[2024-01-25 19:47:05,838] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:05,839] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:05,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ee16724-c2e4-443a-ba56-02817280b525/dqc_reference
[2024-01-25 19:47:07,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:07,017] [INFO] Task started: Prodigal
[2024-01-25 19:47:07,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c1e7816-9235-4e88-8e4a-0ce4374d282d/GCF_024347055.1_ASM2434705v1_genomic.fna.gz | prodigal -d GCF_024347055.1_ASM2434705v1_genomic.fna/cds.fna -a GCF_024347055.1_ASM2434705v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:20,683] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:20,683] [INFO] Task started: HMMsearch
[2024-01-25 19:47:20,683] [INFO] Running command: hmmsearch --tblout GCF_024347055.1_ASM2434705v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ee16724-c2e4-443a-ba56-02817280b525/dqc_reference/reference_markers.hmm GCF_024347055.1_ASM2434705v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:20,946] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:20,948] [INFO] Found 6/6 markers.
[2024-01-25 19:47:20,989] [INFO] Query marker FASTA was written to GCF_024347055.1_ASM2434705v1_genomic.fna/markers.fasta
[2024-01-25 19:47:20,989] [INFO] Task started: Blastn
[2024-01-25 19:47:20,989] [INFO] Running command: blastn -query GCF_024347055.1_ASM2434705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ee16724-c2e4-443a-ba56-02817280b525/dqc_reference/reference_markers.fasta -out GCF_024347055.1_ASM2434705v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:21,766] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:21,768] [INFO] Selected 20 target genomes.
[2024-01-25 19:47:21,769] [INFO] Target genome list was writen to GCF_024347055.1_ASM2434705v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:21,780] [INFO] Task started: fastANI
[2024-01-25 19:47:21,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c1e7816-9235-4e88-8e4a-0ce4374d282d/GCF_024347055.1_ASM2434705v1_genomic.fna.gz --refList GCF_024347055.1_ASM2434705v1_genomic.fna/target_genomes.txt --output GCF_024347055.1_ASM2434705v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:39,289] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:39,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ee16724-c2e4-443a-ba56-02817280b525/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:39,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ee16724-c2e4-443a-ba56-02817280b525/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:39,301] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:39,302] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:39,302] [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 porteresiae	strain=MSSRF30	GCA_024347055.1	435912	435912	type	True	100.0	1831	1833	95	conclusive
Vibrio tritonius	strain=JCM 16456	GCA_001547935.1	1435069	1435069	type	True	87.0023	1390	1833	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	80.9467	712	1833	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	79.9584	423	1833	95	below_threshold
Vibrio fluvialis	strain=NCTC11327	GCA_900460245.1	676	676	type	True	79.8611	410	1833	95	below_threshold
Vibrio furnissii	strain=NCTC13120	GCA_900460225.1	29494	29494	type	True	79.7846	418	1833	95	below_threshold
Vibrio fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	79.7815	421	1833	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	79.7609	262	1833	95	below_threshold
Vibrio furnissii	strain=FDAARGOS_777	GCA_006364355.1	29494	29494	type	True	79.674	419	1833	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.5014	279	1833	95	below_threshold
Vibrio furnissii	strain=CIP 102972	GCA_000176175.1	29494	29494	type	True	79.4468	406	1833	95	below_threshold
Vibrio navarrensis	strain=ATCC 51183	GCA_000764325.1	29495	29495	type	True	79.3448	273	1833	95	below_threshold
Vibrio artabrorum	strain=CECT 7226	GCA_024347295.1	446374	446374	type	True	79.2749	264	1833	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	79.096	356	1833	95	below_threshold
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	79.0869	286	1833	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	78.7972	219	1833	95	below_threshold
Vibrio sagamiensis	strain=NBRC 104589	GCA_007990935.1	512650	512650	type	True	78.7925	181	1833	95	below_threshold
Vibrio aestuarianus subsp. cardii	strain=12/122 3T3	GCA_011090275.1	2807650	28171	type	True	78.7108	297	1833	95	below_threshold
Vibrio sagamiensis	strain=NBRC 104589	GCA_000400425.1	512650	512650	type	True	78.6433	184	1833	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	78.4296	289	1833	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:39,303] [INFO] DFAST Taxonomy check result was written to GCF_024347055.1_ASM2434705v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:39,304] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:39,304] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:39,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ee16724-c2e4-443a-ba56-02817280b525/dqc_reference/checkm_data
[2024-01-25 19:47:39,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:39,357] [INFO] Task started: CheckM
[2024-01-25 19:47:39,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347055.1_ASM2434705v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347055.1_ASM2434705v1_genomic.fna/checkm_input GCF_024347055.1_ASM2434705v1_genomic.fna/checkm_result
[2024-01-25 19:48:24,134] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:24,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:24,169] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:24,170] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:24,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347055.1_ASM2434705v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:24,171] [INFO] Task started: Blastn
[2024-01-25 19:48:24,171] [INFO] Running command: blastn -query GCF_024347055.1_ASM2434705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ee16724-c2e4-443a-ba56-02817280b525/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347055.1_ASM2434705v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:25,380] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:25,383] [INFO] Selected 23 target genomes.
[2024-01-25 19:48:25,383] [INFO] Target genome list was writen to GCF_024347055.1_ASM2434705v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:25,421] [INFO] Task started: fastANI
[2024-01-25 19:48:25,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c1e7816-9235-4e88-8e4a-0ce4374d282d/GCF_024347055.1_ASM2434705v1_genomic.fna.gz --refList GCF_024347055.1_ASM2434705v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347055.1_ASM2434705v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:46,348] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:46,361] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:48:46,362] [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_001547935.1	s__Vibrio tritonius	87.0083	1391	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015686695.1	s__Vibrio nitrifigilis	80.9556	712	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.79	98.79	0.95	0.95	2	-
GCF_900460245.1	s__Vibrio fluvialis	79.8453	408	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
GCF_009938165.1	s__Vibrio taketomensis	79.679	286	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_011064285.1	s__Vibrio ziniensis	79.5597	379	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009938205.1	s__Vibrio panuliri	79.5423	279	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	-
GCF_002224265.1	s__Vibrio vulnificus	79.4559	282	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.11	95.22	0.91	0.85	225	-
GCF_000176175.1	s__Vibrio furnissii	79.4164	407	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.58	97.97	0.95	0.91	12	-
GCF_009938225.1	s__Vibrio ponticus	79.4018	306	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.69	97.39	0.92	0.85	3	-
GCF_000772105.1	s__Vibrio tubiashii	79.331	293	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_000764325.1	s__Vibrio navarrensis	79.2985	273	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.19	97.06	0.93	0.87	22	-
GCF_014596725.1	s__Vibrio sp014596725	79.2274	342	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.52	0.94	0.94	2	-
GCF_000740015.1	s__Vibrio diazotrophicus	79.1016	355	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
GCF_003350325.1	s__Vibrio rhodolitus	79.0783	287	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
GCF_000775715.1	s__Vibrio tubiashii_A	78.9266	261	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967545.1	s__Vibrio galatheae	78.905	260	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006124995.1	s__Vibrio sp006124995	78.8489	275	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990935.1	s__Vibrio sagamiensis	78.7925	181	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.95	99.91	0.97	0.96	3	-
GCF_000171815.1	s__Vibrio sp000171815	78.7286	219	1833	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	78.7232	277	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013113835.1	s__Vibrio sp013113835	78.6753	283	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827885.1	s__Vibrio renipiscarius	78.4303	290	1833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000272105.2	s__Vibrio splendidus_I	78.3184	270	1833	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 19:48:46,363] [INFO] GTDB search result was written to GCF_024347055.1_ASM2434705v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:46,364] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:46,367] [INFO] DFAST_QC result json was written to GCF_024347055.1_ASM2434705v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:46,367] [INFO] DFAST_QC completed!
[2024-01-25 19:48:46,367] [INFO] Total running time: 0h1m41s