[2024-01-24 13:25:31,303] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,305] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg045ca59a-efd1-4d1b-9273-c37b9b673e68/dqc_reference
[2024-01-24 13:25:32,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,686] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,686] [INFO] Running command: gunzip -c /var/lib/cwl/stg8797a8ca-be9b-4ea8-8a7f-bafaca9e9c31/GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/cds.fna -a GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:44,416] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:44,416] [INFO] Task started: HMMsearch
[2024-01-24 13:25:44,416] [INFO] Running command: hmmsearch --tblout GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg045ca59a-efd1-4d1b-9273-c37b9b673e68/dqc_reference/reference_markers.hmm GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:44,712] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:44,714] [INFO] Found 6/6 markers.
[2024-01-24 13:25:44,765] [INFO] Query marker FASTA was written to GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:25:44,765] [INFO] Task started: Blastn
[2024-01-24 13:25:44,766] [INFO] Running command: blastn -query GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg045ca59a-efd1-4d1b-9273-c37b9b673e68/dqc_reference/reference_markers.fasta -out GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:45,443] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:45,447] [INFO] Selected 16 target genomes.
[2024-01-24 13:25:45,448] [INFO] Target genome list was writen to GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:25:45,456] [INFO] Task started: fastANI
[2024-01-24 13:25:45,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg8797a8ca-be9b-4ea8-8a7f-bafaca9e9c31/GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna.gz --refList GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:59,147] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:59,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg045ca59a-efd1-4d1b-9273-c37b9b673e68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:59,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg045ca59a-efd1-4d1b-9273-c37b9b673e68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:59,165] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:59,165] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:59,166] [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
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	100.0	1187	1189	95	conclusive
Salegentibacter salarius	strain=DSM 23401	GCA_900168265.1	435906	435906	type	True	87.4864	896	1189	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	87.404	896	1189	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_001752425.1	435906	435906	type	True	87.3827	900	1189	95	below_threshold
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	86.8946	923	1189	95	below_threshold
Salegentibacter mishustinae	strain=DSM 23404	GCA_003254095.1	270918	270918	type	True	86.8914	932	1189	95	below_threshold
Salegentibacter mishustinae	strain=KCTC 12263	GCA_001431365.1	270918	270918	type	True	86.8786	918	1189	95	below_threshold
Salegentibacter mishustinae	strain=KCTC 12263	GCA_014651335.1	270918	270918	type	True	86.7998	930	1189	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	84.361	832	1189	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	84.3387	850	1189	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	84.0298	828	1189	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	83.1838	822	1189	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	82.6385	801	1189	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	76.2799	53	1189	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	75.8051	74	1189	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	75.7419	73	1189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:59,169] [INFO] DFAST Taxonomy check result was written to GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:25:59,169] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:59,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:59,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg045ca59a-efd1-4d1b-9273-c37b9b673e68/dqc_reference/checkm_data
[2024-01-24 13:25:59,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:59,213] [INFO] Task started: CheckM
[2024-01-24 13:25:59,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/checkm_input GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:26:36,371] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:36,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:36,396] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:36,396] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:36,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:26:36,397] [INFO] Task started: Blastn
[2024-01-24 13:26:36,397] [INFO] Running command: blastn -query GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg045ca59a-efd1-4d1b-9273-c37b9b673e68/dqc_reference/reference_markers_gtdb.fasta -out GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:37,261] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:37,265] [INFO] Selected 8 target genomes.
[2024-01-24 13:26:37,265] [INFO] Target genome list was writen to GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:37,278] [INFO] Task started: fastANI
[2024-01-24 13:26:37,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg8797a8ca-be9b-4ea8-8a7f-bafaca9e9c31/GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna.gz --refList GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:44,517] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:44,529] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:44,529] [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_900168045.1	s__Salegentibacter holothuriorum	100.0	1187	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900168265.1	s__Salegentibacter salarius	87.516	893	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_002900095.1	s__Salegentibacter mishustinae	86.8966	923	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	-
GCF_016236915.1	s__Salegentibacter maritimus	84.4708	927	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	98.25	98.21	0.91	0.91	3	-
GCF_900142975.1	s__Salegentibacter salegens	84.3442	849	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900113135.1	s__Salegentibacter agarivorans	84.0499	826	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_000745315.1	s__Salegentibacter sp000745315	83.5295	805	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168115.1	s__Salegentibacter salinarum	82.5084	781	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:44,531] [INFO] GTDB search result was written to GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:44,531] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:44,535] [INFO] DFAST_QC result json was written to GCF_900168045.1_IMG-taxon_2595698246_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:26:44,535] [INFO] DFAST_QC completed!
[2024-01-24 13:26:44,535] [INFO] Total running time: 0h1m13s