[2024-01-24 14:55:05,317] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:05,319] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:05,319] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dad160a-b224-430c-bdca-ba409c51c4d3/dqc_reference
[2024-01-24 14:55:09,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:09,470] [INFO] Task started: Prodigal
[2024-01-24 14:55:09,471] [INFO] Running command: gunzip -c /var/lib/cwl/stg096c8758-6d4d-4237-8900-3469b1c3e664/GCF_003144035.1_ASM314403v1_genomic.fna.gz | prodigal -d GCF_003144035.1_ASM314403v1_genomic.fna/cds.fna -a GCF_003144035.1_ASM314403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:19,534] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:19,534] [INFO] Task started: HMMsearch
[2024-01-24 14:55:19,534] [INFO] Running command: hmmsearch --tblout GCF_003144035.1_ASM314403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dad160a-b224-430c-bdca-ba409c51c4d3/dqc_reference/reference_markers.hmm GCF_003144035.1_ASM314403v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:19,828] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:19,830] [INFO] Found 6/6 markers.
[2024-01-24 14:55:20,069] [INFO] Query marker FASTA was written to GCF_003144035.1_ASM314403v1_genomic.fna/markers.fasta
[2024-01-24 14:55:20,069] [INFO] Task started: Blastn
[2024-01-24 14:55:20,070] [INFO] Running command: blastn -query GCF_003144035.1_ASM314403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dad160a-b224-430c-bdca-ba409c51c4d3/dqc_reference/reference_markers.fasta -out GCF_003144035.1_ASM314403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:20,898] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:20,902] [INFO] Selected 25 target genomes.
[2024-01-24 14:55:20,902] [INFO] Target genome list was writen to GCF_003144035.1_ASM314403v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:20,914] [INFO] Task started: fastANI
[2024-01-24 14:55:20,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg096c8758-6d4d-4237-8900-3469b1c3e664/GCF_003144035.1_ASM314403v1_genomic.fna.gz --refList GCF_003144035.1_ASM314403v1_genomic.fna/target_genomes.txt --output GCF_003144035.1_ASM314403v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:40,923] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:40,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dad160a-b224-430c-bdca-ba409c51c4d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:40,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dad160a-b224-430c-bdca-ba409c51c4d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:40,956] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:40,957] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:40,957] [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 albus	strain=E4404	GCA_003144035.1	2200953	2200953	type	True	100.0	1399	1403	95	conclusive
Vibrio penaeicida	strain=CAIM 285	GCA_003970425.1	104609	104609	type	True	79.4802	164	1403	95	below_threshold
Vibrio penaeicida	strain=IFO 15640	GCA_019977755.1	104609	104609	type	True	79.4561	174	1403	95	below_threshold
Vibrio nigripulchritudo	strain=ATCC 27043	GCA_000222685.2	28173	28173	type	True	79.3497	198	1403	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_002224265.1	672	672	type	True	79.0974	190	1403	95	below_threshold
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	79.06	204	1403	95	below_threshold
Vibrio furnissii	strain=FDAARGOS_777	GCA_006364355.1	29494	29494	type	True	79.0591	195	1403	95	below_threshold
Vibrio vulnificus	strain=NCTC13647	GCA_900460565.1	672	672	type	True	78.9974	195	1403	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	78.9942	217	1403	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	78.9535	198	1403	95	below_threshold
Vibrio coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	78.9141	194	1403	95	below_threshold
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001011015.1	670	670	type	True	78.8943	203	1403	95	below_threshold
Vibrio barjaei	strain=3062	GCA_001639065.2	1676683	1676683	type	True	78.8873	169	1403	95	below_threshold
Vibrio furnissii	strain=NCTC13120	GCA_900460225.1	29494	29494	type	True	78.8711	194	1403	95	below_threshold
Vibrio ichthyoenteri	strain=ATCC 700023	GCA_000222605.2	142461	142461	type	True	78.8255	171	1403	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	78.8155	164	1403	95	below_threshold
Vibrio parahaemolyticus	strain=NBRC 12711	GCA_000813305.1	670	670	type	True	78.8091	199	1403	95	below_threshold
Vibrio furnissii	strain=CIP 102972	GCA_000176175.1	29494	29494	type	True	78.7923	187	1403	95	below_threshold
Vibrio vulnificus	strain=NBRC 15645	GCA_001591065.1	672	672	type	True	78.7579	188	1403	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	78.6188	175	1403	95	below_threshold
Photobacterium proteolyticum	strain=13-12	GCA_001939735.1	1903952	1903952	type	True	78.5543	151	1403	95	below_threshold
Photobacterium alginatilyticum	strain=P03D4	GCA_009910675.1	1775171	1775171	type	True	78.4126	155	1403	95	below_threshold
Vibrio rhizosphaerae	strain=LMG 23790	GCA_024347095.1	398736	398736	type	True	78.1209	156	1403	95	below_threshold
Photobacterium ganghwense	strain=JCM 12487	GCA_003025595.1	320778	320778	type	True	78.1203	180	1403	95	below_threshold
Photobacterium ganghwense	strain=DSM 22954	GCA_001029455.1	320778	320778	type	True	77.9922	173	1403	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:40,959] [INFO] DFAST Taxonomy check result was written to GCF_003144035.1_ASM314403v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:40,959] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:40,959] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:40,960] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dad160a-b224-430c-bdca-ba409c51c4d3/dqc_reference/checkm_data
[2024-01-24 14:55:40,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:41,004] [INFO] Task started: CheckM
[2024-01-24 14:55:41,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003144035.1_ASM314403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003144035.1_ASM314403v1_genomic.fna/checkm_input GCF_003144035.1_ASM314403v1_genomic.fna/checkm_result
[2024-01-24 14:56:16,966] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:16,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:16,988] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:16,988] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:16,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003144035.1_ASM314403v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:16,989] [INFO] Task started: Blastn
[2024-01-24 14:56:16,989] [INFO] Running command: blastn -query GCF_003144035.1_ASM314403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dad160a-b224-430c-bdca-ba409c51c4d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003144035.1_ASM314403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:18,232] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:18,235] [INFO] Selected 22 target genomes.
[2024-01-24 14:56:18,236] [INFO] Target genome list was writen to GCF_003144035.1_ASM314403v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:18,254] [INFO] Task started: fastANI
[2024-01-24 14:56:18,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg096c8758-6d4d-4237-8900-3469b1c3e664/GCF_003144035.1_ASM314403v1_genomic.fna.gz --refList GCF_003144035.1_ASM314403v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003144035.1_ASM314403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:36,193] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:36,218] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:36,218] [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_003144035.1	s__Vibrio sp003144035	100.0	1399	1403	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_002812955.1	s__Vibrio sp002812955	81.2394	621	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970425.1	s__Vibrio penaeicida	79.4703	164	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.14	96.14	0.85	0.85	2	-
GCF_000222685.1	s__Vibrio nigripulchritudo	79.3497	198	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.90	96.77	0.92	0.87	18	-
GCF_002224265.1	s__Vibrio vulnificus	79.0756	190	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.11	95.22	0.91	0.85	225	-
GCF_009811315.1	s__Vibrio atypicus	79.046	181	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_900460245.1	s__Vibrio fluvialis	79.0101	237	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
GCF_001591105.1	s__Vibrio nereis	78.982	192	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009938165.1	s__Vibrio taketomensis	78.9739	181	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_013113835.1	s__Vibrio sp013113835	78.9371	193	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000417905.1	s__Vibrio natriegens	78.9356	214	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.60	95.57	0.95	0.90	11	-
GCF_000176135.1	s__Vibrio coralliilyticus	78.8916	196	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_013041605.1	s__Vibrio plantisponsor	78.8598	203	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.35	98.35	0.93	0.93	2	-
GCF_001639065.2	s__Vibrio barjaei	78.8596	169	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.1582	N/A	N/A	N/A	N/A	1	-
GCF_000222605.1	s__Vibrio ichthyoenteri	78.8143	172	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176175.1	s__Vibrio furnissii	78.8139	185	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.58	97.97	0.95	0.91	12	-
GCF_000467125.1	s__Vibrio proteolyticus	78.7672	223	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.93	98.89	0.93	0.91	5	-
GCF_001939735.1	s__Photobacterium proteolyticum	78.5887	147	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107935.1	s__Vibrio hangzhouensis	78.5826	211	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331515.1	s__Photobacterium marinum	78.5535	166	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
GCF_009910675.1	s__Photobacterium alginatilyticum	78.3801	154	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003025595.1	s__Photobacterium ganghwense	78.1428	177	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.50	98.82	0.97	0.96	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:36,220] [INFO] GTDB search result was written to GCF_003144035.1_ASM314403v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:36,220] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:36,225] [INFO] DFAST_QC result json was written to GCF_003144035.1_ASM314403v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:36,225] [INFO] DFAST_QC completed!
[2024-01-24 14:56:36,225] [INFO] Total running time: 0h1m31s