[2024-01-24 12:15:20,760] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:20,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:20,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f90364e-4976-44dd-8434-a3c3716b33a8/dqc_reference
[2024-01-24 12:15:22,193] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:22,194] [INFO] Task started: Prodigal
[2024-01-24 12:15:22,194] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9c2988a-982c-4d65-b8c4-8da37e59ce5b/GCF_001591085.1_ASM159108v1_genomic.fna.gz | prodigal -d GCF_001591085.1_ASM159108v1_genomic.fna/cds.fna -a GCF_001591085.1_ASM159108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:34,881] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:34,881] [INFO] Task started: HMMsearch
[2024-01-24 12:15:34,881] [INFO] Running command: hmmsearch --tblout GCF_001591085.1_ASM159108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f90364e-4976-44dd-8434-a3c3716b33a8/dqc_reference/reference_markers.hmm GCF_001591085.1_ASM159108v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:35,172] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:35,173] [INFO] Found 6/6 markers.
[2024-01-24 12:15:35,217] [INFO] Query marker FASTA was written to GCF_001591085.1_ASM159108v1_genomic.fna/markers.fasta
[2024-01-24 12:15:35,217] [INFO] Task started: Blastn
[2024-01-24 12:15:35,218] [INFO] Running command: blastn -query GCF_001591085.1_ASM159108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f90364e-4976-44dd-8434-a3c3716b33a8/dqc_reference/reference_markers.fasta -out GCF_001591085.1_ASM159108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:36,040] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:36,043] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:36,044] [INFO] Target genome list was writen to GCF_001591085.1_ASM159108v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:36,053] [INFO] Task started: fastANI
[2024-01-24 12:15:36,053] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9c2988a-982c-4d65-b8c4-8da37e59ce5b/GCF_001591085.1_ASM159108v1_genomic.fna.gz --refList GCF_001591085.1_ASM159108v1_genomic.fna/target_genomes.txt --output GCF_001591085.1_ASM159108v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:45,185] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:45,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f90364e-4976-44dd-8434-a3c3716b33a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:45,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f90364e-4976-44dd-8434-a3c3716b33a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:45,199] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:15:45,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:45,199] [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 natriegens	strain=NBRC 15636	GCA_001591085.1	691	691	type	True	100.0	1687	1688	95	conclusive
Vibrio natriegens	strain=ATCC 14048	GCA_001680025.1	691	691	type	True	99.9993	1686	1688	95	conclusive
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	99.9941	1688	1688	95	conclusive
Vibrio natriegens	strain=ATCC 14048	GCA_000417905.1	691	691	type	True	99.9797	1673	1688	95	conclusive
Vibrio natriegens	strain=DSM 759	GCA_000438785.2	691	691	type	True	99.9369	1603	1688	95	conclusive
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.2846	360	1688	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.2031	359	1688	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.7799	443	1688	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	79.7258	445	1688	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:45,200] [INFO] DFAST Taxonomy check result was written to GCF_001591085.1_ASM159108v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:45,201] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:45,201] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:45,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f90364e-4976-44dd-8434-a3c3716b33a8/dqc_reference/checkm_data
[2024-01-24 12:15:45,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:45,251] [INFO] Task started: CheckM
[2024-01-24 12:15:45,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591085.1_ASM159108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591085.1_ASM159108v1_genomic.fna/checkm_input GCF_001591085.1_ASM159108v1_genomic.fna/checkm_result
[2024-01-24 12:16:25,402] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:25,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:25,427] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:25,427] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:25,428] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591085.1_ASM159108v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:25,428] [INFO] Task started: Blastn
[2024-01-24 12:16:25,428] [INFO] Running command: blastn -query GCF_001591085.1_ASM159108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f90364e-4976-44dd-8434-a3c3716b33a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591085.1_ASM159108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:26,625] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:26,630] [INFO] Selected 9 target genomes.
[2024-01-24 12:16:26,630] [INFO] Target genome list was writen to GCF_001591085.1_ASM159108v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:26,642] [INFO] Task started: fastANI
[2024-01-24 12:16:26,642] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9c2988a-982c-4d65-b8c4-8da37e59ce5b/GCF_001591085.1_ASM159108v1_genomic.fna.gz --refList GCF_001591085.1_ASM159108v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591085.1_ASM159108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:36,335] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:36,349] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:36,349] [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_000417905.1	s__Vibrio natriegens	99.9797	1673	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.60	95.57	0.95	0.90	11	conclusive
GCA_018223135.1	s__Vibrio sp018223135	91.4497	1220	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222805.1	s__Vibrio sp018222805	90.0012	1202	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905175385.1	s__Vibrio sp903986855	83.7029	1035	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.95	0.95	0.92	4	-
GCF_900460535.1	s__Vibrio parahaemolyticus	83.3113	922	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
GCA_001048675.1	s__Vibrio diabolicus	82.9958	905	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_000354175.2	s__Vibrio alginolyticus	82.6804	892	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_002741985.1	s__Vibrio rotiferianus	82.058	794	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_000830505.1	s__Vibrio mytili	81.7106	767	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:36,351] [INFO] GTDB search result was written to GCF_001591085.1_ASM159108v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:36,352] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:36,356] [INFO] DFAST_QC result json was written to GCF_001591085.1_ASM159108v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:36,356] [INFO] DFAST_QC completed!
[2024-01-24 12:16:36,356] [INFO] Total running time: 0h1m16s