[2024-01-24 14:46:55,561] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,563] [INFO] DQC Reference Directory: /var/lib/cwl/stg54368e8c-529b-45a7-b8f5-1154c90ad30c/dqc_reference
[2024-01-24 14:46:58,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,018] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg1795476e-68ed-4eb9-a953-e8f6eeefee59/GCF_007990935.1_ASM799093v1_genomic.fna.gz | prodigal -d GCF_007990935.1_ASM799093v1_genomic.fna/cds.fna -a GCF_007990935.1_ASM799093v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:08,167] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:08,167] [INFO] Task started: HMMsearch
[2024-01-24 14:47:08,168] [INFO] Running command: hmmsearch --tblout GCF_007990935.1_ASM799093v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54368e8c-529b-45a7-b8f5-1154c90ad30c/dqc_reference/reference_markers.hmm GCF_007990935.1_ASM799093v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:08,495] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:08,496] [INFO] Found 6/6 markers.
[2024-01-24 14:47:08,538] [INFO] Query marker FASTA was written to GCF_007990935.1_ASM799093v1_genomic.fna/markers.fasta
[2024-01-24 14:47:08,538] [INFO] Task started: Blastn
[2024-01-24 14:47:08,538] [INFO] Running command: blastn -query GCF_007990935.1_ASM799093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54368e8c-529b-45a7-b8f5-1154c90ad30c/dqc_reference/reference_markers.fasta -out GCF_007990935.1_ASM799093v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:09,387] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:09,390] [INFO] Selected 10 target genomes.
[2024-01-24 14:47:09,390] [INFO] Target genome list was writen to GCF_007990935.1_ASM799093v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:09,403] [INFO] Task started: fastANI
[2024-01-24 14:47:09,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg1795476e-68ed-4eb9-a953-e8f6eeefee59/GCF_007990935.1_ASM799093v1_genomic.fna.gz --refList GCF_007990935.1_ASM799093v1_genomic.fna/target_genomes.txt --output GCF_007990935.1_ASM799093v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:19,247] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:19,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54368e8c-529b-45a7-b8f5-1154c90ad30c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:19,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54368e8c-529b-45a7-b8f5-1154c90ad30c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:19,256] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:19,256] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:19,257] [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 sagamiensis	strain=NBRC 104589	GCA_007990935.1	512650	512650	type	True	100.0	1414	1418	95	conclusive
Vibrio sagamiensis	strain=NBRC 104589	GCA_000400425.1	512650	512650	type	True	99.9698	1355	1418	95	conclusive
Vibrio azureus	strain=NBRC 104587	GCA_000400265.1	512649	512649	type	True	91.3411	1049	1418	95	below_threshold
Vibrio azureus	strain=NBRC 104587	GCA_000467165.1	512649	512649	type	True	91.1369	1107	1418	95	below_threshold
Vibrio azureus	strain=LC2-005	GCA_002849855.1	512649	512649	type	True	91.0894	1149	1418	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.3198	394	1418	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.7243	252	1418	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.6676	247	1418	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	79.3255	272	1418	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	79.3065	289	1418	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:19,258] [INFO] DFAST Taxonomy check result was written to GCF_007990935.1_ASM799093v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:19,259] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:19,259] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:19,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54368e8c-529b-45a7-b8f5-1154c90ad30c/dqc_reference/checkm_data
[2024-01-24 14:47:19,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:19,308] [INFO] Task started: CheckM
[2024-01-24 14:47:19,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007990935.1_ASM799093v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007990935.1_ASM799093v1_genomic.fna/checkm_input GCF_007990935.1_ASM799093v1_genomic.fna/checkm_result
[2024-01-24 14:47:54,576] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:54,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:54,600] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:54,600] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:54,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007990935.1_ASM799093v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:54,601] [INFO] Task started: Blastn
[2024-01-24 14:47:54,601] [INFO] Running command: blastn -query GCF_007990935.1_ASM799093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54368e8c-529b-45a7-b8f5-1154c90ad30c/dqc_reference/reference_markers_gtdb.fasta -out GCF_007990935.1_ASM799093v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:56,014] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:56,017] [INFO] Selected 11 target genomes.
[2024-01-24 14:47:56,018] [INFO] Target genome list was writen to GCF_007990935.1_ASM799093v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:56,029] [INFO] Task started: fastANI
[2024-01-24 14:47:56,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg1795476e-68ed-4eb9-a953-e8f6eeefee59/GCF_007990935.1_ASM799093v1_genomic.fna.gz --refList GCF_007990935.1_ASM799093v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007990935.1_ASM799093v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:06,933] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:06,946] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:06,947] [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_007990935.1	s__Vibrio sagamiensis	100.0	1414	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.95	99.91	0.97	0.96	3	conclusive
GCF_002849855.1	s__Vibrio azureus	91.0876	1149	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002163755.1	s__Vibrio campbellii	81.4966	489	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_002741985.1	s__Vibrio rotiferianus	81.3056	443	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_001591145.1	s__Vibrio harveyi	81.3056	446	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_000817815.1	s__Vibrio owensii	80.9841	470	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_002906655.1	s__Vibrio hyugaensis	80.9245	478	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCF_000171815.1	s__Vibrio sp000171815	80.6666	420	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544875.1	s__Vibrio alfacsensis	80.6242	443	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.49	96.49	0.89	0.89	2	-
GCF_000354175.2	s__Vibrio alginolyticus	80.6219	439	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCA_001048675.1	s__Vibrio diabolicus	80.4494	438	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:06,949] [INFO] GTDB search result was written to GCF_007990935.1_ASM799093v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:06,949] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:06,953] [INFO] DFAST_QC result json was written to GCF_007990935.1_ASM799093v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:06,953] [INFO] DFAST_QC completed!
[2024-01-24 14:48:06,954] [INFO] Total running time: 0h1m11s