[2024-01-24 15:27:19,494] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:19,496] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:19,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg5754cb25-4b52-43b0-879a-569260894607/dqc_reference
[2024-01-24 15:27:20,756] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:20,757] [INFO] Task started: Prodigal
[2024-01-24 15:27:20,757] [INFO] Running command: gunzip -c /var/lib/cwl/stgac7730c5-953a-4414-9750-ef64abfb0d0c/GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/cds.fna -a GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:38,879] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:38,880] [INFO] Task started: HMMsearch
[2024-01-24 15:27:38,880] [INFO] Running command: hmmsearch --tblout GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5754cb25-4b52-43b0-879a-569260894607/dqc_reference/reference_markers.hmm GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:39,188] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:39,189] [INFO] Found 6/6 markers.
[2024-01-24 15:27:39,243] [INFO] Query marker FASTA was written to GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:27:39,243] [INFO] Task started: Blastn
[2024-01-24 15:27:39,244] [INFO] Running command: blastn -query GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5754cb25-4b52-43b0-879a-569260894607/dqc_reference/reference_markers.fasta -out GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:39,968] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:39,972] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:39,972] [INFO] Target genome list was writen to GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:27:39,979] [INFO] Task started: fastANI
[2024-01-24 15:27:39,980] [INFO] Running command: fastANI --query /var/lib/cwl/stgac7730c5-953a-4414-9750-ef64abfb0d0c/GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna.gz --refList GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:56,771] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:56,772] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5754cb25-4b52-43b0-879a-569260894607/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:56,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5754cb25-4b52-43b0-879a-569260894607/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:56,791] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:56,791] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:56,792] [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
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	100.0	1711	1712	95	conclusive
Chryseobacterium artocarpi	strain=UTM-3	GCA_001684975.1	1414727	1414727	type	True	93.9463	1383	1712	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	85.132	1199	1712	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	84.8922	1116	1712	95	below_threshold
Chryseobacterium contaminans	strain=C-26	GCA_001684955.1	1423959	1423959	type	True	84.8811	1004	1712	95	below_threshold
Chryseobacterium joostei	strain=DSM 16927	GCA_003815775.1	112234	112234	type	True	84.5944	1164	1712	95	below_threshold
Chryseobacterium nakagawai	strain=NCTC13529	GCA_900637665.1	1241982	1241982	type	True	84.3518	1190	1712	95	below_threshold
Chryseobacterium pennae	strain=1_F178	GCA_003385515.1	2258962	2258962	type	True	84.3485	1197	1712	95	below_threshold
Chryseobacterium oncorhynchi	strain=701B-08	GCA_002899895.2	741074	741074	type	True	84.2875	1138	1712	95	below_threshold
Chryseobacterium arthrosphaerae	strain=CC-VM-7	GCA_001684965.1	651561	651561	type	True	83.0888	1078	1712	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.9493	700	1712	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.6107	741	1712	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.4042	736	1712	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.5718	606	1712	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.2618	546	1712	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:56,793] [INFO] DFAST Taxonomy check result was written to GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:27:56,794] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:56,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:56,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5754cb25-4b52-43b0-879a-569260894607/dqc_reference/checkm_data
[2024-01-24 15:27:56,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:56,852] [INFO] Task started: CheckM
[2024-01-24 15:27:56,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/checkm_input GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:28:50,794] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:50,795] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:50,819] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:50,820] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:50,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:28:50,821] [INFO] Task started: Blastn
[2024-01-24 15:28:50,822] [INFO] Running command: blastn -query GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5754cb25-4b52-43b0-879a-569260894607/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:51,757] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:51,761] [INFO] Selected 16 target genomes.
[2024-01-24 15:28:51,761] [INFO] Target genome list was writen to GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:51,774] [INFO] Task started: fastANI
[2024-01-24 15:28:51,774] [INFO] Running command: fastANI --query /var/lib/cwl/stgac7730c5-953a-4414-9750-ef64abfb0d0c/GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna.gz --refList GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:11,288] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:11,306] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:11,307] [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_900156735.1	s__Chryseobacterium ureilyticum	100.0	1711	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001684975.1	s__Chryseobacterium artocarpi	93.9463	1383	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100075.1	s__Chryseobacterium jejuense	85.1186	1200	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_017877355.1	s__Chryseobacterium jejuense_A	85.0346	1154	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829375.1	s__Chryseobacterium sp000829375	84.9269	1199	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001684955.1	s__Chryseobacterium contaminans	84.852	1007	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014218825.1	s__Chryseobacterium bernardetii	84.6956	1167	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.97	99.97	0.99	0.99	3	-
GCF_003815975.1	s__Chryseobacterium bernardetii_A	84.6273	1158	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.62	98.62	0.90	0.90	2	-
GCF_003815715.1	s__Chryseobacterium sp003815715	84.5606	1183	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009900745.1	s__Chryseobacterium sp009900745	84.5229	1167	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637665.1	s__Chryseobacterium nakagawai	84.3694	1187	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003385515.1	s__Chryseobacterium sp003385515	84.3515	1197	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.92	97.92	0.86	0.86	2	-
GCF_002899895.1	s__Chryseobacterium oncorhynchi	84.3027	1136	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815675.1	s__Chryseobacterium sp003815675	84.0794	1154	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019203745.1	s__Chryseobacterium sp019203745	83.3915	1079	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001684965.1	s__Chryseobacterium arthrosphaerae	83.0807	1079	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.97	97.80	0.92	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:11,308] [INFO] GTDB search result was written to GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:11,309] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:11,315] [INFO] DFAST_QC result json was written to GCF_900156735.1_IMG-taxon_2681813509_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:29:11,316] [INFO] DFAST_QC completed!
[2024-01-24 15:29:11,316] [INFO] Total running time: 0h1m52s