[2024-01-24 10:48:09,166] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,168] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,168] [INFO] DQC Reference Directory: /var/lib/cwl/stgec8c8509-6a0b-4dee-add8-36bcbb9f7dfb/dqc_reference
[2024-01-24 10:48:23,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,955] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,955] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7ff4dbd-3080-40fe-9733-69b7dbb1c48b/GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna.gz | prodigal -d GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/cds.fna -a GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:32,746] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:32,746] [INFO] Task started: HMMsearch
[2024-01-24 10:48:32,746] [INFO] Running command: hmmsearch --tblout GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec8c8509-6a0b-4dee-add8-36bcbb9f7dfb/dqc_reference/reference_markers.hmm GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:33,040] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:33,042] [INFO] Found 6/6 markers.
[2024-01-24 10:48:33,076] [INFO] Query marker FASTA was written to GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/markers.fasta
[2024-01-24 10:48:33,077] [INFO] Task started: Blastn
[2024-01-24 10:48:33,077] [INFO] Running command: blastn -query GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/markers.fasta -db /var/lib/cwl/stgec8c8509-6a0b-4dee-add8-36bcbb9f7dfb/dqc_reference/reference_markers.fasta -out GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:33,855] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:33,862] [INFO] Selected 12 target genomes.
[2024-01-24 10:48:33,863] [INFO] Target genome list was writen to GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/target_genomes.txt
[2024-01-24 10:48:33,869] [INFO] Task started: fastANI
[2024-01-24 10:48:33,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7ff4dbd-3080-40fe-9733-69b7dbb1c48b/GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna.gz --refList GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/target_genomes.txt --output GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:43,925] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:43,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec8c8509-6a0b-4dee-add8-36bcbb9f7dfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:43,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec8c8509-6a0b-4dee-add8-36bcbb9f7dfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:43,937] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:43,937] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:43,937] [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_900162645.1	1918946	1918946	type	True	100.0	1222	1222	95	conclusive
Vibrio palustris	strain=CECT 9027	GCA_024346995.1	1918946	1918946	type	True	99.9996	1218	1222	95	conclusive
Vibrio zhugei	strain=HBUAS61001	GCA_003716875.1	2479546	2479546	type	True	82.2621	766	1222	95	below_threshold
Vibrio zhugei	strain=KCTC 62784	GCA_024347155.1	2479546	2479546	type	True	82.2583	779	1222	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	79.3569	340	1222	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	79.0103	164	1222	95	below_threshold
Vibrio tritonius	strain=JCM 16456	GCA_001547935.1	1435069	1435069	type	True	78.9234	331	1222	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	78.757	167	1222	95	below_threshold
Vibrio qinghaiensis	strain=Q67	GCA_002257545.1	2025808	2025808	type	True	78.6032	194	1222	95	below_threshold
Vibrio proteolyticus	strain=NBRC 13287	GCA_000467125.1	671	671	type	True	78.5559	170	1222	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	78.4677	179	1222	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	78.2774	189	1222	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:43,939] [INFO] DFAST Taxonomy check result was written to GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/tc_result.tsv
[2024-01-24 10:48:43,940] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:43,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:43,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec8c8509-6a0b-4dee-add8-36bcbb9f7dfb/dqc_reference/checkm_data
[2024-01-24 10:48:43,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:43,979] [INFO] Task started: CheckM
[2024-01-24 10:48:43,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/checkm_input GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/checkm_result
[2024-01-24 10:49:18,630] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:18,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:19,459] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:19,460] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:19,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/markers.fasta)
[2024-01-24 10:49:19,461] [INFO] Task started: Blastn
[2024-01-24 10:49:19,461] [INFO] Running command: blastn -query GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/markers.fasta -db /var/lib/cwl/stgec8c8509-6a0b-4dee-add8-36bcbb9f7dfb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:20,945] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:20,949] [INFO] Selected 17 target genomes.
[2024-01-24 10:49:20,949] [INFO] Target genome list was writen to GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:20,961] [INFO] Task started: fastANI
[2024-01-24 10:49:20,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7ff4dbd-3080-40fe-9733-69b7dbb1c48b/GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna.gz --refList GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/target_genomes_gtdb.txt --output GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:37,964] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:37,981] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:37,981] [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	100.0	1222	1222	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	82.2727	765	1222	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	79.3532	343	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.79	98.79	0.95	0.95	2	-
GCF_001547935.1	s__Vibrio tritonius	78.943	328	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764325.1	s__Vibrio navarrensis	78.7706	159	1222	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	78.6312	144	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001048675.1	s__Vibrio diabolicus	78.6057	185	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_001989995.2	s__Vibrio anguillarum	78.5919	195	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.39	98.01	0.89	0.80	121	-
GCF_019226825.1	s__Vibrio sp004804295	78.5895	209	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.23	99.23	0.93	0.93	2	-
GCF_000772105.1	s__Vibrio tubiashii	78.5362	183	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_000467125.1	s__Vibrio proteolyticus	78.5325	171	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.93	98.89	0.93	0.91	5	-
GCF_002934045.1	s__Vibrio gangliei	78.521	155	1222	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	78.4574	167	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107935.1	s__Vibrio hangzhouensis	78.4477	140	1222	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	78.441	194	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
GCF_005281815.1	s__Vibrio chagasii	78.3694	162	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	-
GCF_000417905.1	s__Vibrio natriegens	78.1021	191	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.60	95.57	0.95	0.90	11	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:37,983] [INFO] GTDB search result was written to GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:37,984] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:37,987] [INFO] DFAST_QC result json was written to GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL_genomic.fna/dqc_result.json
[2024-01-24 10:49:37,987] [INFO] DFAST_QC completed!
[2024-01-24 10:49:37,988] [INFO] Total running time: 0h1m29s