[2024-01-24 12:13:24,531] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:24,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:24,537] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e069c0e-0b8f-4188-8a7e-5fad1bae023a/dqc_reference
[2024-01-24 12:13:26,482] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:26,484] [INFO] Task started: Prodigal
[2024-01-24 12:13:26,484] [INFO] Running command: gunzip -c /var/lib/cwl/stgb591132e-9ae3-451e-930d-616697f30dbb/GCF_003568985.1_Vezurae_genomic.fna.gz | prodigal -d GCF_003568985.1_Vezurae_genomic.fna/cds.fna -a GCF_003568985.1_Vezurae_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:36,059] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:36,060] [INFO] Task started: HMMsearch
[2024-01-24 12:13:36,060] [INFO] Running command: hmmsearch --tblout GCF_003568985.1_Vezurae_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e069c0e-0b8f-4188-8a7e-5fad1bae023a/dqc_reference/reference_markers.hmm GCF_003568985.1_Vezurae_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:36,364] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:36,365] [INFO] Found 6/6 markers.
[2024-01-24 12:13:36,398] [INFO] Query marker FASTA was written to GCF_003568985.1_Vezurae_genomic.fna/markers.fasta
[2024-01-24 12:13:36,399] [INFO] Task started: Blastn
[2024-01-24 12:13:36,399] [INFO] Running command: blastn -query GCF_003568985.1_Vezurae_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e069c0e-0b8f-4188-8a7e-5fad1bae023a/dqc_reference/reference_markers.fasta -out GCF_003568985.1_Vezurae_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:37,238] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:37,245] [INFO] Selected 9 target genomes.
[2024-01-24 12:13:37,245] [INFO] Target genome list was writen to GCF_003568985.1_Vezurae_genomic.fna/target_genomes.txt
[2024-01-24 12:13:37,253] [INFO] Task started: fastANI
[2024-01-24 12:13:37,253] [INFO] Running command: fastANI --query /var/lib/cwl/stgb591132e-9ae3-451e-930d-616697f30dbb/GCF_003568985.1_Vezurae_genomic.fna.gz --refList GCF_003568985.1_Vezurae_genomic.fna/target_genomes.txt --output GCF_003568985.1_Vezurae_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:45,544] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:45,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e069c0e-0b8f-4188-8a7e-5fad1bae023a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:45,545] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e069c0e-0b8f-4188-8a7e-5fad1bae023a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:45,554] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:13:45,554] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:45,554] [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 ezurae	strain=HDS1-1	GCA_003568985.1	252583	252583	type	True	99.9999	1227	1231	95	conclusive
Vibrio ezurae	strain=NBRC 102218	GCA_000467185.1	252583	252583	type	True	99.9581	1184	1231	95	conclusive
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	89.0446	1022	1231	95	below_threshold
Vibrio halioticoli	strain=IAM 14596	GCA_003568965.1	71388	71388	type	True	88.3259	1008	1231	95	below_threshold
Vibrio halioticoli	strain=NBRC 102217	GCA_000496695.1	71388	71388	type	True	88.2702	964	1231	95	below_threshold
Vibrio inusitatus	strain=LMG 23434	GCA_024346935.1	413402	413402	type	True	81.2503	559	1231	95	below_threshold
Vibrio rarus	strain=LMG 23674	GCA_024347075.1	413403	413403	type	True	81.0298	588	1231	95	below_threshold
Vibrio comitans	strain=LMG 23416	GCA_024346835.1	413401	413401	type	True	81.0139	577	1231	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	79.4139	233	1231	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:45,561] [INFO] DFAST Taxonomy check result was written to GCF_003568985.1_Vezurae_genomic.fna/tc_result.tsv
[2024-01-24 12:13:45,562] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:45,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:45,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e069c0e-0b8f-4188-8a7e-5fad1bae023a/dqc_reference/checkm_data
[2024-01-24 12:13:45,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:45,601] [INFO] Task started: CheckM
[2024-01-24 12:13:45,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003568985.1_Vezurae_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003568985.1_Vezurae_genomic.fna/checkm_input GCF_003568985.1_Vezurae_genomic.fna/checkm_result
[2024-01-24 12:14:19,244] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:19,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:19,275] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:19,276] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:19,276] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003568985.1_Vezurae_genomic.fna/markers.fasta)
[2024-01-24 12:14:19,276] [INFO] Task started: Blastn
[2024-01-24 12:14:19,276] [INFO] Running command: blastn -query GCF_003568985.1_Vezurae_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e069c0e-0b8f-4188-8a7e-5fad1bae023a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003568985.1_Vezurae_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:20,529] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:20,532] [INFO] Selected 8 target genomes.
[2024-01-24 12:14:20,533] [INFO] Target genome list was writen to GCF_003568985.1_Vezurae_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:20,543] [INFO] Task started: fastANI
[2024-01-24 12:14:20,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgb591132e-9ae3-451e-930d-616697f30dbb/GCF_003568985.1_Vezurae_genomic.fna.gz --refList GCF_003568985.1_Vezurae_genomic.fna/target_genomes_gtdb.txt --output GCF_003568985.1_Vezurae_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:28,133] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:28,141] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:28,141] [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_000467185.1	s__Vibrio ezurae	99.9581	1184	1231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000496695.1	s__Vibrio halioticoli	88.2893	964	1231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.31	0.94	0.87	3	-
GCF_001676025.1	s__Vibrio sp001676025	81.3523	624	1231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_006538525.1	s__Vibrio inusitatus	81.2718	543	1231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569005.1	s__Vibrio superstes	81.2236	548	1231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001677275.1	s__Vibrio breoganii	81.1792	570	1231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.22	96.88	0.90	0.86	59	-
GCF_006538565.1	s__Vibrio comitans	80.9051	574	1231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591145.1	s__Vibrio harveyi	79.0541	220	1231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:28,143] [INFO] GTDB search result was written to GCF_003568985.1_Vezurae_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:28,143] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:28,146] [INFO] DFAST_QC result json was written to GCF_003568985.1_Vezurae_genomic.fna/dqc_result.json
[2024-01-24 12:14:28,146] [INFO] DFAST_QC completed!
[2024-01-24 12:14:28,146] [INFO] Total running time: 0h1m4s