[2024-01-24 11:59:05,239] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:05,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:05,241] [INFO] DQC Reference Directory: /var/lib/cwl/stgfda07852-b0cf-4a11-99c5-4eb4b670fbb3/dqc_reference
[2024-01-24 11:59:06,455] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:06,456] [INFO] Task started: Prodigal
[2024-01-24 11:59:06,456] [INFO] Running command: gunzip -c /var/lib/cwl/stga1a29933-acf3-455e-ac10-a93459a05ad2/GCF_900460385.1_42650_F01_genomic.fna.gz | prodigal -d GCF_900460385.1_42650_F01_genomic.fna/cds.fna -a GCF_900460385.1_42650_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:18,438] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:18,439] [INFO] Task started: HMMsearch
[2024-01-24 11:59:18,439] [INFO] Running command: hmmsearch --tblout GCF_900460385.1_42650_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfda07852-b0cf-4a11-99c5-4eb4b670fbb3/dqc_reference/reference_markers.hmm GCF_900460385.1_42650_F01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:18,741] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:18,743] [INFO] Found 6/6 markers.
[2024-01-24 11:59:18,784] [INFO] Query marker FASTA was written to GCF_900460385.1_42650_F01_genomic.fna/markers.fasta
[2024-01-24 11:59:18,785] [INFO] Task started: Blastn
[2024-01-24 11:59:18,785] [INFO] Running command: blastn -query GCF_900460385.1_42650_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stgfda07852-b0cf-4a11-99c5-4eb4b670fbb3/dqc_reference/reference_markers.fasta -out GCF_900460385.1_42650_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:19,650] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:19,655] [INFO] Selected 10 target genomes.
[2024-01-24 11:59:19,656] [INFO] Target genome list was writen to GCF_900460385.1_42650_F01_genomic.fna/target_genomes.txt
[2024-01-24 11:59:19,660] [INFO] Task started: fastANI
[2024-01-24 11:59:19,660] [INFO] Running command: fastANI --query /var/lib/cwl/stga1a29933-acf3-455e-ac10-a93459a05ad2/GCF_900460385.1_42650_F01_genomic.fna.gz --refList GCF_900460385.1_42650_F01_genomic.fna/target_genomes.txt --output GCF_900460385.1_42650_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:31,849] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:31,850] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfda07852-b0cf-4a11-99c5-4eb4b670fbb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:31,850] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfda07852-b0cf-4a11-99c5-4eb4b670fbb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:31,862] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:59:31,862] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:31,863] [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 mimicus	strain=NCTC11435	GCA_900460385.1	674	674	type	True	100.0	1472	1480	95	conclusive
Vibrio mimicus	strain=CAIM 602	GCA_000338875.1	674	674	type	True	99.9309	1374	1480	95	conclusive
Vibrio metoecus	strain=OP3H	GCA_000696385.1	1481663	1481663	type	True	87.6307	1063	1480	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	87.165	1110	1480	95	below_threshold
Vibrio cholerae	strain=ATCC 14035	GCA_000621645.1	666	666	type	True	86.5152	1036	1480	95	below_threshold
Vibrio paracholerae	strain=EDC-792	GCA_017169525.1	650003	650003	type	True	86.3346	993	1480	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	79.8607	545	1480	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.2433	310	1480	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	79.1254	343	1480	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.896	310	1480	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:31,864] [INFO] DFAST Taxonomy check result was written to GCF_900460385.1_42650_F01_genomic.fna/tc_result.tsv
[2024-01-24 11:59:31,865] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:31,865] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:31,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfda07852-b0cf-4a11-99c5-4eb4b670fbb3/dqc_reference/checkm_data
[2024-01-24 11:59:31,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:31,908] [INFO] Task started: CheckM
[2024-01-24 11:59:31,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900460385.1_42650_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900460385.1_42650_F01_genomic.fna/checkm_input GCF_900460385.1_42650_F01_genomic.fna/checkm_result
[2024-01-24 12:00:12,017] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:12,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:12,043] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:12,043] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:12,043] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900460385.1_42650_F01_genomic.fna/markers.fasta)
[2024-01-24 12:00:12,044] [INFO] Task started: Blastn
[2024-01-24 12:00:12,044] [INFO] Running command: blastn -query GCF_900460385.1_42650_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stgfda07852-b0cf-4a11-99c5-4eb4b670fbb3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900460385.1_42650_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:13,327] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:13,332] [INFO] Selected 5 target genomes.
[2024-01-24 12:00:13,333] [INFO] Target genome list was writen to GCF_900460385.1_42650_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:13,337] [INFO] Task started: fastANI
[2024-01-24 12:00:13,338] [INFO] Running command: fastANI --query /var/lib/cwl/stga1a29933-acf3-455e-ac10-a93459a05ad2/GCF_900460385.1_42650_F01_genomic.fna.gz --refList GCF_900460385.1_42650_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900460385.1_42650_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:20,696] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:20,707] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:20,707] [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_000338875.1	s__Vibrio mimicus	99.9309	1374	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.81	0.94	0.91	26	conclusive
GCF_019048845.1	s__Vibrio sp000176715	89.7486	1123	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.20	96.20	0.92	0.92	2	-
GCF_009665255.1	s__Vibrio metoecus_B	88.5687	1107	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.11	98.11	0.94	0.94	2	-
GCF_000696385.1	s__Vibrio metoecus	87.6307	1063	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.79	97.58	0.93	0.89	26	-
GCF_001471585.2	s__Vibrio cholerae	86.6884	1066	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.72	95.09	0.90	0.82	1544	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:20,709] [INFO] GTDB search result was written to GCF_900460385.1_42650_F01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:20,710] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:20,715] [INFO] DFAST_QC result json was written to GCF_900460385.1_42650_F01_genomic.fna/dqc_result.json
[2024-01-24 12:00:20,715] [INFO] DFAST_QC completed!
[2024-01-24 12:00:20,715] [INFO] Total running time: 0h1m15s