[2024-01-24 12:22:14,143] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:14,148] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:14,148] [INFO] DQC Reference Directory: /var/lib/cwl/stg485e8e7d-3f38-4112-8edb-afabe5acc9df/dqc_reference
[2024-01-24 12:22:15,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:15,736] [INFO] Task started: Prodigal
[2024-01-24 12:22:15,736] [INFO] Running command: gunzip -c /var/lib/cwl/stg3339a2d0-1fc7-49cc-9a6e-a3a6ca22d183/GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/cds.fna -a GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:25,312] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:25,313] [INFO] Task started: HMMsearch
[2024-01-24 12:22:25,313] [INFO] Running command: hmmsearch --tblout GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg485e8e7d-3f38-4112-8edb-afabe5acc9df/dqc_reference/reference_markers.hmm GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:25,630] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:25,634] [INFO] Found 6/6 markers.
[2024-01-24 12:22:25,675] [INFO] Query marker FASTA was written to GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:22:25,675] [INFO] Task started: Blastn
[2024-01-24 12:22:25,675] [INFO] Running command: blastn -query GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg485e8e7d-3f38-4112-8edb-afabe5acc9df/dqc_reference/reference_markers.fasta -out GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:26,364] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:26,370] [INFO] Selected 14 target genomes.
[2024-01-24 12:22:26,370] [INFO] Target genome list was writen to GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:22:26,381] [INFO] Task started: fastANI
[2024-01-24 12:22:26,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg3339a2d0-1fc7-49cc-9a6e-a3a6ca22d183/GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna.gz --refList GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:36,493] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:36,494] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg485e8e7d-3f38-4112-8edb-afabe5acc9df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:36,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg485e8e7d-3f38-4112-8edb-afabe5acc9df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:36,504] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:22:36,504] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:36,505] [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
Cloacibacterium normanense	strain=DSM 15886	GCA_900104195.1	237258	237258	type	True	100.0	889	891	95	conclusive
Cloacibacterium normanense	strain=NRS-1	GCA_003860565.1	237258	237258	type	True	99.9942	888	891	95	conclusive
Cloacibacterium normanense	strain=NRS-1	GCA_001747495.1	237258	237258	type	True	99.9761	866	891	95	conclusive
Cloacibacterium rupense	strain=CGMCC 1.7656	GCA_014645495.1	517423	517423	type	True	82.1585	590	891	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	77.7081	205	891	95	below_threshold
Epilithonimonas arachidiradicis	strain=CCM 8490	GCA_014635405.1	1617282	1617282	type	True	77.6982	160	891	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	77.5426	219	891	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	77.5143	235	891	95	below_threshold
Chryseobacterium balustinum	strain=DSM 16775	GCA_900168205.1	246	246	type	True	77.4941	230	891	95	below_threshold
Chryseobacterium antibioticum	strain=RP-3-3	GCA_012927325.1	2728847	2728847	type	True	77.4727	154	891	95	below_threshold
Chryseobacterium aquaticum	strain=KCTC 12483	GCA_001420285.1	452084	452084	type	True	77.4128	230	891	95	below_threshold
Chryseobacterium taeanense	strain=DSM 17071	GCA_900099685.1	311334	311334	type	True	77.3919	169	891	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	75.8865	59	891	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:36,506] [INFO] DFAST Taxonomy check result was written to GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:22:36,507] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:36,507] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:36,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg485e8e7d-3f38-4112-8edb-afabe5acc9df/dqc_reference/checkm_data
[2024-01-24 12:22:36,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:36,540] [INFO] Task started: CheckM
[2024-01-24 12:22:36,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/checkm_input GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:23:10,630] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:10,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:10,655] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:10,655] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:10,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:23:10,656] [INFO] Task started: Blastn
[2024-01-24 12:23:10,656] [INFO] Running command: blastn -query GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg485e8e7d-3f38-4112-8edb-afabe5acc9df/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:11,558] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:11,562] [INFO] Selected 6 target genomes.
[2024-01-24 12:23:11,562] [INFO] Target genome list was writen to GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:11,567] [INFO] Task started: fastANI
[2024-01-24 12:23:11,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg3339a2d0-1fc7-49cc-9a6e-a3a6ca22d183/GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna.gz --refList GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:16,051] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:16,057] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 12:23:16,057] [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_003860565.1	s__Cloacibacterium normanense	99.9942	888	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.1075	98.41	95.23	0.95	0.87	4	inconclusive
GCF_907163105.1	s__Cloacibacterium caeni_A	95.0101	752	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_907163125.1	s__Cloacibacterium caeni_B	94.9768	729	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.1075	N/A	N/A	N/A	N/A	1	-
GCF_002943105.1	s__Cloacibacterium sp002422665	94.9263	730	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0662	95.27	95.25	0.87	0.85	3	-
GCF_014645495.1	s__Cloacibacterium rupense	82.1546	590	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337005.1	s__Cloacibacterium sp002337005	81.7704	545	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:16,058] [INFO] GTDB search result was written to GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:16,059] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:16,064] [INFO] DFAST_QC result json was written to GCF_900104195.1_IMG-taxon_2634166320_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:23:16,064] [INFO] DFAST_QC completed!
[2024-01-24 12:23:16,065] [INFO] Total running time: 0h1m2s