[2024-01-24 13:50:26,273] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:26,275] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:26,275] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb76c902-7cac-48ff-870c-e217d5177837/dqc_reference
[2024-01-24 13:50:27,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:27,646] [INFO] Task started: Prodigal
[2024-01-24 13:50:27,646] [INFO] Running command: gunzip -c /var/lib/cwl/stg165dcf43-f28d-4988-8e96-ecd3749db8b6/GCF_009938225.1_ASM993822v1_genomic.fna.gz | prodigal -d GCF_009938225.1_ASM993822v1_genomic.fna/cds.fna -a GCF_009938225.1_ASM993822v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:40,179] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:40,180] [INFO] Task started: HMMsearch
[2024-01-24 13:50:40,180] [INFO] Running command: hmmsearch --tblout GCF_009938225.1_ASM993822v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb76c902-7cac-48ff-870c-e217d5177837/dqc_reference/reference_markers.hmm GCF_009938225.1_ASM993822v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:40,466] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:40,468] [INFO] Found 6/6 markers.
[2024-01-24 13:50:40,515] [INFO] Query marker FASTA was written to GCF_009938225.1_ASM993822v1_genomic.fna/markers.fasta
[2024-01-24 13:50:40,515] [INFO] Task started: Blastn
[2024-01-24 13:50:40,515] [INFO] Running command: blastn -query GCF_009938225.1_ASM993822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb76c902-7cac-48ff-870c-e217d5177837/dqc_reference/reference_markers.fasta -out GCF_009938225.1_ASM993822v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:41,332] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:41,336] [INFO] Selected 10 target genomes.
[2024-01-24 13:50:41,337] [INFO] Target genome list was writen to GCF_009938225.1_ASM993822v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:41,354] [INFO] Task started: fastANI
[2024-01-24 13:50:41,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg165dcf43-f28d-4988-8e96-ecd3749db8b6/GCF_009938225.1_ASM993822v1_genomic.fna.gz --refList GCF_009938225.1_ASM993822v1_genomic.fna/target_genomes.txt --output GCF_009938225.1_ASM993822v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:51,291] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:51,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb76c902-7cac-48ff-870c-e217d5177837/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:51,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb76c902-7cac-48ff-870c-e217d5177837/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:51,305] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:51,305] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:51,305] [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 ponticus	strain=DSM 16217	GCA_009938225.1	265668	265668	type	True	100.0	1598	1598	95	conclusive
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	88.2118	1059	1598	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	83.7373	911	1598	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	83.6871	918	1598	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	81.9888	814	1598	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	81.181	637	1598	95	below_threshold
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	81.1138	467	1598	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.7435	416	1598	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	79.9438	450	1598	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	79.4233	349	1598	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:51,307] [INFO] DFAST Taxonomy check result was written to GCF_009938225.1_ASM993822v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:51,308] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:51,308] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:51,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb76c902-7cac-48ff-870c-e217d5177837/dqc_reference/checkm_data
[2024-01-24 13:50:51,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:51,358] [INFO] Task started: CheckM
[2024-01-24 13:50:51,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009938225.1_ASM993822v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009938225.1_ASM993822v1_genomic.fna/checkm_input GCF_009938225.1_ASM993822v1_genomic.fna/checkm_result
[2024-01-24 13:51:32,756] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:32,757] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:32,779] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:32,780] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:32,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009938225.1_ASM993822v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:32,781] [INFO] Task started: Blastn
[2024-01-24 13:51:32,781] [INFO] Running command: blastn -query GCF_009938225.1_ASM993822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb76c902-7cac-48ff-870c-e217d5177837/dqc_reference/reference_markers_gtdb.fasta -out GCF_009938225.1_ASM993822v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:34,029] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:34,032] [INFO] Selected 8 target genomes.
[2024-01-24 13:51:34,033] [INFO] Target genome list was writen to GCF_009938225.1_ASM993822v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:34,042] [INFO] Task started: fastANI
[2024-01-24 13:51:34,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg165dcf43-f28d-4988-8e96-ecd3749db8b6/GCF_009938225.1_ASM993822v1_genomic.fna.gz --refList GCF_009938225.1_ASM993822v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009938225.1_ASM993822v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:43,024] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:43,038] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:43,039] [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_009938225.1	s__Vibrio ponticus	100.0	1598	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.69	97.39	0.92	0.85	3	conclusive
GCF_015278125.1	s__Vibrio sp015278125	91.4742	1263	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350325.1	s__Vibrio rhodolitus	88.2067	1060	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
GCF_009938205.1	s__Vibrio panuliri	83.7429	910	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	-
GCF_009938165.1	s__Vibrio taketomensis	83.0009	773	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_014050145.1	s__Vibrio marinisediminis	81.9977	813	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222585.1	s__Vibrio scophthalmi	81.1793	638	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCF_900460535.1	s__Vibrio parahaemolyticus	81.0671	463	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:43,040] [INFO] GTDB search result was written to GCF_009938225.1_ASM993822v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:43,041] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:43,044] [INFO] DFAST_QC result json was written to GCF_009938225.1_ASM993822v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:43,045] [INFO] DFAST_QC completed!
[2024-01-24 13:51:43,045] [INFO] Total running time: 0h1m17s