[2024-01-24 12:47:49,751] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:49,753] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:49,753] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bd85b78-9aad-48dd-bdd4-e21c031260d7/dqc_reference
[2024-01-24 12:47:50,952] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:50,953] [INFO] Task started: Prodigal
[2024-01-24 12:47:50,954] [INFO] Running command: gunzip -c /var/lib/cwl/stg601b3247-d4b7-40f7-81c8-73e29553bc34/GCF_024346995.1_ASM2434699v1_genomic.fna.gz | prodigal -d GCF_024346995.1_ASM2434699v1_genomic.fna/cds.fna -a GCF_024346995.1_ASM2434699v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:59,808] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:59,809] [INFO] Task started: HMMsearch
[2024-01-24 12:47:59,809] [INFO] Running command: hmmsearch --tblout GCF_024346995.1_ASM2434699v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bd85b78-9aad-48dd-bdd4-e21c031260d7/dqc_reference/reference_markers.hmm GCF_024346995.1_ASM2434699v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:00,074] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:00,076] [INFO] Found 6/6 markers.
[2024-01-24 12:48:00,112] [INFO] Query marker FASTA was written to GCF_024346995.1_ASM2434699v1_genomic.fna/markers.fasta
[2024-01-24 12:48:00,113] [INFO] Task started: Blastn
[2024-01-24 12:48:00,113] [INFO] Running command: blastn -query GCF_024346995.1_ASM2434699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bd85b78-9aad-48dd-bdd4-e21c031260d7/dqc_reference/reference_markers.fasta -out GCF_024346995.1_ASM2434699v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:00,898] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:00,902] [INFO] Selected 12 target genomes.
[2024-01-24 12:48:00,903] [INFO] Target genome list was writen to GCF_024346995.1_ASM2434699v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:00,925] [INFO] Task started: fastANI
[2024-01-24 12:48:00,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg601b3247-d4b7-40f7-81c8-73e29553bc34/GCF_024346995.1_ASM2434699v1_genomic.fna.gz --refList GCF_024346995.1_ASM2434699v1_genomic.fna/target_genomes.txt --output GCF_024346995.1_ASM2434699v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:11,340] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:11,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bd85b78-9aad-48dd-bdd4-e21c031260d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:11,342] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bd85b78-9aad-48dd-bdd4-e21c031260d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:11,354] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:48:11,354] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:11,355] [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 palustris	strain=CECT 9027	GCA_024346995.1	1918946	1918946	type	True	100.0	1244	1244	95	conclusive
Vibrio palustris	strain=CECT 9027	GCA_900162645.1	1918946	1918946	type	True	99.9776	1221	1244	95	conclusive
Vibrio zhugei	strain=HBUAS61001	GCA_003716875.1	2479546	2479546	type	True	82.593	788	1244	95	below_threshold
Vibrio zhugei	strain=KCTC 62784	GCA_024347155.1	2479546	2479546	type	True	82.5714	775	1244	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	80.0895	339	1244	95	below_threshold
Vibrio tritonius	strain=JCM 16456	GCA_001547935.1	1435069	1435069	type	True	79.6357	334	1244	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	79.5473	173	1244	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	79.3858	184	1244	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	79.378	193	1244	95	below_threshold
Vibrio qinghaiensis	strain=Q67	GCA_002257545.1	2025808	2025808	type	True	79.3644	219	1244	95	below_threshold
Vibrio proteolyticus	strain=NBRC 13287	GCA_000467125.1	671	671	type	True	78.7022	166	1244	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	78.5223	180	1244	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:11,356] [INFO] DFAST Taxonomy check result was written to GCF_024346995.1_ASM2434699v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:11,357] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:11,357] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:11,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bd85b78-9aad-48dd-bdd4-e21c031260d7/dqc_reference/checkm_data
[2024-01-24 12:48:11,360] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:11,399] [INFO] Task started: CheckM
[2024-01-24 12:48:11,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024346995.1_ASM2434699v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024346995.1_ASM2434699v1_genomic.fna/checkm_input GCF_024346995.1_ASM2434699v1_genomic.fna/checkm_result
[2024-01-24 12:48:43,079] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:43,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:43,103] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:43,103] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:43,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024346995.1_ASM2434699v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:43,104] [INFO] Task started: Blastn
[2024-01-24 12:48:43,104] [INFO] Running command: blastn -query GCF_024346995.1_ASM2434699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bd85b78-9aad-48dd-bdd4-e21c031260d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_024346995.1_ASM2434699v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:44,253] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:44,257] [INFO] Selected 17 target genomes.
[2024-01-24 12:48:44,257] [INFO] Target genome list was writen to GCF_024346995.1_ASM2434699v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:44,281] [INFO] Task started: fastANI
[2024-01-24 12:48:44,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg601b3247-d4b7-40f7-81c8-73e29553bc34/GCF_024346995.1_ASM2434699v1_genomic.fna.gz --refList GCF_024346995.1_ASM2434699v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024346995.1_ASM2434699v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:57,963] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:57,990] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:57,990] [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_900162645.1	s__Vibrio palustris	99.9776	1221	1244	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_003716875.1	s__Vibrio zhugei	82.5783	788	1244	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	80.1854	343	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.79	98.79	0.95	0.95	2	-
GCF_019226825.1	s__Vibrio sp004804295	79.8098	216	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.23	99.23	0.93	0.93	2	-
GCF_001547935.1	s__Vibrio tritonius	79.721	335	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900460535.1	s__Vibrio parahaemolyticus	79.5632	208	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
GCF_000772105.1	s__Vibrio tubiashii	79.5113	200	1244	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	79.4152	173	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.19	97.06	0.93	0.87	22	-
GCF_002157735.2	s__Vibrio aphrogenes	79.3308	153	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934045.1	s__Vibrio gangliei	78.8362	155	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000467125.1	s__Vibrio proteolyticus	78.7023	167	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.93	98.89	0.93	0.91	5	-
GCA_001048675.1	s__Vibrio diabolicus	78.6303	187	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_000967545.1	s__Vibrio galatheae	78.6087	163	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001989995.2	s__Vibrio anguillarum	78.5231	198	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.39	98.01	0.89	0.80	121	-
GCF_900107935.1	s__Vibrio hangzhouensis	78.4874	141	1244	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	78.3077	184	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.60	95.57	0.95	0.90	11	-
GCF_005281815.1	s__Vibrio chagasii	78.0148	179	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:57,992] [INFO] GTDB search result was written to GCF_024346995.1_ASM2434699v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:57,993] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:57,998] [INFO] DFAST_QC result json was written to GCF_024346995.1_ASM2434699v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:57,998] [INFO] DFAST_QC completed!
[2024-01-24 12:48:57,998] [INFO] Total running time: 0h1m8s