -query GCF_016900875.1_ASM1690087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e74153e-2d26-4699-aa98-8b9603accc6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_016900875.1_ASM1690087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:11,908] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:11,911] [INFO] Selected 21 target genomes.
[2024-01-25 17:49:11,911] [INFO] Target genome list was writen to GCF_016900875.1_ASM1690087v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:11,926] [INFO] Task started: fastANI
[2024-01-25 17:49:11,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg96a3e661-6e28-431f-a233-36296107d6cb/GCF_016900875.1_ASM1690087v1_genomic.fna.gz --refList GCF_016900875.1_ASM1690087v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016900875.1_ASM1690087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:29,499] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:29,511] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:29,511] [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_016900875.1	s__Vibrio sp016900875	100.0	1447	1447	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_002100145.1	s__Vibrio sp002100145	92.9886	1190	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000467185.1	s__Vibrio ezurae	79.4529	190	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000176135.1	s__Vibrio coralliilyticus	79.1627	182	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_003970385.1	s__Vibrio aquaticus	79.1594	197	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013114545.1	s__Vibrio sp013114545	79.1063	196	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000775715.1	s__Vibrio tubiashii_A	79.091	178	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538565.1	s__Vibrio comitans	79.0572	188	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001695575.1	s__Vibrio europaeus	79.0208	190	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCA_000830415.1	s__Vibrio ishigakensis	79.0147	178	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.42	95.17	0.89	0.89	4	-
GCF_000496695.1	s__Vibrio halioticoli	78.9353	191	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.31	0.94	0.87	3	-
GCA_003263845.1	s__Vibrio aestivus	78.9148	191	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811315.1	s__Vibrio atypicus	78.8694	187	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_000827885.1	s__Vibrio renipiscarius	78.7416	184	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000222605.1	s__Vibrio ichthyoenteri	78.6304	182	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967545.1	s__Vibrio galatheae	78.6222	177	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064285.1	s__Vibrio ziniensis	78.6113	167	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900233005.1	s__Vibrio tapetis	78.5491	189	1447	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	78.5482	194	1447	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	78.4664	147	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.23	99.23	0.93	0.93	2	-
GCF_009763805.1	s__Vibrio cidicii	78.3814	167	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.20	97.77	0.90	0.87	8	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:29,515] [INFO] GTDB search result was written to GCF_016900875.1_ASM1690087v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:29,516] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:29,521] [INFO] DFAST_QC result json was written to GCF_016900875.1_ASM1690087v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:29,521] [INFO] DFAST_QC completed!
[2024-01-25 17:49:29,521] [INFO] Total running time: 0h1m24s