[2024-01-25 18:06:05,644] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:05,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:05,645] [INFO] DQC Reference Directory: /var/lib/cwl/stgde6a8da2-aeae-41b1-8993-612fb03424f9/dqc_reference
[2024-01-25 18:06:06,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:06,740] [INFO] Task started: Prodigal
[2024-01-25 18:06:06,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c8e52b9-4a04-46f9-b83b-fa5af5a19285/GCF_003415655.1_ASM341565v1_genomic.fna.gz | prodigal -d GCF_003415655.1_ASM341565v1_genomic.fna/cds.fna -a GCF_003415655.1_ASM341565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:16,655] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:16,655] [INFO] Task started: HMMsearch
[2024-01-25 18:06:16,655] [INFO] Running command: hmmsearch --tblout GCF_003415655.1_ASM341565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde6a8da2-aeae-41b1-8993-612fb03424f9/dqc_reference/reference_markers.hmm GCF_003415655.1_ASM341565v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:16,893] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:16,894] [INFO] Found 6/6 markers.
[2024-01-25 18:06:16,932] [INFO] Query marker FASTA was written to GCF_003415655.1_ASM341565v1_genomic.fna/markers.fasta
[2024-01-25 18:06:16,932] [INFO] Task started: Blastn
[2024-01-25 18:06:16,932] [INFO] Running command: blastn -query GCF_003415655.1_ASM341565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde6a8da2-aeae-41b1-8993-612fb03424f9/dqc_reference/reference_markers.fasta -out GCF_003415655.1_ASM341565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:17,706] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:17,709] [INFO] Selected 23 target genomes.
[2024-01-25 18:06:17,709] [INFO] Target genome list was writen to GCF_003415655.1_ASM341565v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:17,730] [INFO] Task started: fastANI
[2024-01-25 18:06:17,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c8e52b9-4a04-46f9-b83b-fa5af5a19285/GCF_003415655.1_ASM341565v1_genomic.fna.gz --refList GCF_003415655.1_ASM341565v1_genomic.fna/target_genomes.txt --output GCF_003415655.1_ASM341565v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:38,816] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:38,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde6a8da2-aeae-41b1-8993-612fb03424f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:38,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde6a8da2-aeae-41b1-8993-612fb03424f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:38,830] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:38,830] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:38,830] [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 maerlii	strain=G62	GCA_003415655.1	2231648	2231648	type	True	100.0	1567	1567	95	conclusive
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	81.1368	450	1567	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_005281815.1	170679	170679	suspected-type	True	80.9078	417	1567	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	80.8214	423	1567	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.7345	445	1567	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	80.7111	406	1567	95	below_threshold
Vibrio mexicanus	strain=CAIM 1540	GCA_001012815.1	1004326	1004326	type	True	80.5416	361	1567	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_002906655.1	1534743	1534743	type	True	80.3354	411	1567	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	80.2783	411	1567	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	80.2652	434	1567	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	80.1911	427	1567	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	80.1726	404	1567	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	80.0874	433	1567	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	80.0831	411	1567	95	below_threshold
Vibrio ponticus	strain=DSM 16217	GCA_009938225.1	265668	265668	type	True	79.9507	360	1567	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.8107	341	1567	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.6289	344	1567	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	79.4067	341	1567	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	79.2035	299	1567	95	below_threshold
Vibrio hippocampi	strain=CECT 8226	GCA_921292975.1	654686	654686	type	True	79.0109	269	1567	95	below_threshold
Vibrio fluvialis	strain=NCTC11327	GCA_900460245.1	676	676	type	True	78.6325	283	1567	95	below_threshold
Vibrio fluvialis	strain=NBRC 103150	GCA_001598835.1	676	676	type	True	78.5979	280	1567	95	below_threshold
Vibrio fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	78.5266	282	1567	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:38,831] [INFO] DFAST Taxonomy check result was written to GCF_003415655.1_ASM341565v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:38,832] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:38,832] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:38,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde6a8da2-aeae-41b1-8993-612fb03424f9/dqc_reference/checkm_data
[2024-01-25 18:06:38,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:38,883] [INFO] Task started: CheckM
[2024-01-25 18:06:38,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003415655.1_ASM341565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003415655.1_ASM341565v1_genomic.fna/checkm_input GCF_003415655.1_ASM341565v1_genomic.fna/checkm_result
[2024-01-25 18:07:12,300] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:12,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:12,322] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:12,322] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:12,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003415655.1_ASM341565v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:12,322] [INFO] Task started: Blastn
[2024-01-25 18:07:12,323] [INFO] Running command: blastn -query GCF_003415655.1_ASM341565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde6a8da2-aeae-41b1-8993-612fb03424f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003415655.1_ASM341565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:13,506] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:13,509] [INFO] Selected 23 target genomes.
[2024-01-25 18:07:13,509] [INFO] Target genome list was writen to GCF_003415655.1_ASM341565v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:13,535] [INFO] Task started: fastANI
[2024-01-25 18:07:13,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c8e52b9-4a04-46f9-b83b-fa5af5a19285/GCF_003415655.1_ASM341565v1_genomic.fna.gz --refList GCF_003415655.1_ASM341565v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003415655.1_ASM341565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:34,589] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:34,603] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:34,603] [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_003415655.1	s__Vibrio maerlii	100.0	1567	1567	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_005281815.1	s__Vibrio chagasii	80.898	416	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	-
GCF_002954585.1	s__Vibrio chagasii_A	80.8873	422	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.42	95.44	0.90	0.87	4	-
GCF_000695685.1	s__Vibrio fortis	80.8819	448	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.41	96.21	0.90	0.88	4	-
GCF_001635455.1	s__Vibrio sp001635455	80.7944	404	1567	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	80.7926	414	1567	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	80.537	362	1567	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	80.4352	391	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741985.1	s__Vibrio rotiferianus	80.4262	399	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_010587385.1	s__Vibrio astriarenae	80.4012	341	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	96.60	0.82	0.82	2	-
GCF_002906655.1	s__Vibrio hyugaensis	80.3353	411	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCF_002163755.1	s__Vibrio campbellii	80.332	419	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_000189255.1	s__Vibrio brasiliensis	80.1835	377	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156475.1	s__Vibrio gigantis	80.1744	429	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	-
GCF_001274785.1	s__Vibrio hepatarius	80.1657	362	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
GCF_001695575.1	s__Vibrio europaeus	80.0822	409	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_001591145.1	s__Vibrio harveyi	80.0776	440	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_009938225.1	s__Vibrio ponticus	79.9521	361	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.69	97.39	0.92	0.85	3	-
GCA_003263775.1	s__Vibrio maritimus	79.8932	374	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009938165.1	s__Vibrio taketomensis	79.7827	341	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_000222585.1	s__Vibrio scophthalmi	79.3793	342	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCF_002873395.1	s__Vibrio sp002873395	79.236	271	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900460245.1	s__Vibrio fluvialis	78.6279	282	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:34,605] [INFO] GTDB search result was written to GCF_003415655.1_ASM341565v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:34,607] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:34,615] [INFO] DFAST_QC result json was written to GCF_003415655.1_ASM341565v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:34,615] [INFO] DFAST_QC completed!
[2024-01-25 18:07:34,615] [INFO] Total running time: 0h1m29s