[2024-01-25 18:40:21,066] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:21,068] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:21,068] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fd19c36-1c8f-49af-91e1-1df41ed679dd/dqc_reference
[2024-01-25 18:40:22,235] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:22,236] [INFO] Task started: Prodigal
[2024-01-25 18:40:22,236] [INFO] Running command: gunzip -c /var/lib/cwl/stg598ec3f2-9735-49f5-9e25-a636c3727fca/GCF_002954715.1_ASM295471v1_genomic.fna.gz | prodigal -d GCF_002954715.1_ASM295471v1_genomic.fna/cds.fna -a GCF_002954715.1_ASM295471v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:30,403] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:30,404] [INFO] Task started: HMMsearch
[2024-01-25 18:40:30,404] [INFO] Running command: hmmsearch --tblout GCF_002954715.1_ASM295471v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fd19c36-1c8f-49af-91e1-1df41ed679dd/dqc_reference/reference_markers.hmm GCF_002954715.1_ASM295471v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:30,650] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:30,651] [INFO] Found 6/6 markers.
[2024-01-25 18:40:30,689] [INFO] Query marker FASTA was written to GCF_002954715.1_ASM295471v1_genomic.fna/markers.fasta
[2024-01-25 18:40:30,690] [INFO] Task started: Blastn
[2024-01-25 18:40:30,690] [INFO] Running command: blastn -query GCF_002954715.1_ASM295471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fd19c36-1c8f-49af-91e1-1df41ed679dd/dqc_reference/reference_markers.fasta -out GCF_002954715.1_ASM295471v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:31,440] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:31,443] [INFO] Selected 14 target genomes.
[2024-01-25 18:40:31,443] [INFO] Target genome list was writen to GCF_002954715.1_ASM295471v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:31,451] [INFO] Task started: fastANI
[2024-01-25 18:40:31,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg598ec3f2-9735-49f5-9e25-a636c3727fca/GCF_002954715.1_ASM295471v1_genomic.fna.gz --refList GCF_002954715.1_ASM295471v1_genomic.fna/target_genomes.txt --output GCF_002954715.1_ASM295471v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:43,645] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:43,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fd19c36-1c8f-49af-91e1-1df41ed679dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:43,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fd19c36-1c8f-49af-91e1-1df41ed679dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:43,655] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:40:43,655] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:43,655] [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
Aliivibrio sifiae	strain=NBRC 105001	GCA_002954715.1	566293	566293	type	True	99.99	1554	1576	95	conclusive
Aliivibrio finisterrensis	strain=LMG 23869	GCA_008933155.1	511998	511998	suspected-type	True	85.3777	975	1576	95	below_threshold
Aliivibrio fischeri	strain=ATCC 7744	GCA_016464335.1	668	668	suspected-type	True	83.198	948	1576	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	83.1168	997	1576	95	below_threshold
Vibrio echinoideorum	strain=DSM 107264	GCA_024347455.1	2100116	2100116	type	True	79.2221	293	1576	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	79.0781	290	1576	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_900089765.1	1194427	1194427	type	True	78.8828	282	1576	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	78.564	290	1576	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.4444	208	1576	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.434	205	1576	95	below_threshold
Vibrio casei	strain=DSM 22364	GCA_002218025.2	673372	673372	type	True	78.3497	205	1576	95	below_threshold
Photobacterium aquimaris	strain=DSM 23343	GCA_003025415.1	512643	512643	suspected-type	True	78.05	225	1576	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	77.9783	205	1576	95	below_threshold
Photobacterium malacitanum	strain=CECT 9190	GCA_900185615.1	2204294	2204294	type	True	77.8027	235	1576	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:43,656] [INFO] DFAST Taxonomy check result was written to GCF_002954715.1_ASM295471v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:43,657] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:43,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:43,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fd19c36-1c8f-49af-91e1-1df41ed679dd/dqc_reference/checkm_data
[2024-01-25 18:40:43,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:43,702] [INFO] Task started: CheckM
[2024-01-25 18:40:43,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002954715.1_ASM295471v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002954715.1_ASM295471v1_genomic.fna/checkm_input GCF_002954715.1_ASM295471v1_genomic.fna/checkm_result
[2024-01-25 18:41:13,023] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:13,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:13,049] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:13,049] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:13,049] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002954715.1_ASM295471v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:13,050] [INFO] Task started: Blastn
[2024-01-25 18:41:13,050] [INFO] Running command: blastn -query GCF_002954715.1_ASM295471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fd19c36-1c8f-49af-91e1-1df41ed679dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_002954715.1_ASM295471v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:14,191] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:14,194] [INFO] Selected 7 target genomes.
[2024-01-25 18:41:14,194] [INFO] Target genome list was writen to GCF_002954715.1_ASM295471v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:14,199] [INFO] Task started: fastANI
[2024-01-25 18:41:14,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg598ec3f2-9735-49f5-9e25-a636c3727fca/GCF_002954715.1_ASM295471v1_genomic.fna.gz --refList GCF_002954715.1_ASM295471v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002954715.1_ASM295471v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:23,079] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:23,085] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:23,085] [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_002954715.1	s__Aliivibrio sifiae	99.99	1554	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	98.51	98.40	0.92	0.91	7	conclusive
GCF_002954705.1	s__Aliivibrio sifiae_A	91.8832	1241	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001690985.1	s__Aliivibrio sp001690985	88.4287	1164	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	99.59	99.19	0.97	0.95	3	-
GCF_900312675.1	s__Aliivibrio sp900312675	86.6742	1105	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000953695.1	s__Aliivibrio wodanis	86.139	1013	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008933155.1	s__Aliivibrio finisterrensis	85.3841	972	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	95.53	95.03	0.81	0.80	11	-
GCF_000196495.1	s__Aliivibrio salmonicida_A	84.3641	973	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	97.90	97.13	0.84	0.80	5	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:23,087] [INFO] GTDB search result was written to GCF_002954715.1_ASM295471v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:23,087] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:23,090] [INFO] DFAST_QC result json was written to GCF_002954715.1_ASM295471v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:23,091] [INFO] DFAST_QC completed!
[2024-01-25 18:41:23,091] [INFO] Total running time: 0h1m2s