[2024-01-24 14:14:00,270] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:00,272] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:00,273] [INFO] DQC Reference Directory: /var/lib/cwl/stga3cccd92-1ecd-4ee0-8a6d-77e5d82e8525/dqc_reference
[2024-01-24 14:14:01,536] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:01,537] [INFO] Task started: Prodigal
[2024-01-24 14:14:01,537] [INFO] Running command: gunzip -c /var/lib/cwl/stg75521db7-4a0d-4a43-8454-7d2f07a52d30/GCF_006333845.1_ASM633384v1_genomic.fna.gz | prodigal -d GCF_006333845.1_ASM633384v1_genomic.fna/cds.fna -a GCF_006333845.1_ASM633384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:13,925] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:13,926] [INFO] Task started: HMMsearch
[2024-01-24 14:14:13,926] [INFO] Running command: hmmsearch --tblout GCF_006333845.1_ASM633384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3cccd92-1ecd-4ee0-8a6d-77e5d82e8525/dqc_reference/reference_markers.hmm GCF_006333845.1_ASM633384v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:14,375] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:14,377] [INFO] Found 6/6 markers.
[2024-01-24 14:14:14,520] [INFO] Query marker FASTA was written to GCF_006333845.1_ASM633384v1_genomic.fna/markers.fasta
[2024-01-24 14:14:14,521] [INFO] Task started: Blastn
[2024-01-24 14:14:14,521] [INFO] Running command: blastn -query GCF_006333845.1_ASM633384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3cccd92-1ecd-4ee0-8a6d-77e5d82e8525/dqc_reference/reference_markers.fasta -out GCF_006333845.1_ASM633384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:15,510] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:15,513] [INFO] Selected 11 target genomes.
[2024-01-24 14:14:15,513] [INFO] Target genome list was writen to GCF_006333845.1_ASM633384v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:15,519] [INFO] Task started: fastANI
[2024-01-24 14:14:15,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg75521db7-4a0d-4a43-8454-7d2f07a52d30/GCF_006333845.1_ASM633384v1_genomic.fna.gz --refList GCF_006333845.1_ASM633384v1_genomic.fna/target_genomes.txt --output GCF_006333845.1_ASM633384v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:32,499] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:32,500] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3cccd92-1ecd-4ee0-8a6d-77e5d82e8525/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:32,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3cccd92-1ecd-4ee0-8a6d-77e5d82e8525/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:32,526] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:14:32,527] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:32,527] [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 tasmaniensis	strain=LMG 20012	GCA_006333845.1	212663	212663	suspected-type	True	100.0	1538	1545	95	conclusive
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	99.9979	1543	1545	95	conclusive
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	94.3609	1349	1545	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	94.2798	1367	1545	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	90.7625	1311	1545	95	below_threshold
Vibrio lentus	strain=40M4T	GCA_014878155.1	136468	136468	type	True	89.9981	1265	1545	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	89.78	1268	1545	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	89.6876	1282	1545	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	89.3399	1301	1545	95	below_threshold
Vibrio crassostreae	strain=LGP7	GCA_001048535.1	246167	246167	type	True	89.3279	1281	1545	95	below_threshold
Vibrio bathopelagicus	strain=Sal10	GCA_014879975.1	2777577	2777577	type	True	88.976	1259	1545	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:32,529] [INFO] DFAST Taxonomy check result was written to GCF_006333845.1_ASM633384v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:32,529] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:32,530] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:32,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3cccd92-1ecd-4ee0-8a6d-77e5d82e8525/dqc_reference/checkm_data
[2024-01-24 14:14:32,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:32,625] [INFO] Task started: CheckM
[2024-01-24 14:14:32,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006333845.1_ASM633384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006333845.1_ASM633384v1_genomic.fna/checkm_input GCF_006333845.1_ASM633384v1_genomic.fna/checkm_result
[2024-01-24 14:15:11,407] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:11,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:11,431] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:11,432] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:11,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006333845.1_ASM633384v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:11,433] [INFO] Task started: Blastn
[2024-01-24 14:15:11,433] [INFO] Running command: blastn -query GCF_006333845.1_ASM633384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3cccd92-1ecd-4ee0-8a6d-77e5d82e8525/dqc_reference/reference_markers_gtdb.fasta -out GCF_006333845.1_ASM633384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:12,664] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:12,668] [INFO] Selected 12 target genomes.
[2024-01-24 14:15:12,668] [INFO] Target genome list was writen to GCF_006333845.1_ASM633384v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:12,679] [INFO] Task started: fastANI
[2024-01-24 14:15:12,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg75521db7-4a0d-4a43-8454-7d2f07a52d30/GCF_006333845.1_ASM633384v1_genomic.fna.gz --refList GCF_006333845.1_ASM633384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006333845.1_ASM633384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:27,418] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:27,434] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:27,435] [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_006333845.1	s__Vibrio tasmaniensis	100.0	1538	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	conclusive
GCF_900089855.1	s__Vibrio atlanticus	94.3461	1350	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	N/A	N/A	N/A	N/A	1	-
GCF_000272405.2	s__Vibrio tasmaniensis_A	94.1931	1273	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
GCF_002873455.1	s__Vibrio splendidus_J	90.0333	1290	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.45	97.37	0.93	0.92	7	-
GCF_014878155.1	s__Vibrio lentus	89.9755	1267	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.56	0.86	0.83	91	-
GCF_002156455.1	s__Vibrio coralliirubri	89.8063	1249	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	96.55	95.77	0.88	0.83	22	-
GCF_000272045.2	s__Vibrio crassostreae_C	89.6994	1256	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_000272105.2	s__Vibrio splendidus_I	89.5506	1231	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002875945.1	s__Vibrio lentus_A	89.516	1257	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001048535.1	s__Vibrio crassostreae	89.3279	1281	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.86	96.20	0.91	0.83	177	-
GCF_007858795.1	s__Vibrio sp007858795	89.2768	1251	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014879975.1	s__Vibrio bathopelagicus	88.976	1259	1545	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 14:15:27,437] [INFO] GTDB search result was written to GCF_006333845.1_ASM633384v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:27,438] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:27,443] [INFO] DFAST_QC result json was written to GCF_006333845.1_ASM633384v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:27,444] [INFO] DFAST_QC completed!
[2024-01-24 14:15:27,444] [INFO] Total running time: 0h1m27s