[2024-01-24 11:12:40,008] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:40,010] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:40,010] [INFO] DQC Reference Directory: /var/lib/cwl/stgf529dff2-2a4d-4670-acd2-f046e74d47c8/dqc_reference
[2024-01-24 11:12:41,330] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,331] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,331] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd3357ed-cde4-439e-88df-c295dbcd983f/GCF_007997155.1_ASM799715v1_genomic.fna.gz | prodigal -d GCF_007997155.1_ASM799715v1_genomic.fna/cds.fna -a GCF_007997155.1_ASM799715v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:57,984] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:57,985] [INFO] Task started: HMMsearch
[2024-01-24 11:12:57,985] [INFO] Running command: hmmsearch --tblout GCF_007997155.1_ASM799715v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf529dff2-2a4d-4670-acd2-f046e74d47c8/dqc_reference/reference_markers.hmm GCF_007997155.1_ASM799715v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:58,284] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:58,286] [INFO] Found 6/6 markers.
[2024-01-24 11:12:58,324] [INFO] Query marker FASTA was written to GCF_007997155.1_ASM799715v1_genomic.fna/markers.fasta
[2024-01-24 11:12:58,325] [INFO] Task started: Blastn
[2024-01-24 11:12:58,325] [INFO] Running command: blastn -query GCF_007997155.1_ASM799715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf529dff2-2a4d-4670-acd2-f046e74d47c8/dqc_reference/reference_markers.fasta -out GCF_007997155.1_ASM799715v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:59,025] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:59,030] [INFO] Selected 12 target genomes.
[2024-01-24 11:12:59,031] [INFO] Target genome list was writen to GCF_007997155.1_ASM799715v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:59,037] [INFO] Task started: fastANI
[2024-01-24 11:12:59,037] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd3357ed-cde4-439e-88df-c295dbcd983f/GCF_007997155.1_ASM799715v1_genomic.fna.gz --refList GCF_007997155.1_ASM799715v1_genomic.fna/target_genomes.txt --output GCF_007997155.1_ASM799715v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:09,532] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:09,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf529dff2-2a4d-4670-acd2-f046e74d47c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:09,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf529dff2-2a4d-4670-acd2-f046e74d47c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:09,551] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:09,551] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:09,551] [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
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	100.0	1252	1256	95	conclusive
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	81.7705	748	1256	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	81.3916	714	1256	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	80.8372	731	1256	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	80.5864	642	1256	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	80.296	627	1256	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	80.2919	674	1256	95	below_threshold
Aequorivita capsosiphonis	strain=DSM 23843	GCA_000429125.1	487317	487317	type	True	79.0975	540	1256	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.5548	147	1256	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.3672	65	1256	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	76.1498	59	1256	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.1089	56	1256	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:09,554] [INFO] DFAST Taxonomy check result was written to GCF_007997155.1_ASM799715v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:09,555] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:09,555] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:09,555] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf529dff2-2a4d-4670-acd2-f046e74d47c8/dqc_reference/checkm_data
[2024-01-24 11:13:09,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:09,595] [INFO] Task started: CheckM
[2024-01-24 11:13:09,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007997155.1_ASM799715v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007997155.1_ASM799715v1_genomic.fna/checkm_input GCF_007997155.1_ASM799715v1_genomic.fna/checkm_result
[2024-01-24 11:13:59,268] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:59,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:59,292] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:59,293] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:59,293] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007997155.1_ASM799715v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:59,294] [INFO] Task started: Blastn
[2024-01-24 11:13:59,294] [INFO] Running command: blastn -query GCF_007997155.1_ASM799715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf529dff2-2a4d-4670-acd2-f046e74d47c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_007997155.1_ASM799715v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:00,164] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:00,169] [INFO] Selected 10 target genomes.
[2024-01-24 11:14:00,169] [INFO] Target genome list was writen to GCF_007997155.1_ASM799715v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:00,180] [INFO] Task started: fastANI
[2024-01-24 11:14:00,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd3357ed-cde4-439e-88df-c295dbcd983f/GCF_007997155.1_ASM799715v1_genomic.fna.gz --refList GCF_007997155.1_ASM799715v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007997155.1_ASM799715v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:08,104] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:08,123] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:08,123] [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_007997155.1	s__Aequorivita antarctica	100.0	1252	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_900489465.1	s__Aequorivita sp900489465	83.1601	814	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641085.1	s__Aequorivita soesokkakensis	81.7746	747	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCA_016649715.1	s__Aequorivita sp016649715	81.7363	758	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997135.1	s__Aequorivita lipolytica	81.3918	714	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000265385.1	s__Aequorivita sublithincola	80.8457	730	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364215.1	s__Aequorivita sp002364215	80.7486	695	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_001573155.1	s__Aequorivita aquimaris	80.5927	641	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757735.1	s__Aequorivita sp016757735	80.3052	672	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429125.1	s__Aequorivita capsosiphonis	79.0939	541	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:08,125] [INFO] GTDB search result was written to GCF_007997155.1_ASM799715v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:08,125] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:08,129] [INFO] DFAST_QC result json was written to GCF_007997155.1_ASM799715v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:08,130] [INFO] DFAST_QC completed!
[2024-01-24 11:14:08,130] [INFO] Total running time: 0h1m28s