[2024-01-24 13:48:59,474] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,476] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,477] [INFO] DQC Reference Directory: /var/lib/cwl/stg936a69ae-94ec-4b35-b848-f956ed9b8d3c/dqc_reference
[2024-01-24 13:49:00,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:00,863] [INFO] Task started: Prodigal
[2024-01-24 13:49:00,863] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c1d3f67-d931-4124-8394-4b511aa200f9/GCF_900460255.1_34500_B01_genomic.fna.gz | prodigal -d GCF_900460255.1_34500_B01_genomic.fna/cds.fna -a GCF_900460255.1_34500_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:10,251] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:10,252] [INFO] Task started: HMMsearch
[2024-01-24 13:49:10,252] [INFO] Running command: hmmsearch --tblout GCF_900460255.1_34500_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg936a69ae-94ec-4b35-b848-f956ed9b8d3c/dqc_reference/reference_markers.hmm GCF_900460255.1_34500_B01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:10,549] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:10,550] [INFO] Found 6/6 markers.
[2024-01-24 13:49:10,600] [INFO] Query marker FASTA was written to GCF_900460255.1_34500_B01_genomic.fna/markers.fasta
[2024-01-24 13:49:10,601] [INFO] Task started: Blastn
[2024-01-24 13:49:10,601] [INFO] Running command: blastn -query GCF_900460255.1_34500_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg936a69ae-94ec-4b35-b848-f956ed9b8d3c/dqc_reference/reference_markers.fasta -out GCF_900460255.1_34500_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:11,434] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:11,438] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:11,438] [INFO] Target genome list was writen to GCF_900460255.1_34500_B01_genomic.fna/target_genomes.txt
[2024-01-24 13:49:11,444] [INFO] Task started: fastANI
[2024-01-24 13:49:11,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c1d3f67-d931-4124-8394-4b511aa200f9/GCF_900460255.1_34500_B01_genomic.fna.gz --refList GCF_900460255.1_34500_B01_genomic.fna/target_genomes.txt --output GCF_900460255.1_34500_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:26,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:26,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg936a69ae-94ec-4b35-b848-f956ed9b8d3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:26,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg936a69ae-94ec-4b35-b848-f956ed9b8d3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:26,476] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:26,476] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:26,476] [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 cincinnatiensis	strain=NCTC12012	GCA_900460255.1	675	675	type	True	100.0	1263	1265	95	conclusive
Vibrio cincinnatiensis	strain=DSM 19608	GCA_900167345.1	675	675	type	True	99.9573	1189	1265	95	conclusive
Vibrio fujianensis	strain=FJ201301	GCA_002749895.1	1974215	1974215	type	True	84.5818	848	1265	95	below_threshold
Vibrio metschnikovii	strain=NCTC8443	GCA_900460295.1	28172	28172	type	True	80.9587	535	1265	95	below_threshold
Vibrio metschnikovii	strain=CIP 69.14	GCA_000176155.1	28172	28172	type	True	80.8456	534	1265	95	below_threshold
Vibrio injensis	strain=M12-1144	GCA_001895205.1	1307414	1307414	type	True	80.3578	502	1265	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	80.1782	416	1265	95	below_threshold
Vibrio fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	80.1565	416	1265	95	below_threshold
Vibrio fluvialis	strain=NCTC11327	GCA_900460245.1	676	676	type	True	80.0422	418	1265	95	below_threshold
Vibrio fluvialis	strain=NBRC 103150	GCA_001598835.1	676	676	type	True	79.5816	406	1265	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	79.3342	328	1265	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	79.1605	383	1265	95	below_threshold
Vibrio paracholerae	strain=EDC-792	GCA_017169525.1	650003	650003	type	True	79.1423	334	1265	95	below_threshold
Vibrio porteresiae	strain=MSSRF30	GCA_024347055.1	435912	435912	type	True	78.9424	292	1265	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.9363	262	1265	95	below_threshold
Vibrio cholerae	strain=ATCC 14035	GCA_000621645.1	666	666	type	True	78.7941	360	1265	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.6657	257	1265	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:26,478] [INFO] DFAST Taxonomy check result was written to GCF_900460255.1_34500_B01_genomic.fna/tc_result.tsv
[2024-01-24 13:49:26,483] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:26,483] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:26,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg936a69ae-94ec-4b35-b848-f956ed9b8d3c/dqc_reference/checkm_data
[2024-01-24 13:49:26,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:26,530] [INFO] Task started: CheckM
[2024-01-24 13:49:26,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900460255.1_34500_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900460255.1_34500_B01_genomic.fna/checkm_input GCF_900460255.1_34500_B01_genomic.fna/checkm_result
[2024-01-24 13:50:00,859] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:00,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:00,881] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:00,882] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:00,882] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900460255.1_34500_B01_genomic.fna/markers.fasta)
[2024-01-24 13:50:00,883] [INFO] Task started: Blastn
[2024-01-24 13:50:00,883] [INFO] Running command: blastn -query GCF_900460255.1_34500_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg936a69ae-94ec-4b35-b848-f956ed9b8d3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900460255.1_34500_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:02,148] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:02,152] [INFO] Selected 13 target genomes.
[2024-01-24 13:50:02,152] [INFO] Target genome list was writen to GCF_900460255.1_34500_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:02,173] [INFO] Task started: fastANI
[2024-01-24 13:50:02,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c1d3f67-d931-4124-8394-4b511aa200f9/GCF_900460255.1_34500_B01_genomic.fna.gz --refList GCF_900460255.1_34500_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900460255.1_34500_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:12,539] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:12,555] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:12,555] [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_900167345.1	s__Vibrio cincinnatiensis	99.9573	1189	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	99.06	0.97	0.94	6	conclusive
GCF_002749895.1	s__Vibrio fujianensis	84.5921	846	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.21	99.14	0.95	0.93	8	-
GCF_000176155.1	s__Vibrio metschnikovii	80.8303	532	1265	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	80.3366	504	1265	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	80.0069	418	1265	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	79.775	399	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.58	97.97	0.95	0.91	12	-
GCF_009665255.1	s__Vibrio metoecus_B	79.6309	341	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.11	98.11	0.94	0.94	2	-
GCF_011064285.1	s__Vibrio ziniensis	79.3628	328	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001547935.1	s__Vibrio tritonius	79.3062	282	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001471585.2	s__Vibrio cholerae	79.2866	366	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.72	95.09	0.90	0.82	1544	-
GCA_007124475.1	s__Vibrio sp007124475	78.86	297	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.98	98.98	0.80	0.80	2	-
GCF_014596725.1	s__Vibrio sp014596725	78.8571	307	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.52	0.94	0.94	2	-
GCF_012395185.1	s__Vibrio aestuarianus	78.6725	362	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.70	96.75	0.86	0.80	14	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:12,557] [INFO] GTDB search result was written to GCF_900460255.1_34500_B01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:12,558] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:12,563] [INFO] DFAST_QC result json was written to GCF_900460255.1_34500_B01_genomic.fna/dqc_result.json
[2024-01-24 13:50:12,563] [INFO] DFAST_QC completed!
[2024-01-24 13:50:12,563] [INFO] Total running time: 0h1m13s