[2024-01-25 18:39:20,396] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:20,397] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:20,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c5ca3b6-9180-4d48-9d3c-f5c67b61771f/dqc_reference
[2024-01-25 18:39:21,535] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:21,535] [INFO] Task started: Prodigal
[2024-01-25 18:39:21,535] [INFO] Running command: gunzip -c /var/lib/cwl/stg1eeea811-264e-4e87-aeda-a14e09b0e6f5/GCF_001895205.1_ASM189520v1_genomic.fna.gz | prodigal -d GCF_001895205.1_ASM189520v1_genomic.fna/cds.fna -a GCF_001895205.1_ASM189520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:39:28,872] [INFO] Task succeeded: Prodigal
[2024-01-25 18:39:28,873] [INFO] Task started: HMMsearch
[2024-01-25 18:39:28,873] [INFO] Running command: hmmsearch --tblout GCF_001895205.1_ASM189520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c5ca3b6-9180-4d48-9d3c-f5c67b61771f/dqc_reference/reference_markers.hmm GCF_001895205.1_ASM189520v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:39:29,087] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:39:29,088] [INFO] Found 6/6 markers.
[2024-01-25 18:39:29,117] [INFO] Query marker FASTA was written to GCF_001895205.1_ASM189520v1_genomic.fna/markers.fasta
[2024-01-25 18:39:29,117] [INFO] Task started: Blastn
[2024-01-25 18:39:29,117] [INFO] Running command: blastn -query GCF_001895205.1_ASM189520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c5ca3b6-9180-4d48-9d3c-f5c67b61771f/dqc_reference/reference_markers.fasta -out GCF_001895205.1_ASM189520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:39:29,832] [INFO] Task succeeded: Blastn
[2024-01-25 18:39:29,835] [INFO] Selected 16 target genomes.
[2024-01-25 18:39:29,835] [INFO] Target genome list was writen to GCF_001895205.1_ASM189520v1_genomic.fna/target_genomes.txt
[2024-01-25 18:39:29,864] [INFO] Task started: fastANI
[2024-01-25 18:39:29,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eeea811-264e-4e87-aeda-a14e09b0e6f5/GCF_001895205.1_ASM189520v1_genomic.fna.gz --refList GCF_001895205.1_ASM189520v1_genomic.fna/target_genomes.txt --output GCF_001895205.1_ASM189520v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:39:42,565] [INFO] Task succeeded: fastANI
[2024-01-25 18:39:42,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c5ca3b6-9180-4d48-9d3c-f5c67b61771f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:39:42,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c5ca3b6-9180-4d48-9d3c-f5c67b61771f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:39:42,575] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:39:42,575] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:39:42,575] [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 injensis	strain=M12-1144	GCA_001895205.1	1307414	1307414	type	True	100.0	1208	1208	95	conclusive
Vibrio metschnikovii	strain=CIP 69.14	GCA_000176155.1	28172	28172	type	True	92.8731	1042	1208	95	below_threshold
Vibrio metschnikovii	strain=NCTC8443	GCA_900460295.1	28172	28172	type	True	92.8098	1056	1208	95	below_threshold
Vibrio fujianensis	strain=FJ201301	GCA_002749895.1	1974215	1974215	type	True	80.796	521	1208	95	below_threshold
Vibrio cincinnatiensis	strain=NCTC12012	GCA_900460255.1	675	675	type	True	80.2674	499	1208	95	below_threshold
Vibrio cincinnatiensis	strain=DSM 19608	GCA_900167345.1	675	675	type	True	80.1968	502	1208	95	below_threshold
Vibrio anguillarum	strain=NCTC12159	GCA_900452855.1	55601	55601	type	True	78.8666	340	1208	95	below_threshold
Vibrio anguillarum	strain=DSM 21597	GCA_001989995.2	55601	55601	type	True	78.7071	312	1208	95	below_threshold
Vibrio metoecus	strain=OP3H	GCA_000696385.1	1481663	1481663	type	True	78.3033	309	1208	95	below_threshold
Vibrio porteresiae	strain=MSSRF30	GCA_024347055.1	435912	435912	type	True	78.2399	254	1208	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	78.2375	185	1208	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	78.1317	218	1208	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	78.0993	193	1208	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	78.0423	237	1208	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	78.0263	234	1208	95	below_threshold
Vibrio spartinae	strain=CECT 9026	GCA_024347135.1	1918945	1918945	type	True	77.9668	166	1208	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:39:42,577] [INFO] DFAST Taxonomy check result was written to GCF_001895205.1_ASM189520v1_genomic.fna/tc_result.tsv
[2024-01-25 18:39:42,577] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:39:42,577] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:39:42,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c5ca3b6-9180-4d48-9d3c-f5c67b61771f/dqc_reference/checkm_data
[2024-01-25 18:39:42,578] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:39:42,617] [INFO] Task started: CheckM
[2024-01-25 18:39:42,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001895205.1_ASM189520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001895205.1_ASM189520v1_genomic.fna/checkm_input GCF_001895205.1_ASM189520v1_genomic.fna/checkm_result
[2024-01-25 18:40:09,459] [INFO] Task succeeded: CheckM
[2024-01-25 18:40:09,460] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:40:09,478] [INFO] ===== Completeness check finished =====
[2024-01-25 18:40:09,478] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:40:09,479] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001895205.1_ASM189520v1_genomic.fna/markers.fasta)
[2024-01-25 18:40:09,479] [INFO] Task started: Blastn
[2024-01-25 18:40:09,480] [INFO] Running command: blastn -query GCF_001895205.1_ASM189520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c5ca3b6-9180-4d48-9d3c-f5c67b61771f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001895205.1_ASM189520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:10,680] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:10,682] [INFO] Selected 15 target genomes.
[2024-01-25 18:40:10,683] [INFO] Target genome list was writen to GCF_001895205.1_ASM189520v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:40:10,693] [INFO] Task started: fastANI
[2024-01-25 18:40:10,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eeea811-264e-4e87-aeda-a14e09b0e6f5/GCF_001895205.1_ASM189520v1_genomic.fna.gz --refList GCF_001895205.1_ASM189520v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001895205.1_ASM189520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:40:21,917] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:21,926] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:40:21,926] [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_001895205.1	s__Vibrio injensis	100.0	1208	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.81	98.81	0.92	0.92	2	conclusive
GCF_000176155.1	s__Vibrio metschnikovii	92.8731	1042	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.65	97.32	0.91	0.86	50	-
GCA_007124475.1	s__Vibrio sp007124475	83.9834	511	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.98	98.98	0.80	0.80	2	-
GCF_002749895.1	s__Vibrio fujianensis	80.8368	519	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.21	99.14	0.95	0.93	8	-
GCF_900167345.1	s__Vibrio cincinnatiensis	80.1965	502	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	99.06	0.97	0.94	6	-
GCF_011306175.1	s__Vibrio sp011306175	79.0411	300	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000257205.1	s__Vibrio ordalii	78.8687	304	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.90	98.90	0.96	0.96	2	-
GCF_001989995.2	s__Vibrio anguillarum	78.7103	312	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.39	98.01	0.89	0.80	121	-
GCF_000967545.1	s__Vibrio galatheae	78.5933	193	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064285.1	s__Vibrio ziniensis	78.3878	267	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000696385.1	s__Vibrio metoecus	78.3258	305	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.79	97.58	0.93	0.89	26	-
GCF_000354175.2	s__Vibrio alginolyticus	78.2791	219	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_001695575.1	s__Vibrio europaeus	78.1601	234	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_002849855.1	s__Vibrio azureus	78.0902	193	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000772105.1	s__Vibrio tubiashii	78.0085	238	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:40:21,928] [INFO] GTDB search result was written to GCF_001895205.1_ASM189520v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:40:21,928] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:40:21,931] [INFO] DFAST_QC result json was written to GCF_001895205.1_ASM189520v1_genomic.fna/dqc_result.json
[2024-01-25 18:40:21,931] [INFO] DFAST_QC completed!
[2024-01-25 18:40:21,931] [INFO] Total running time: 0h1m2s