[2024-01-24 15:26:50,849] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:50,853] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:50,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a34a350-a04c-43f7-85af-4d7ae91edae8/dqc_reference
[2024-01-24 15:26:52,909] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:52,910] [INFO] Task started: Prodigal
[2024-01-24 15:26:52,910] [INFO] Running command: gunzip -c /var/lib/cwl/stg60b821c0-90c1-4b87-8948-c181697be1ab/GCF_003970425.1_ASM397042v1_genomic.fna.gz | prodigal -d GCF_003970425.1_ASM397042v1_genomic.fna/cds.fna -a GCF_003970425.1_ASM397042v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:07,087] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:07,087] [INFO] Task started: HMMsearch
[2024-01-24 15:27:07,087] [INFO] Running command: hmmsearch --tblout GCF_003970425.1_ASM397042v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a34a350-a04c-43f7-85af-4d7ae91edae8/dqc_reference/reference_markers.hmm GCF_003970425.1_ASM397042v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:07,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:07,418] [INFO] Found 6/6 markers.
[2024-01-24 15:27:07,480] [INFO] Query marker FASTA was written to GCF_003970425.1_ASM397042v1_genomic.fna/markers.fasta
[2024-01-24 15:27:07,481] [INFO] Task started: Blastn
[2024-01-24 15:27:07,481] [INFO] Running command: blastn -query GCF_003970425.1_ASM397042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a34a350-a04c-43f7-85af-4d7ae91edae8/dqc_reference/reference_markers.fasta -out GCF_003970425.1_ASM397042v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:08,298] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:08,301] [INFO] Selected 21 target genomes.
[2024-01-24 15:27:08,301] [INFO] Target genome list was writen to GCF_003970425.1_ASM397042v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:08,319] [INFO] Task started: fastANI
[2024-01-24 15:27:08,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg60b821c0-90c1-4b87-8948-c181697be1ab/GCF_003970425.1_ASM397042v1_genomic.fna.gz --refList GCF_003970425.1_ASM397042v1_genomic.fna/target_genomes.txt --output GCF_003970425.1_ASM397042v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:28,689] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:28,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a34a350-a04c-43f7-85af-4d7ae91edae8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:28,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a34a350-a04c-43f7-85af-4d7ae91edae8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:28,707] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:28,708] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:28,708] [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 penaeicida	strain=CAIM 285	GCA_003970425.1	104609	104609	type	True	100.0	1896	1932	95	conclusive
Vibrio penaeicida	strain=IFO 15640	GCA_019977755.1	104609	104609	type	True	99.9831	1905	1932	95	conclusive
Vibrio nigripulchritudo	strain=ATCC 27043	GCA_000222685.2	28173	28173	type	True	81.7338	870	1932	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	79.9722	258	1932	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	79.8305	269	1932	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	79.5909	287	1932	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	79.5241	260	1932	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	79.4131	270	1932	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	79.3857	270	1932	95	below_threshold
Vibrio nereis	strain=NBRC 15637	GCA_001591105.1	693	693	type	True	79.2912	238	1932	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	79.2871	274	1932	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	79.2544	282	1932	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	79.2123	262	1932	95	below_threshold
Vibrio coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	79.1624	265	1932	95	below_threshold
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	79.1252	271	1932	95	below_threshold
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001011015.1	670	670	type	True	79.1057	262	1932	95	below_threshold
Vibrio bivalvicida	strain=605	GCA_001399455.2	1276888	1276888	type	True	79.0309	254	1932	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	78.9498	240	1932	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	78.9265	230	1932	95	below_threshold
Vibrio sonorensis	strain=CAIM 1076	GCA_001854765.1	1004316	1004316	type	True	78.8528	227	1932	95	below_threshold
Vibrio aestuarianus subsp. cardii	strain=12/122 3T3	GCA_011090275.1	2807650	28171	type	True	78.671	245	1932	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:28,710] [INFO] DFAST Taxonomy check result was written to GCF_003970425.1_ASM397042v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:28,710] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:28,710] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:28,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a34a350-a04c-43f7-85af-4d7ae91edae8/dqc_reference/checkm_data
[2024-01-24 15:27:28,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:28,775] [INFO] Task started: CheckM
[2024-01-24 15:27:28,775] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003970425.1_ASM397042v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003970425.1_ASM397042v1_genomic.fna/checkm_input GCF_003970425.1_ASM397042v1_genomic.fna/checkm_result
[2024-01-24 15:28:15,081] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:15,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:15,112] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:15,112] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:15,112] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003970425.1_ASM397042v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:15,113] [INFO] Task started: Blastn
[2024-01-24 15:28:15,113] [INFO] Running command: blastn -query GCF_003970425.1_ASM397042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a34a350-a04c-43f7-85af-4d7ae91edae8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003970425.1_ASM397042v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:16,221] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:16,224] [INFO] Selected 14 target genomes.
[2024-01-24 15:28:16,224] [INFO] Target genome list was writen to GCF_003970425.1_ASM397042v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:16,233] [INFO] Task started: fastANI
[2024-01-24 15:28:16,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg60b821c0-90c1-4b87-8948-c181697be1ab/GCF_003970425.1_ASM397042v1_genomic.fna.gz --refList GCF_003970425.1_ASM397042v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003970425.1_ASM397042v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:30,685] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:30,698] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:30,698] [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_003970425.1	s__Vibrio penaeicida	100.0	1897	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.14	96.14	0.85	0.85	2	conclusive
GCF_002933855.1	s__Vibrio penaeicida_A	92.742	1596	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014694455.1	s__Vibrio sp014694455	85.5188	1280	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222685.1	s__Vibrio nigripulchritudo	81.7258	872	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.90	96.77	0.92	0.87	18	-
GCF_000772105.1	s__Vibrio tubiashii	79.8095	270	1932	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	79.4023	269	1932	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	79.3124	247	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000189255.1	s__Vibrio brasiliensis	79.2655	233	1932	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	79.1748	257	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_900233005.1	s__Vibrio tapetis	79.1747	312	1932	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	79.1122	279	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_000222585.1	s__Vibrio scophthalmi	78.9652	228	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCF_009938165.1	s__Vibrio taketomensis	78.9591	225	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCA_018223135.1	s__Vibrio sp018223135	78.9145	224	1932	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 15:28:30,700] [INFO] GTDB search result was written to GCF_003970425.1_ASM397042v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:30,701] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:30,705] [INFO] DFAST_QC result json was written to GCF_003970425.1_ASM397042v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:30,705] [INFO] DFAST_QC completed!
[2024-01-24 15:28:30,705] [INFO] Total running time: 0h1m40s