[2024-01-24 15:02:46,768] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:46,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:46,773] [INFO] DQC Reference Directory: /var/lib/cwl/stg13618cdd-cda4-4de4-b684-aaaa51d0cd63/dqc_reference
[2024-01-24 15:02:48,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:48,091] [INFO] Task started: Prodigal
[2024-01-24 15:02:48,091] [INFO] Running command: gunzip -c /var/lib/cwl/stgefcd73d9-05a2-4c71-9c8e-7398c8f4e2a1/GCF_030161235.1_ASM3016123v1_genomic.fna.gz | prodigal -d GCF_030161235.1_ASM3016123v1_genomic.fna/cds.fna -a GCF_030161235.1_ASM3016123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:59,997] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:59,998] [INFO] Task started: HMMsearch
[2024-01-24 15:02:59,998] [INFO] Running command: hmmsearch --tblout GCF_030161235.1_ASM3016123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13618cdd-cda4-4de4-b684-aaaa51d0cd63/dqc_reference/reference_markers.hmm GCF_030161235.1_ASM3016123v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:00,395] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:00,396] [INFO] Found 6/6 markers.
[2024-01-24 15:03:00,441] [INFO] Query marker FASTA was written to GCF_030161235.1_ASM3016123v1_genomic.fna/markers.fasta
[2024-01-24 15:03:00,441] [INFO] Task started: Blastn
[2024-01-24 15:03:00,442] [INFO] Running command: blastn -query GCF_030161235.1_ASM3016123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13618cdd-cda4-4de4-b684-aaaa51d0cd63/dqc_reference/reference_markers.fasta -out GCF_030161235.1_ASM3016123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:01,325] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:01,330] [INFO] Selected 20 target genomes.
[2024-01-24 15:03:01,331] [INFO] Target genome list was writen to GCF_030161235.1_ASM3016123v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:01,341] [INFO] Task started: fastANI
[2024-01-24 15:03:01,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgefcd73d9-05a2-4c71-9c8e-7398c8f4e2a1/GCF_030161235.1_ASM3016123v1_genomic.fna.gz --refList GCF_030161235.1_ASM3016123v1_genomic.fna/target_genomes.txt --output GCF_030161235.1_ASM3016123v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:17,749] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:17,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13618cdd-cda4-4de4-b684-aaaa51d0cd63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:17,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13618cdd-cda4-4de4-b684-aaaa51d0cd63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:17,768] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:03:17,768] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:03:17,768] [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	82.8834	945	1535	95	below_threshold
Vibrio pectenicida	strain=LMG 19642	GCA_024347015.1	62763	62763	type	True	81.2653	890	1535	95	below_threshold
Vibrio pectenicida	strain=CAIM 594	GCA_003937805.1	62763	62763	type	True	81.1573	822	1535	95	below_threshold
Vibrio coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	79.6081	439	1535	95	below_threshold
Vibrio sonorensis	strain=CAIM 1076	GCA_001854765.1	1004316	1004316	type	True	79.3745	225	1535	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	79.348	321	1535	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	79.2025	317	1535	95	below_threshold
Vibrio hippocampi	strain=CECT 8226	GCA_921292975.1	654686	654686	type	True	79.1224	166	1535	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	78.9931	317	1535	95	below_threshold
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	78.986	231	1535	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	78.9712	307	1535	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.9352	245	1535	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.9182	248	1535	95	below_threshold
Vibrio cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	78.7647	189	1535	95	below_threshold
Vibrio ichthyoenteri	strain=ATCC 700023	GCA_000222605.2	142461	142461	type	True	78.7183	238	1535	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	78.7054	176	1535	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	78.6488	239	1535	95	below_threshold
Vibrio anguillarum	strain=NCTC12159	GCA_900452855.1	55601	55601	type	True	78.5239	240	1535	95	below_threshold
Vibrio anguillarum	strain=DSM 21597	GCA_001989995.2	55601	55601	type	True	78.3269	232	1535	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	78.1622	221	1535	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:17,770] [INFO] DFAST Taxonomy check result was written to GCF_030161235.1_ASM3016123v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:17,770] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:17,770] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:17,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13618cdd-cda4-4de4-b684-aaaa51d0cd63/dqc_reference/checkm_data
[2024-01-24 15:03:17,771] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:17,819] [INFO] Task started: CheckM
[2024-01-24 15:03:17,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161235.1_ASM3016123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161235.1_ASM3016123v1_genomic.fna/checkm_input GCF_030161235.1_ASM3016123v1_genomic.fna/checkm_result
[2024-01-24 15:03:57,005] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:57,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:57,022] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:57,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:57,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161235.1_ASM3016123v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:57,024] [INFO] Task started: Blastn
[2024-01-24 15:03:57,024] [INFO] Running command: blastn -query GCF_030161235.1_ASM3016123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13618cdd-cda4-4de4-b684-aaaa51d0cd63/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161235.1_ASM3016123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:58,238] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:58,241] [INFO] Selected 15 target genomes.
[2024-01-24 15:03:58,242] [INFO] Target genome list was writen to GCF_030161235.1_ASM3016123v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:58,253] [INFO] Task started: fastANI
[2024-01-24 15:03:58,253] [INFO] Running command: fastANI --query /var/lib/cwl/stgefcd73d9-05a2-4c71-9c8e-7398c8f4e2a1/GCF_030161235.1_ASM3016123v1_genomic.fna.gz --refList GCF_030161235.1_ASM3016123v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161235.1_ASM3016123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:11,481] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:11,494] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:04:11,494] [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_009363415.1	s__Vibrio aquimaris	82.8835	945	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350295.1	s__Vibrio tetraodonis	82.2231	883	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.28	95.28	0.88	0.88	2	-
GCF_018860525.1	s__Vibrio hepatarius_B	81.2316	824	1535	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	81.1358	824	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.20	98.20	0.85	0.85	2	-
GCF_013113835.1	s__Vibrio sp013113835	79.6836	424	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176135.1	s__Vibrio coralliilyticus	79.6105	438	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_001274785.1	s__Vibrio hepatarius	79.3378	294	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
GCF_000775715.1	s__Vibrio tubiashii_A	79.2519	285	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002811245.1	s__Vibrio salilacus	79.0274	298	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.5386	N/A	N/A	N/A	N/A	1	-
GCF_000176235.1	s__Vibrio orientalis	78.9931	317	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000808535.1	s__Vibrio sinaloensis	78.9334	319	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_000189255.1	s__Vibrio brasiliensis	78.9226	310	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000257205.1	s__Vibrio ordalii	78.6892	214	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.90	98.90	0.96	0.96	2	-
GCF_014050145.1	s__Vibrio marinisediminis	78.6697	237	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605645.1	s__Vibrio sinensis	78.5409	252	1535	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 15:04:11,496] [INFO] GTDB search result was written to GCF_030161235.1_ASM3016123v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:11,496] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:11,501] [INFO] DFAST_QC result json was written to GCF_030161235.1_ASM3016123v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:11,501] [INFO] DFAST_QC completed!
[2024-01-24 15:04:11,501] [INFO] Total running time: 0h1m25s