[2024-01-24 13:22:01,809] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:01,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:01,811] [INFO] DQC Reference Directory: /var/lib/cwl/stga5fde22d-40d8-496c-94f7-a134bb2b9a88/dqc_reference
[2024-01-24 13:22:03,193] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,194] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,194] [INFO] Running command: gunzip -c /var/lib/cwl/stg945fd42a-e52c-4ae9-8a7d-39607217520c/GCF_025996475.1_ASM2599647v1_genomic.fna.gz | prodigal -d GCF_025996475.1_ASM2599647v1_genomic.fna/cds.fna -a GCF_025996475.1_ASM2599647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:15,138] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:15,139] [INFO] Task started: HMMsearch
[2024-01-24 13:22:15,139] [INFO] Running command: hmmsearch --tblout GCF_025996475.1_ASM2599647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5fde22d-40d8-496c-94f7-a134bb2b9a88/dqc_reference/reference_markers.hmm GCF_025996475.1_ASM2599647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:15,465] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:15,466] [INFO] Found 6/6 markers.
[2024-01-24 13:22:15,509] [INFO] Query marker FASTA was written to GCF_025996475.1_ASM2599647v1_genomic.fna/markers.fasta
[2024-01-24 13:22:15,510] [INFO] Task started: Blastn
[2024-01-24 13:22:15,510] [INFO] Running command: blastn -query GCF_025996475.1_ASM2599647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5fde22d-40d8-496c-94f7-a134bb2b9a88/dqc_reference/reference_markers.fasta -out GCF_025996475.1_ASM2599647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:16,362] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:16,365] [INFO] Selected 31 target genomes.
[2024-01-24 13:22:16,366] [INFO] Target genome list was writen to GCF_025996475.1_ASM2599647v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:16,384] [INFO] Task started: fastANI
[2024-01-24 13:22:16,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg945fd42a-e52c-4ae9-8a7d-39607217520c/GCF_025996475.1_ASM2599647v1_genomic.fna.gz --refList GCF_025996475.1_ASM2599647v1_genomic.fna/target_genomes.txt --output GCF_025996475.1_ASM2599647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:44,464] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:44,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5fde22d-40d8-496c-94f7-a134bb2b9a88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:44,465] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5fde22d-40d8-496c-94f7-a134bb2b9a88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:44,488] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:44,488] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:44,488] [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	80.4495	346	1556	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	80.4021	349	1556	95	below_threshold
Vibrio mexicanus	strain=CAIM 1540	GCA_001012815.1	1004326	1004326	type	True	80.3718	340	1556	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_002906655.1	1534743	1534743	type	True	80.3108	365	1556	95	below_threshold
Vibrio maerlii	strain=G62	GCA_003415655.1	2231648	2231648	type	True	80.2896	355	1556	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	80.2458	336	1556	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.1744	357	1556	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	80.1352	320	1556	95	below_threshold
Vibrio thalassae	strain=CECT8203	GCA_900089835.1	1243014	1243014	type	True	80.0894	271	1556	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.0861	328	1556	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.0487	343	1556	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	80.0416	349	1556	95	below_threshold
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	80.0412	343	1556	95	below_threshold
Vibrio profundi	strain=TP187	GCA_005281835.1	1774960	1774960	type	True	80.016	298	1556	95	below_threshold
Vibrio owensii	strain=DY05	GCA_000817815.1	696485	696485	type	True	80.014	353	1556	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	79.9974	358	1556	95	below_threshold
Vibrio variabilis	strain=CAIM 1454	GCA_003263785.1	990271	990271	type	True	79.966	316	1556	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	79.9293	198	1556	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	79.9184	330	1556	95	below_threshold
Vibrio ponticus	strain=DSM 16217	GCA_009938225.1	265668	265668	type	True	79.7766	340	1556	95	below_threshold
Vibrio harveyi	strain=NBRC 15634	GCA_001591145.1	669	669	type	True	79.7583	340	1556	95	below_threshold
Vibrio mediterranei	strain=NBRC 15635	GCA_001591125.1	689	689	type	True	79.7056	292	1556	95	below_threshold
Vibrio mediterranei		GCA_900088415.1	689	689	type	True	79.6946	304	1556	95	below_threshold
Vibrio hangzhouensis	strain=CGMCC 1.7062	GCA_900107935.1	462991	462991	type	True	79.635	274	1556	95	below_threshold
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001011015.1	670	670	type	True	79.624	339	1556	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	79.6208	272	1556	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	79.2307	317	1556	95	below_threshold
Vibrio fluvialis	strain=NCTC11327	GCA_900460245.1	676	676	type	True	79.2082	284	1556	95	below_threshold
Vibrio fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	79.1541	286	1556	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	79.0761	281	1556	95	below_threshold
Vibrio fluvialis	strain=NBRC 103150	GCA_001598835.1	676	676	type	True	78.8239	272	1556	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:44,490] [INFO] DFAST Taxonomy check result was written to GCF_025996475.1_ASM2599647v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:44,490] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:44,491] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:44,491] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5fde22d-40d8-496c-94f7-a134bb2b9a88/dqc_reference/checkm_data
[2024-01-24 13:22:44,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:44,540] [INFO] Task started: CheckM
[2024-01-24 13:22:44,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025996475.1_ASM2599647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025996475.1_ASM2599647v1_genomic.fna/checkm_input GCF_025996475.1_ASM2599647v1_genomic.fna/checkm_result
[2024-01-24 13:23:24,837] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:24,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:24,857] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:24,857] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:24,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025996475.1_ASM2599647v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:24,858] [INFO] Task started: Blastn
[2024-01-24 13:23:24,858] [INFO] Running command: blastn -query GCF_025996475.1_ASM2599647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5fde22d-40d8-496c-94f7-a134bb2b9a88/dqc_reference/reference_markers_gtdb.fasta -out GCF_025996475.1_ASM2599647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:26,043] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:26,047] [INFO] Selected 25 target genomes.
[2024-01-24 13:23:26,047] [INFO] Target genome list was writen to GCF_025996475.1_ASM2599647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:26,102] [INFO] Task started: fastANI
[2024-01-24 13:23:26,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg945fd42a-e52c-4ae9-8a7d-39607217520c/GCF_025996475.1_ASM2599647v1_genomic.fna.gz --refList GCF_025996475.1_ASM2599647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025996475.1_ASM2599647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:47,279] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:47,303] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:23:47,303] [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_010587385.1	s__Vibrio astriarenae	83.3871	915	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	96.60	0.82	0.82	2	-
GCF_013114545.1	s__Vibrio sp013114545	80.4958	346	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544875.1	s__Vibrio alfacsensis	80.4702	311	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.49	96.49	0.89	0.89	2	-
GCF_000772105.1	s__Vibrio tubiashii	80.4417	347	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_003970385.1	s__Vibrio aquaticus	80.4109	349	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001012815.1	s__Vibrio mexicanus	80.3708	340	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002906655.1	s__Vibrio hyugaensis	80.347	369	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCF_003415655.1	s__Vibrio maerlii	80.315	358	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163755.1	s__Vibrio campbellii	80.2733	352	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCA_003263845.1	s__Vibrio aestivus	80.2159	337	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004551525.1	s__Vibrio ouci	80.1795	356	1556	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	80.0798	293	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806575.1	s__Vibrio hepatarius_A	80.0633	305	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.94	98.94	0.97	0.97	2	-
GCF_000817815.1	s__Vibrio owensii	80.0545	350	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_000400365.1	s__Vibrio jasicida	80.0323	344	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_005281835.1	s__Vibrio profundi	80.0151	298	1556	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	80.0111	354	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_006124995.1	s__Vibrio sp006124995	80.0086	315	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274785.1	s__Vibrio hepatarius	79.9377	326	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
GCF_001635455.1	s__Vibrio sp001635455	79.8417	312	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013113835.1	s__Vibrio sp013113835	79.7901	312	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967495.1	s__Vibrio neptunius	79.6444	281	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.83	96.84	0.91	0.89	7	-
GCF_011064285.1	s__Vibrio ziniensis	79.5206	270	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222585.1	s__Vibrio scophthalmi	79.2259	318	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCF_900460245.1	s__Vibrio fluvialis	79.1768	285	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:47,305] [INFO] GTDB search result was written to GCF_025996475.1_ASM2599647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:47,305] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:47,310] [INFO] DFAST_QC result json was written to GCF_025996475.1_ASM2599647v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:47,310] [INFO] DFAST_QC completed!
[2024-01-24 13:23:47,310] [INFO] Total running time: 0h1m46s