[2024-01-24 14:04:31,711] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:04:31,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:04:31,713] [INFO] DQC Reference Directory: /var/lib/cwl/stg58e9c36a-8bf6-4fb7-bbcc-1c93d265137a/dqc_reference
[2024-01-24 14:04:33,031] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:04:33,032] [INFO] Task started: Prodigal
[2024-01-24 14:04:33,032] [INFO] Running command: gunzip -c /var/lib/cwl/stga83a5ada-d3b0-4111-b517-633e0e8a9207/GCF_000426765.1_ASM42676v1_genomic.fna.gz | prodigal -d GCF_000426765.1_ASM42676v1_genomic.fna/cds.fna -a GCF_000426765.1_ASM42676v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:04:41,667] [INFO] Task succeeded: Prodigal
[2024-01-24 14:04:41,668] [INFO] Task started: HMMsearch
[2024-01-24 14:04:41,668] [INFO] Running command: hmmsearch --tblout GCF_000426765.1_ASM42676v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58e9c36a-8bf6-4fb7-bbcc-1c93d265137a/dqc_reference/reference_markers.hmm GCF_000426765.1_ASM42676v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:04:42,003] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:04:42,005] [INFO] Found 6/6 markers.
[2024-01-24 14:04:42,040] [INFO] Query marker FASTA was written to GCF_000426765.1_ASM42676v1_genomic.fna/markers.fasta
[2024-01-24 14:04:42,041] [INFO] Task started: Blastn
[2024-01-24 14:04:42,041] [INFO] Running command: blastn -query GCF_000426765.1_ASM42676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58e9c36a-8bf6-4fb7-bbcc-1c93d265137a/dqc_reference/reference_markers.fasta -out GCF_000426765.1_ASM42676v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:42,949] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:42,952] [INFO] Selected 12 target genomes.
[2024-01-24 14:04:42,953] [INFO] Target genome list was writen to GCF_000426765.1_ASM42676v1_genomic.fna/target_genomes.txt
[2024-01-24 14:04:43,036] [INFO] Task started: fastANI
[2024-01-24 14:04:43,037] [INFO] Running command: fastANI --query /var/lib/cwl/stga83a5ada-d3b0-4111-b517-633e0e8a9207/GCF_000426765.1_ASM42676v1_genomic.fna.gz --refList GCF_000426765.1_ASM42676v1_genomic.fna/target_genomes.txt --output GCF_000426765.1_ASM42676v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:04:54,561] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:54,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58e9c36a-8bf6-4fb7-bbcc-1c93d265137a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:04:54,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58e9c36a-8bf6-4fb7-bbcc-1c93d265137a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:04:54,573] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:04:54,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:04:54,573] [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 litoralis	strain=DSM 17657	GCA_000426765.1	335972	335972	type	True	100.0	1262	1264	95	conclusive
Vibrio algivorus	strain=SA2	GCA_002218005.2	1667024	1667024	type	True	88.9001	1001	1264	95	below_threshold
Vibrio rumoiensis	strain=FERM P-14531	GCA_002218045.2	76258	76258	type	True	85.3092	990	1264	95	below_threshold
Vibrio casei	strain=DSM 22364	GCA_002218025.2	673372	673372	type	True	82.7241	650	1264	95	below_threshold
Vibrio gangliei	strain=SZDIS-1	GCA_002934045.1	2077090	2077090	type	True	81.1887	654	1264	95	below_threshold
Vibrio aphrogenes	strain=CA-1004	GCA_002157735.2	1891186	1891186	type	True	80.6311	591	1264	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	79.561	474	1264	95	below_threshold
Vibrio hibernica	strain=B1.19	GCA_015223435.1	2587465	2587465	type	True	79.5555	420	1264	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	78.6194	207	1264	95	below_threshold
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	78.6125	203	1264	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.5784	210	1264	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.5525	211	1264	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:04:54,577] [INFO] DFAST Taxonomy check result was written to GCF_000426765.1_ASM42676v1_genomic.fna/tc_result.tsv
[2024-01-24 14:04:54,579] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:04:54,579] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:04:54,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58e9c36a-8bf6-4fb7-bbcc-1c93d265137a/dqc_reference/checkm_data
[2024-01-24 14:04:54,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:04:54,623] [INFO] Task started: CheckM
[2024-01-24 14:04:54,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000426765.1_ASM42676v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000426765.1_ASM42676v1_genomic.fna/checkm_input GCF_000426765.1_ASM42676v1_genomic.fna/checkm_result
[2024-01-24 14:05:27,141] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:27,143] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:27,165] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:27,165] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:27,166] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000426765.1_ASM42676v1_genomic.fna/markers.fasta)
[2024-01-24 14:05:27,166] [INFO] Task started: Blastn
[2024-01-24 14:05:27,166] [INFO] Running command: blastn -query GCF_000426765.1_ASM42676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58e9c36a-8bf6-4fb7-bbcc-1c93d265137a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000426765.1_ASM42676v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:28,362] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:28,365] [INFO] Selected 8 target genomes.
[2024-01-24 14:05:28,365] [INFO] Target genome list was writen to GCF_000426765.1_ASM42676v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:28,429] [INFO] Task started: fastANI
[2024-01-24 14:05:28,429] [INFO] Running command: fastANI --query /var/lib/cwl/stga83a5ada-d3b0-4111-b517-633e0e8a9207/GCF_000426765.1_ASM42676v1_genomic.fna.gz --refList GCF_000426765.1_ASM42676v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000426765.1_ASM42676v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:35,729] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:35,741] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:05:35,741] [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_000426765.1	s__Vibrio litoralis	100.0	1262	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.36	97.06	0.89	0.86	3	conclusive
GCF_002218005.2	s__Vibrio algivorus	88.9285	999	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.65	98.65	0.88	0.88	2	-
GCF_002218045.2	s__Vibrio rumoiensis	85.3192	989	1264	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	82.6808	654	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.63	99.33	0.95	0.89	5	-
GCF_002934045.1	s__Vibrio gangliei	81.1901	653	1264	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	80.6105	595	1264	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	80.492	590	1264	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	79.5054	465	1264	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 14:05:35,743] [INFO] GTDB search result was written to GCF_000426765.1_ASM42676v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:35,744] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:35,747] [INFO] DFAST_QC result json was written to GCF_000426765.1_ASM42676v1_genomic.fna/dqc_result.json
[2024-01-24 14:05:35,747] [INFO] DFAST_QC completed!
[2024-01-24 14:05:35,747] [INFO] Total running time: 0h1m4s