[2024-01-24 13:32:16,113] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:16,116] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:16,116] [INFO] DQC Reference Directory: /var/lib/cwl/stg98465e8c-2cae-4a5b-a943-a29ecf83642a/dqc_reference
[2024-01-24 13:32:17,435] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:17,436] [INFO] Task started: Prodigal
[2024-01-24 13:32:17,436] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e4cb72c-1a9e-4566-9d55-96fe6ffffb96/GCF_004764665.1_ASM476466v1_genomic.fna.gz | prodigal -d GCF_004764665.1_ASM476466v1_genomic.fna/cds.fna -a GCF_004764665.1_ASM476466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:31,216] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:31,217] [INFO] Task started: HMMsearch
[2024-01-24 13:32:31,217] [INFO] Running command: hmmsearch --tblout GCF_004764665.1_ASM476466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98465e8c-2cae-4a5b-a943-a29ecf83642a/dqc_reference/reference_markers.hmm GCF_004764665.1_ASM476466v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:31,569] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:31,571] [INFO] Found 6/6 markers.
[2024-01-24 13:32:31,616] [INFO] Query marker FASTA was written to GCF_004764665.1_ASM476466v1_genomic.fna/markers.fasta
[2024-01-24 13:32:31,617] [INFO] Task started: Blastn
[2024-01-24 13:32:31,617] [INFO] Running command: blastn -query GCF_004764665.1_ASM476466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98465e8c-2cae-4a5b-a943-a29ecf83642a/dqc_reference/reference_markers.fasta -out GCF_004764665.1_ASM476466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:32,488] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:32,492] [INFO] Selected 14 target genomes.
[2024-01-24 13:32:32,492] [INFO] Target genome list was writen to GCF_004764665.1_ASM476466v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:32,493] [INFO] Task started: fastANI
[2024-01-24 13:32:32,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e4cb72c-1a9e-4566-9d55-96fe6ffffb96/GCF_004764665.1_ASM476466v1_genomic.fna.gz --refList GCF_004764665.1_ASM476466v1_genomic.fna/target_genomes.txt --output GCF_004764665.1_ASM476466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:50,718] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:50,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98465e8c-2cae-4a5b-a943-a29ecf83642a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:50,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98465e8c-2cae-4a5b-a943-a29ecf83642a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:50,731] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:50,731] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:50,732] [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 echinoideorum	strain=NFH.MB010	GCA_004764665.1	2100116	2100116	type	True	100.0	1841	1845	95	conclusive
Vibrio echinoideorum	strain=DSM 107264	GCA_024347455.1	2100116	2100116	type	True	99.9984	1842	1845	95	conclusive
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	90.2535	1512	1845	95	below_threshold
Vibrio splendidus	strain=NCCB 53037	GCA_001558015.1	29497	29497	type	True	90.2335	1510	1845	95	below_threshold
Vibrio cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	89.8829	1448	1845	95	below_threshold
Vibrio lentus	strain=40M4T	GCA_014878155.1	136468	136468	type	True	89.3216	1458	1845	95	below_threshold
Vibrio bathopelagicus	strain=Sal10	GCA_014879975.1	2777577	2777577	type	True	88.7089	1462	1845	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	88.639	1306	1845	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	88.6128	1320	1845	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	88.4632	1307	1845	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	88.4336	1451	1845	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	88.2905	1448	1845	95	below_threshold
Vibrio crassostreae	strain=LGP7	GCA_001048535.1	246167	246167	type	True	88.2262	1431	1845	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	87.545	1390	1845	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:50,734] [INFO] DFAST Taxonomy check result was written to GCF_004764665.1_ASM476466v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:50,734] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:50,734] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:50,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98465e8c-2cae-4a5b-a943-a29ecf83642a/dqc_reference/checkm_data
[2024-01-24 13:32:50,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:50,790] [INFO] Task started: CheckM
[2024-01-24 13:32:50,790] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004764665.1_ASM476466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004764665.1_ASM476466v1_genomic.fna/checkm_input GCF_004764665.1_ASM476466v1_genomic.fna/checkm_result
[2024-01-24 13:33:35,072] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:35,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:35,096] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:35,096] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:35,097] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004764665.1_ASM476466v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:35,097] [INFO] Task started: Blastn
[2024-01-24 13:33:35,097] [INFO] Running command: blastn -query GCF_004764665.1_ASM476466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98465e8c-2cae-4a5b-a943-a29ecf83642a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004764665.1_ASM476466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:36,309] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:36,312] [INFO] Selected 14 target genomes.
[2024-01-24 13:33:36,312] [INFO] Target genome list was writen to GCF_004764665.1_ASM476466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:36,313] [INFO] Task started: fastANI
[2024-01-24 13:33:36,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e4cb72c-1a9e-4566-9d55-96fe6ffffb96/GCF_004764665.1_ASM476466v1_genomic.fna.gz --refList GCF_004764665.1_ASM476466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004764665.1_ASM476466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:53,383] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:53,401] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:53,402] [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_004764665.1	s__Vibrio echinoideorum	100.0	1841	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.83	0.88	0.82	5	conclusive
GCF_001558015.1	s__Vibrio splendidus	90.2454	1508	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.85	95.03	0.88	0.83	97	-
GCF_002873455.1	s__Vibrio splendidus_J	90.0492	1463	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.45	97.37	0.93	0.92	7	-
GCF_002875945.1	s__Vibrio lentus_A	89.3784	1441	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014878155.1	s__Vibrio lentus	89.3216	1458	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.56	0.86	0.83	91	-
GCF_014879975.1	s__Vibrio bathopelagicus	88.7187	1460	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089855.1	s__Vibrio atlanticus	88.6498	1305	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	N/A	N/A	N/A	N/A	1	-
GCF_000272045.2	s__Vibrio crassostreae_C	88.6065	1402	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_000272405.2	s__Vibrio tasmaniensis_A	88.5979	1247	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
GCF_006333845.1	s__Vibrio tasmaniensis	88.3948	1265	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	-
GCF_007858795.1	s__Vibrio sp007858795	88.2439	1383	1845	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	88.234	1430	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.86	96.20	0.91	0.83	177	-
GCF_001557875.1	s__Vibrio splendidus_F	88.1256	1376	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_013394185.1	s__Vibrio sp013394185	87.8896	1436	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:53,403] [INFO] GTDB search result was written to GCF_004764665.1_ASM476466v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:53,404] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:53,407] [INFO] DFAST_QC result json was written to GCF_004764665.1_ASM476466v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:53,408] [INFO] DFAST_QC completed!
[2024-01-24 13:33:53,408] [INFO] Total running time: 0h1m37s