[2024-01-24 12:14:49,101] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:49,103] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:49,103] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ebdf45f-8643-454d-8ef5-44b38cd98667/dqc_reference
[2024-01-24 12:14:50,390] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,391] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,392] [INFO] Running command: gunzip -c /var/lib/cwl/stg32212399-aa06-49a0-b7eb-1c4d7601b99c/GCF_009601765.2_ASM960176v2_genomic.fna.gz | prodigal -d GCF_009601765.2_ASM960176v2_genomic.fna/cds.fna -a GCF_009601765.2_ASM960176v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:59,589] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:59,590] [INFO] Task started: HMMsearch
[2024-01-24 12:14:59,590] [INFO] Running command: hmmsearch --tblout GCF_009601765.2_ASM960176v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ebdf45f-8643-454d-8ef5-44b38cd98667/dqc_reference/reference_markers.hmm GCF_009601765.2_ASM960176v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:59,853] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:59,854] [INFO] Found 6/6 markers.
[2024-01-24 12:14:59,889] [INFO] Query marker FASTA was written to GCF_009601765.2_ASM960176v2_genomic.fna/markers.fasta
[2024-01-24 12:14:59,890] [INFO] Task started: Blastn
[2024-01-24 12:14:59,890] [INFO] Running command: blastn -query GCF_009601765.2_ASM960176v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ebdf45f-8643-454d-8ef5-44b38cd98667/dqc_reference/reference_markers.fasta -out GCF_009601765.2_ASM960176v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:00,825] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:00,829] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:00,829] [INFO] Target genome list was writen to GCF_009601765.2_ASM960176v2_genomic.fna/target_genomes.txt
[2024-01-24 12:15:00,845] [INFO] Task started: fastANI
[2024-01-24 12:15:00,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg32212399-aa06-49a0-b7eb-1c4d7601b99c/GCF_009601765.2_ASM960176v2_genomic.fna.gz --refList GCF_009601765.2_ASM960176v2_genomic.fna/target_genomes.txt --output GCF_009601765.2_ASM960176v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:13,089] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:13,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ebdf45f-8643-454d-8ef5-44b38cd98667/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:13,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ebdf45f-8643-454d-8ef5-44b38cd98667/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:13,101] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:13,102] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:13,102] [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 algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	100.0	1164	1169	95	conclusive
Vibrio hibernica	strain=B1.19	GCA_015223435.1	2587465	2587465	type	True	80.9656	567	1169	95	below_threshold
Vibrio casei	strain=DSM 22364	GCA_002218025.2	673372	673372	type	True	80.1038	415	1169	95	below_threshold
Vibrio rumoiensis	strain=FERM P-14531	GCA_002218045.2	76258	76258	type	True	80.0299	467	1169	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	79.8809	203	1169	95	below_threshold
Vibrio algivorus	strain=SA2	GCA_002218005.2	1667024	1667024	type	True	79.8107	449	1169	95	below_threshold
Vibrio litoralis	strain=DSM 17657	GCA_000426765.1	335972	335972	type	True	79.6161	471	1169	95	below_threshold
Vibrio artabrorum	strain=CECT 7226	GCA_024347295.1	446374	446374	type	True	79.596	211	1169	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	79.3935	216	1169	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.326	173	1169	95	below_threshold
Vibrio gangliei	strain=SZDIS-1	GCA_002934045.1	2077090	2077090	type	True	79.1671	431	1169	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.5925	174	1169	95	below_threshold
Vibrio ezurae	strain=HDS1-1	GCA_003568985.1	252583	252583	type	True	78.4068	180	1169	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:13,104] [INFO] DFAST Taxonomy check result was written to GCF_009601765.2_ASM960176v2_genomic.fna/tc_result.tsv
[2024-01-24 12:15:13,104] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:13,104] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:13,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ebdf45f-8643-454d-8ef5-44b38cd98667/dqc_reference/checkm_data
[2024-01-24 12:15:13,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:13,145] [INFO] Task started: CheckM
[2024-01-24 12:15:13,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009601765.2_ASM960176v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009601765.2_ASM960176v2_genomic.fna/checkm_input GCF_009601765.2_ASM960176v2_genomic.fna/checkm_result
[2024-01-24 12:15:45,119] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:45,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:45,144] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:45,144] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:45,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009601765.2_ASM960176v2_genomic.fna/markers.fasta)
[2024-01-24 12:15:45,145] [INFO] Task started: Blastn
[2024-01-24 12:15:45,145] [INFO] Running command: blastn -query GCF_009601765.2_ASM960176v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ebdf45f-8643-454d-8ef5-44b38cd98667/dqc_reference/reference_markers_gtdb.fasta -out GCF_009601765.2_ASM960176v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:46,330] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:46,334] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:46,335] [INFO] Target genome list was writen to GCF_009601765.2_ASM960176v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:46,343] [INFO] Task started: fastANI
[2024-01-24 12:15:46,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg32212399-aa06-49a0-b7eb-1c4d7601b99c/GCF_009601765.2_ASM960176v2_genomic.fna.gz --refList GCF_009601765.2_ASM960176v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009601765.2_ASM960176v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:53,924] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:53,934] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:53,935] [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_009601765.2	s__Vibrio sp009601765	100.0	1163	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.01	99.01	0.85	0.85	2	conclusive
GCF_015223435.1	s__Vibrio hibernica	80.9619	567	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014694375.1	s__Vibrio sp014694375	80.8134	609	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002218025.2	s__Vibrio casei	80.1532	415	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.63	99.33	0.95	0.89	5	-
GCF_002218045.2	s__Vibrio rumoiensis	80.0599	467	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000286955.2	s__Vibrio rumoiensis_A	79.8774	457	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002218005.2	s__Vibrio algivorus	79.8104	447	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.65	98.65	0.88	0.88	2	-
GCF_000426765.1	s__Vibrio litoralis	79.6184	472	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.36	97.06	0.89	0.86	3	-
GCF_002934045.1	s__Vibrio gangliei	79.1728	430	1169	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 12:15:53,937] [INFO] GTDB search result was written to GCF_009601765.2_ASM960176v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:53,938] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:53,941] [INFO] DFAST_QC result json was written to GCF_009601765.2_ASM960176v2_genomic.fna/dqc_result.json
[2024-01-24 12:15:53,941] [INFO] DFAST_QC completed!
[2024-01-24 12:15:53,941] [INFO] Total running time: 0h1m5s