[2024-01-25 18:02:50,829] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:50,832] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:50,832] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd4bc3e9-bb0e-49ab-8441-f353b335b1e1/dqc_reference
[2024-01-25 18:02:51,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:51,966] [INFO] Task started: Prodigal
[2024-01-25 18:02:51,966] [INFO] Running command: gunzip -c /var/lib/cwl/stg39abdae3-7493-4306-abae-8d1ffdb52515/GCF_002218025.2_ASM221802v2_genomic.fna.gz | prodigal -d GCF_002218025.2_ASM221802v2_genomic.fna/cds.fna -a GCF_002218025.2_ASM221802v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:00,064] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:00,064] [INFO] Task started: HMMsearch
[2024-01-25 18:03:00,065] [INFO] Running command: hmmsearch --tblout GCF_002218025.2_ASM221802v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd4bc3e9-bb0e-49ab-8441-f353b335b1e1/dqc_reference/reference_markers.hmm GCF_002218025.2_ASM221802v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:00,300] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:00,301] [INFO] Found 6/6 markers.
[2024-01-25 18:03:00,337] [INFO] Query marker FASTA was written to GCF_002218025.2_ASM221802v2_genomic.fna/markers.fasta
[2024-01-25 18:03:00,338] [INFO] Task started: Blastn
[2024-01-25 18:03:00,338] [INFO] Running command: blastn -query GCF_002218025.2_ASM221802v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd4bc3e9-bb0e-49ab-8441-f353b335b1e1/dqc_reference/reference_markers.fasta -out GCF_002218025.2_ASM221802v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:01,093] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:01,095] [INFO] Selected 12 target genomes.
[2024-01-25 18:03:01,096] [INFO] Target genome list was writen to GCF_002218025.2_ASM221802v2_genomic.fna/target_genomes.txt
[2024-01-25 18:03:01,123] [INFO] Task started: fastANI
[2024-01-25 18:03:01,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg39abdae3-7493-4306-abae-8d1ffdb52515/GCF_002218025.2_ASM221802v2_genomic.fna.gz --refList GCF_002218025.2_ASM221802v2_genomic.fna/target_genomes.txt --output GCF_002218025.2_ASM221802v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:12,698] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:12,699] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd4bc3e9-bb0e-49ab-8441-f353b335b1e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:12,699] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd4bc3e9-bb0e-49ab-8441-f353b335b1e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:12,707] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:12,707] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:12,707] [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 casei	strain=DSM 22364	GCA_002218025.2	673372	673372	type	True	100.0	1377	1378	95	conclusive
Vibrio litoralis	strain=DSM 17657	GCA_000426765.1	335972	335972	type	True	82.7366	652	1378	95	below_threshold
Vibrio rumoiensis	strain=FERM P-14531	GCA_002218045.2	76258	76258	type	True	81.9695	641	1378	95	below_threshold
Vibrio algivorus	strain=SA2	GCA_002218005.2	1667024	1667024	type	True	81.6723	609	1378	95	below_threshold
Vibrio hibernica	strain=B1.19	GCA_015223435.1	2587465	2587465	type	True	81.3182	471	1378	95	below_threshold
Vibrio gangliei	strain=SZDIS-1	GCA_002934045.1	2077090	2077090	type	True	80.1221	511	1378	95	below_threshold
Vibrio aphrogenes	strain=CA-1004	GCA_002157735.2	1891186	1891186	type	True	80.0788	492	1378	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	80.0776	431	1378	95	below_threshold
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	79.7995	175	1378	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	79.7438	221	1378	95	below_threshold
Vibrio cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	79.6047	223	1378	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	77.6037	162	1378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:12,709] [INFO] DFAST Taxonomy check result was written to GCF_002218025.2_ASM221802v2_genomic.fna/tc_result.tsv
[2024-01-25 18:03:12,710] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:12,710] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:12,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd4bc3e9-bb0e-49ab-8441-f353b335b1e1/dqc_reference/checkm_data
[2024-01-25 18:03:12,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:12,752] [INFO] Task started: CheckM
[2024-01-25 18:03:12,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002218025.2_ASM221802v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002218025.2_ASM221802v2_genomic.fna/checkm_input GCF_002218025.2_ASM221802v2_genomic.fna/checkm_result
[2024-01-25 18:03:40,997] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:40,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:41,015] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:41,016] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:41,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002218025.2_ASM221802v2_genomic.fna/markers.fasta)
[2024-01-25 18:03:41,016] [INFO] Task started: Blastn
[2024-01-25 18:03:41,016] [INFO] Running command: blastn -query GCF_002218025.2_ASM221802v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd4bc3e9-bb0e-49ab-8441-f353b335b1e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002218025.2_ASM221802v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:42,178] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:42,191] [INFO] Selected 10 target genomes.
[2024-01-25 18:03:42,192] [INFO] Target genome list was writen to GCF_002218025.2_ASM221802v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:42,203] [INFO] Task started: fastANI
[2024-01-25 18:03:42,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg39abdae3-7493-4306-abae-8d1ffdb52515/GCF_002218025.2_ASM221802v2_genomic.fna.gz --refList GCF_002218025.2_ASM221802v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002218025.2_ASM221802v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:51,536] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:51,543] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:51,543] [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_002218025.2	s__Vibrio casei	100.0	1378	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.63	99.33	0.95	0.89	5	conclusive
GCF_000426765.1	s__Vibrio litoralis	82.746	651	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.36	97.06	0.89	0.86	3	-
GCF_002218045.2	s__Vibrio rumoiensis	81.9536	643	1378	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	81.8558	735	1378	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	81.5471	607	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.65	98.65	0.88	0.88	2	-
GCF_014694375.1	s__Vibrio sp014694375	81.4392	552	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223435.1	s__Vibrio hibernica	81.3182	471	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157735.2	s__Vibrio aphrogenes	80.1189	495	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934045.1	s__Vibrio gangliei	80.1094	511	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601765.2	s__Vibrio sp009601765	80.077	431	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.01	99.01	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:51,545] [INFO] GTDB search result was written to GCF_002218025.2_ASM221802v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:51,545] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:51,548] [INFO] DFAST_QC result json was written to GCF_002218025.2_ASM221802v2_genomic.fna/dqc_result.json
[2024-01-25 18:03:51,548] [INFO] DFAST_QC completed!
[2024-01-25 18:03:51,548] [INFO] Total running time: 0h1m1s