[2024-01-25 20:15:05,531] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:05,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:05,533] [INFO] DQC Reference Directory: /var/lib/cwl/stg47af1348-6736-4119-b038-859204f69d67/dqc_reference
[2024-01-25 20:15:06,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:06,722] [INFO] Task started: Prodigal
[2024-01-25 20:15:06,722] [INFO] Running command: gunzip -c /var/lib/cwl/stgd364eac1-dd2b-46e9-9b8c-febb23250c63/GCF_009857245.1_ASM985724v1_genomic.fna.gz | prodigal -d GCF_009857245.1_ASM985724v1_genomic.fna/cds.fna -a GCF_009857245.1_ASM985724v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:15,900] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:15,901] [INFO] Task started: HMMsearch
[2024-01-25 20:15:15,901] [INFO] Running command: hmmsearch --tblout GCF_009857245.1_ASM985724v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47af1348-6736-4119-b038-859204f69d67/dqc_reference/reference_markers.hmm GCF_009857245.1_ASM985724v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:16,147] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:16,148] [INFO] Found 6/6 markers.
[2024-01-25 20:15:16,184] [INFO] Query marker FASTA was written to GCF_009857245.1_ASM985724v1_genomic.fna/markers.fasta
[2024-01-25 20:15:16,185] [INFO] Task started: Blastn
[2024-01-25 20:15:16,185] [INFO] Running command: blastn -query GCF_009857245.1_ASM985724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47af1348-6736-4119-b038-859204f69d67/dqc_reference/reference_markers.fasta -out GCF_009857245.1_ASM985724v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:16,914] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:16,917] [INFO] Selected 16 target genomes.
[2024-01-25 20:15:16,917] [INFO] Target genome list was writen to GCF_009857245.1_ASM985724v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:16,923] [INFO] Task started: fastANI
[2024-01-25 20:15:16,923] [INFO] Running command: fastANI --query /var/lib/cwl/stgd364eac1-dd2b-46e9-9b8c-febb23250c63/GCF_009857245.1_ASM985724v1_genomic.fna.gz --refList GCF_009857245.1_ASM985724v1_genomic.fna/target_genomes.txt --output GCF_009857245.1_ASM985724v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:30,589] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:30,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47af1348-6736-4119-b038-859204f69d67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:30,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47af1348-6736-4119-b038-859204f69d67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:30,601] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:15:30,601] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:15:30,601] [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 aquimaris	strain=THAF100	GCA_009363415.1	2587862	2587862	type	True	94.5828	1300	1524	95	below_threshold
Vibrio pectenicida	strain=LMG 19642	GCA_024347015.1	62763	62763	type	True	81.2794	904	1524	95	below_threshold
Vibrio pectenicida	strain=CAIM 594	GCA_003937805.1	62763	62763	type	True	81.2484	829	1524	95	below_threshold
Vibrio coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	79.7276	453	1524	95	below_threshold
Vibrio bivalvicida	strain=605	GCA_001399455.2	1276888	1276888	type	True	79.6135	317	1524	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	79.5185	332	1524	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	79.4426	353	1524	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	79.3458	338	1524	95	below_threshold
Vibrio nereis	strain=DSM 19584	GCA_001274805.1	693	693	type	True	79.3282	307	1524	95	below_threshold
Vibrio nereis	strain=NBRC 15637	GCA_001591105.1	693	693	type	True	79.2545	306	1524	95	below_threshold
Vibrio hippocampi	strain=CECT 8226	GCA_921292975.1	654686	654686	type	True	79.0155	170	1524	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	78.888	185	1524	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	78.7413	255	1524	95	below_threshold
Vibrio sonorensis	strain=CAIM 1076	GCA_001854765.1	1004316	1004316	type	True	78.7136	247	1524	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	78.3573	211	1524	95	below_threshold
Vibrio echinoideorum	strain=DSM 107264	GCA_024347455.1	2100116	2100116	type	True	78.2556	217	1524	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:30,603] [INFO] DFAST Taxonomy check result was written to GCF_009857245.1_ASM985724v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:30,603] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:30,603] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:30,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47af1348-6736-4119-b038-859204f69d67/dqc_reference/checkm_data
[2024-01-25 20:15:30,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:30,649] [INFO] Task started: CheckM
[2024-01-25 20:15:30,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009857245.1_ASM985724v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009857245.1_ASM985724v1_genomic.fna/checkm_input GCF_009857245.1_ASM985724v1_genomic.fna/checkm_result
[2024-01-25 20:16:01,882] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:01,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:01,900] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:01,900] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:01,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009857245.1_ASM985724v1_genomic.fna/markers.fasta)
[2024-01-25 20:16:01,901] [INFO] Task started: Blastn
[2024-01-25 20:16:01,901] [INFO] Running command: blastn -query GCF_009857245.1_ASM985724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47af1348-6736-4119-b038-859204f69d67/dqc_reference/reference_markers_gtdb.fasta -out GCF_009857245.1_ASM985724v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:03,061] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:03,064] [INFO] Selected 14 target genomes.
[2024-01-25 20:16:03,064] [INFO] Target genome list was writen to GCF_009857245.1_ASM985724v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:03,070] [INFO] Task started: fastANI
[2024-01-25 20:16:03,071] [INFO] Running command: fastANI --query /var/lib/cwl/stgd364eac1-dd2b-46e9-9b8c-febb23250c63/GCF_009857245.1_ASM985724v1_genomic.fna.gz --refList GCF_009857245.1_ASM985724v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009857245.1_ASM985724v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:16,316] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:16,325] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:16,325] [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_003350295.1	s__Vibrio tetraodonis	95.2712	1270	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.28	95.28	0.88	0.88	2	conclusive
GCF_009363415.1	s__Vibrio aquimaris	94.5828	1300	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860525.1	s__Vibrio hepatarius_B	81.6196	886	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003937805.1	s__Vibrio pectenicida	81.2484	829	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.20	98.20	0.85	0.85	2	-
GCF_000967495.1	s__Vibrio neptunius	79.7725	443	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.83	96.84	0.91	0.89	7	-
GCF_000176135.1	s__Vibrio coralliilyticus	79.7246	454	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_013113835.1	s__Vibrio sp013113835	79.7212	453	1524	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	79.4629	295	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772105.1	s__Vibrio tubiashii	79.4426	353	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_011806575.1	s__Vibrio hepatarius_A	79.3393	300	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.94	98.94	0.97	0.97	2	-
GCF_000189275.1	s__Vibrio sinaloensis_B	79.2543	312	1524	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	78.9051	251	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_014050145.1	s__Vibrio marinisediminis	78.7447	253	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854765.1	s__Vibrio sonorensis	78.7136	247	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:16,326] [INFO] GTDB search result was written to GCF_009857245.1_ASM985724v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:16,327] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:16,330] [INFO] DFAST_QC result json was written to GCF_009857245.1_ASM985724v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:16,330] [INFO] DFAST_QC completed!
[2024-01-25 20:16:16,330] [INFO] Total running time: 0h1m11s