[2024-01-24 13:43:26,895] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:43:26,897] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:43:26,898] [INFO] DQC Reference Directory: /var/lib/cwl/stgb738a9d4-aa06-466b-b730-4ce4663adc88/dqc_reference
[2024-01-24 13:43:28,122] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:43:28,123] [INFO] Task started: Prodigal
[2024-01-24 13:43:28,123] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcd082db-0db1-4f25-b469-ce315a7b84b2/GCF_002749895.1_ASM274989v1_genomic.fna.gz | prodigal -d GCF_002749895.1_ASM274989v1_genomic.fna/cds.fna -a GCF_002749895.1_ASM274989v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:36,275] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:36,275] [INFO] Task started: HMMsearch
[2024-01-24 13:43:36,275] [INFO] Running command: hmmsearch --tblout GCF_002749895.1_ASM274989v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb738a9d4-aa06-466b-b730-4ce4663adc88/dqc_reference/reference_markers.hmm GCF_002749895.1_ASM274989v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:36,496] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:36,497] [INFO] Found 6/6 markers.
[2024-01-24 13:43:36,533] [INFO] Query marker FASTA was written to GCF_002749895.1_ASM274989v1_genomic.fna/markers.fasta
[2024-01-24 13:43:36,533] [INFO] Task started: Blastn
[2024-01-24 13:43:36,534] [INFO] Running command: blastn -query GCF_002749895.1_ASM274989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb738a9d4-aa06-466b-b730-4ce4663adc88/dqc_reference/reference_markers.fasta -out GCF_002749895.1_ASM274989v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:37,292] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:37,295] [INFO] Selected 16 target genomes.
[2024-01-24 13:43:37,296] [INFO] Target genome list was writen to GCF_002749895.1_ASM274989v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:37,329] [INFO] Task started: fastANI
[2024-01-24 13:43:37,329] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcd082db-0db1-4f25-b469-ce315a7b84b2/GCF_002749895.1_ASM274989v1_genomic.fna.gz --refList GCF_002749895.1_ASM274989v1_genomic.fna/target_genomes.txt --output GCF_002749895.1_ASM274989v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:48,938] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:48,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb738a9d4-aa06-466b-b730-4ce4663adc88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:48,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb738a9d4-aa06-466b-b730-4ce4663adc88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:48,952] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:48,952] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:48,952] [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 fujianensis	strain=FJ201301	GCA_002749895.1	1974215	1974215	type	True	99.9805	1181	1182	95	conclusive
Vibrio cincinnatiensis	strain=NCTC12012	GCA_900460255.1	675	675	type	True	84.6629	838	1182	95	below_threshold
Vibrio cincinnatiensis	strain=DSM 19608	GCA_900167345.1	675	675	type	True	84.6328	817	1182	95	below_threshold
Vibrio metschnikovii	strain=CIP 69.14	GCA_000176155.1	28172	28172	type	True	80.8932	574	1182	95	below_threshold
Vibrio metschnikovii	strain=NCTC8443	GCA_900460295.1	28172	28172	type	True	80.8663	578	1182	95	below_threshold
Vibrio injensis	strain=M12-1144	GCA_001895205.1	1307414	1307414	type	True	80.6539	527	1182	95	below_threshold
Vibrio fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	79.4986	333	1182	95	below_threshold
Vibrio fluvialis	strain=NCTC11327	GCA_900460245.1	676	676	type	True	79.4623	333	1182	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	79.4345	335	1182	95	below_threshold
Vibrio fluvialis	strain=NBRC 103150	GCA_001598835.1	676	676	type	True	79.4215	335	1182	95	below_threshold
Vibrio mimicus	strain=NCTC11435	GCA_900460385.1	674	674	type	True	78.5788	313	1182	95	below_threshold
Vibrio mimicus	strain=CAIM 602	GCA_000338875.1	674	674	type	True	78.5215	312	1182	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	78.4181	325	1182	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	78.2724	203	1182	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	78.2075	159	1182	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	77.9976	222	1182	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:48,954] [INFO] DFAST Taxonomy check result was written to GCF_002749895.1_ASM274989v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:48,954] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:48,954] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:48,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb738a9d4-aa06-466b-b730-4ce4663adc88/dqc_reference/checkm_data
[2024-01-24 13:43:48,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:48,991] [INFO] Task started: CheckM
[2024-01-24 13:43:48,991] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002749895.1_ASM274989v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002749895.1_ASM274989v1_genomic.fna/checkm_input GCF_002749895.1_ASM274989v1_genomic.fna/checkm_result
[2024-01-24 13:44:17,937] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:17,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:17,956] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:17,956] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:17,956] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002749895.1_ASM274989v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:17,956] [INFO] Task started: Blastn
[2024-01-24 13:44:17,957] [INFO] Running command: blastn -query GCF_002749895.1_ASM274989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb738a9d4-aa06-466b-b730-4ce4663adc88/dqc_reference/reference_markers_gtdb.fasta -out GCF_002749895.1_ASM274989v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:19,065] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:19,074] [INFO] Selected 15 target genomes.
[2024-01-24 13:44:19,075] [INFO] Target genome list was writen to GCF_002749895.1_ASM274989v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:19,101] [INFO] Task started: fastANI
[2024-01-24 13:44:19,102] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcd082db-0db1-4f25-b469-ce315a7b84b2/GCF_002749895.1_ASM274989v1_genomic.fna.gz --refList GCF_002749895.1_ASM274989v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002749895.1_ASM274989v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:30,489] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:30,501] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:30,501] [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_002749895.1	s__Vibrio fujianensis	99.9805	1181	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.21	99.14	0.95	0.93	8	conclusive
GCF_900167345.1	s__Vibrio cincinnatiensis	84.6214	821	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	99.06	0.97	0.94	6	-
GCF_000176155.1	s__Vibrio metschnikovii	80.9312	575	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.65	97.32	0.91	0.86	50	-
GCF_001895205.1	s__Vibrio injensis	80.6714	527	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.81	98.81	0.92	0.92	2	-
GCF_900460245.1	s__Vibrio fluvialis	79.4501	335	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
GCF_000176175.1	s__Vibrio furnissii	79.3101	329	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.58	97.97	0.95	0.91	12	-
GCF_009763805.1	s__Vibrio cidicii	79.1118	251	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.20	97.77	0.90	0.87	8	-
GCF_000764325.1	s__Vibrio navarrensis	78.9158	257	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.19	97.06	0.93	0.87	22	-
GCA_007124475.1	s__Vibrio sp007124475	78.8828	323	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.98	98.98	0.80	0.80	2	-
GCF_011064285.1	s__Vibrio ziniensis	78.6207	286	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011306175.1	s__Vibrio sp011306175	78.6085	292	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338875.1	s__Vibrio mimicus	78.5651	310	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.81	0.94	0.91	26	-
GCF_012395185.1	s__Vibrio aestuarianus	78.5516	315	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.70	96.75	0.86	0.80	14	-
GCF_014050145.1	s__Vibrio marinisediminis	78.1862	227	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222585.1	s__Vibrio scophthalmi	78.0109	228	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:30,502] [INFO] GTDB search result was written to GCF_002749895.1_ASM274989v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:30,503] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:30,506] [INFO] DFAST_QC result json was written to GCF_002749895.1_ASM274989v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:30,506] [INFO] DFAST_QC completed!
[2024-01-24 13:44:30,506] [INFO] Total running time: 0h1m4s