[2024-01-25 19:02:35,592] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:35,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:35,597] [INFO] DQC Reference Directory: /var/lib/cwl/stgc26bacef-28e5-429a-a716-ba2cf5ee2bcb/dqc_reference
[2024-01-25 19:02:36,705] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:36,706] [INFO] Task started: Prodigal
[2024-01-25 19:02:36,706] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a80b1fe-dae9-4dc8-bae5-27bfa6667270/GCF_000189255.1_ASM18925v1_genomic.fna.gz | prodigal -d GCF_000189255.1_ASM18925v1_genomic.fna/cds.fna -a GCF_000189255.1_ASM18925v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:45,888] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:45,889] [INFO] Task started: HMMsearch
[2024-01-25 19:02:45,889] [INFO] Running command: hmmsearch --tblout GCF_000189255.1_ASM18925v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc26bacef-28e5-429a-a716-ba2cf5ee2bcb/dqc_reference/reference_markers.hmm GCF_000189255.1_ASM18925v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:46,136] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:46,137] [INFO] Found 6/6 markers.
[2024-01-25 19:02:46,175] [INFO] Query marker FASTA was written to GCF_000189255.1_ASM18925v1_genomic.fna/markers.fasta
[2024-01-25 19:02:46,176] [INFO] Task started: Blastn
[2024-01-25 19:02:46,176] [INFO] Running command: blastn -query GCF_000189255.1_ASM18925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc26bacef-28e5-429a-a716-ba2cf5ee2bcb/dqc_reference/reference_markers.fasta -out GCF_000189255.1_ASM18925v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:46,947] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:46,950] [INFO] Selected 14 target genomes.
[2024-01-25 19:02:46,950] [INFO] Target genome list was writen to GCF_000189255.1_ASM18925v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:46,953] [INFO] Task started: fastANI
[2024-01-25 19:02:46,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a80b1fe-dae9-4dc8-bae5-27bfa6667270/GCF_000189255.1_ASM18925v1_genomic.fna.gz --refList GCF_000189255.1_ASM18925v1_genomic.fna/target_genomes.txt --output GCF_000189255.1_ASM18925v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:59,229] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:59,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc26bacef-28e5-429a-a716-ba2cf5ee2bcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:59,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc26bacef-28e5-429a-a716-ba2cf5ee2bcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:59,238] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:02:59,238] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:02:59,238] [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 tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	82.2523	778	1519	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	82.215	805	1519	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	82.1715	822	1519	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	82.149	760	1519	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	82.1303	783	1519	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	82.013	727	1519	95	below_threshold
Vibrio bivalvicida	strain=605	GCA_001399455.2	1276888	1276888	type	True	81.7894	767	1519	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.4813	407	1519	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	80.3332	448	1519	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.9308	440	1519	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.8516	446	1519	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	79.7057	441	1519	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	79.5193	463	1519	95	below_threshold
Vibrio fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	78.8876	392	1519	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:59,240] [INFO] DFAST Taxonomy check result was written to GCF_000189255.1_ASM18925v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:59,241] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:59,241] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:59,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc26bacef-28e5-429a-a716-ba2cf5ee2bcb/dqc_reference/checkm_data
[2024-01-25 19:02:59,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:59,286] [INFO] Task started: CheckM
[2024-01-25 19:02:59,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000189255.1_ASM18925v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000189255.1_ASM18925v1_genomic.fna/checkm_input GCF_000189255.1_ASM18925v1_genomic.fna/checkm_result
[2024-01-25 19:03:30,343] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:30,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:03:30,364] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:30,364] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:30,364] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000189255.1_ASM18925v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:30,364] [INFO] Task started: Blastn
[2024-01-25 19:03:30,365] [INFO] Running command: blastn -query GCF_000189255.1_ASM18925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc26bacef-28e5-429a-a716-ba2cf5ee2bcb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000189255.1_ASM18925v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:31,548] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:31,552] [INFO] Selected 13 target genomes.
[2024-01-25 19:03:31,552] [INFO] Target genome list was writen to GCF_000189255.1_ASM18925v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:03:31,563] [INFO] Task started: fastANI
[2024-01-25 19:03:31,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a80b1fe-dae9-4dc8-bae5-27bfa6667270/GCF_000189255.1_ASM18925v1_genomic.fna.gz --refList GCF_000189255.1_ASM18925v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000189255.1_ASM18925v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:44,220] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:44,229] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:44,229] [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_000189255.1	s__Vibrio brasiliensis	100.0	1512	1519	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_006124995.1	s__Vibrio sp006124995	85.2406	964	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004551525.1	s__Vibrio ouci	82.3429	769	1519	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	82.217	805	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_001695575.1	s__Vibrio europaeus	82.1803	821	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_000176235.1	s__Vibrio orientalis	82.1303	783	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003970385.1	s__Vibrio aquaticus	82.0031	728	1519	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	81.8906	662	1519	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	81.8048	711	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001399455.2	s__Vibrio bivalvicida	81.7935	766	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.39	98.39	0.93	0.93	2	-
GCF_000967545.1	s__Vibrio galatheae	81.658	648	1519	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	81.3317	688	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_013113835.1	s__Vibrio sp013113835	80.6736	616	1519	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 19:03:44,230] [INFO] GTDB search result was written to GCF_000189255.1_ASM18925v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:44,231] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:44,234] [INFO] DFAST_QC result json was written to GCF_000189255.1_ASM18925v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:44,235] [INFO] DFAST_QC completed!
[2024-01-25 19:03:44,235] [INFO] Total running time: 0h1m9s