[2024-01-24 14:19:20,341] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:20,342] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:20,343] [INFO] DQC Reference Directory: /var/lib/cwl/stg05deb285-a7a1-48b8-8212-d5a5df7edd26/dqc_reference
[2024-01-24 14:19:23,547] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:23,552] [INFO] Task started: Prodigal
[2024-01-24 14:19:23,553] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc1fd7b8-2a7e-48a9-9845-92778945b3a9/GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/cds.fna -a GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:41,906] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:41,906] [INFO] Task started: HMMsearch
[2024-01-24 14:19:41,906] [INFO] Running command: hmmsearch --tblout GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05deb285-a7a1-48b8-8212-d5a5df7edd26/dqc_reference/reference_markers.hmm GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:42,383] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:42,385] [INFO] Found 6/6 markers.
[2024-01-24 14:19:42,442] [INFO] Query marker FASTA was written to GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:19:42,442] [INFO] Task started: Blastn
[2024-01-24 14:19:42,442] [INFO] Running command: blastn -query GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg05deb285-a7a1-48b8-8212-d5a5df7edd26/dqc_reference/reference_markers.fasta -out GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:44,760] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:44,763] [INFO] Selected 16 target genomes.
[2024-01-24 14:19:44,764] [INFO] Target genome list was writen to GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:19:44,776] [INFO] Task started: fastANI
[2024-01-24 14:19:44,776] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc1fd7b8-2a7e-48a9-9845-92778945b3a9/GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna.gz --refList GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:03,152] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:03,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05deb285-a7a1-48b8-8212-d5a5df7edd26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:03,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05deb285-a7a1-48b8-8212-d5a5df7edd26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:03,258] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:03,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:03,259] [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 oranimense	strain=DSM 19055	GCA_900129755.1	421058	421058	type	True	100.0	1522	1523	95	conclusive
Chryseobacterium lathyri	strain=NBRC 105250	GCA_007991435.1	395933	395933	type	True	85.964	1142	1523	95	below_threshold
Chryseobacterium lathyri	strain=KCTC 22544	GCA_003290185.1	395933	395933	type	True	85.9504	1152	1523	95	below_threshold
Chryseobacterium elymi	strain=KCTC 22547	GCA_003385495.1	395936	395936	type	True	85.1733	1086	1523	95	below_threshold
Chryseobacterium luteum	strain=DSM 18605	GCA_000737785.1	421531	421531	type	True	84.7255	1021	1523	95	below_threshold
Chryseobacterium endalhagicum	strain=L7	GCA_016745235.1	2797638	2797638	type	True	84.3127	1083	1523	95	below_threshold
Chryseobacterium angstadtii	strain=KM	GCA_001045465.1	558151	558151	type	True	84.2291	1082	1523	95	below_threshold
Chryseobacterium oleae	strain=DSM 25575	GCA_900115055.1	491207	491207	type	True	84.0836	1073	1523	95	below_threshold
Chryseobacterium kwangjuense	strain=KJ1R5	GCA_001563495.1	267125	267125	type	True	83.7281	1045	1523	95	below_threshold
Chryseobacterium phocaeense	strain=6021061333	GCA_900169075.1	1816690	1816690	type	True	83.6052	1056	1523	95	below_threshold
Chryseobacterium arthrosphaerae	strain=CC-VM-7	GCA_001684965.1	651561	651561	type	True	81.2574	894	1523	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.3719	639	1523	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.2967	704	1523	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.083	754	1523	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.3025	524	1523	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.1059	462	1523	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:03,274] [INFO] DFAST Taxonomy check result was written to GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:20:03,275] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:03,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:03,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05deb285-a7a1-48b8-8212-d5a5df7edd26/dqc_reference/checkm_data
[2024-01-24 14:20:03,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:03,381] [INFO] Task started: CheckM
[2024-01-24 14:20:03,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/checkm_input GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:21:00,099] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:00,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:00,126] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:00,127] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:00,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:21:00,127] [INFO] Task started: Blastn
[2024-01-24 14:21:00,128] [INFO] Running command: blastn -query GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg05deb285-a7a1-48b8-8212-d5a5df7edd26/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:01,050] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:01,054] [INFO] Selected 10 target genomes.
[2024-01-24 14:21:01,054] [INFO] Target genome list was writen to GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:01,063] [INFO] Task started: fastANI
[2024-01-24 14:21:01,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc1fd7b8-2a7e-48a9-9845-92778945b3a9/GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna.gz --refList GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:12,923] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:13,014] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:13,015] [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_900129755.1	s__Chryseobacterium oranimense	100.0	1522	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.88	97.88	0.91	0.91	3	conclusive
GCF_001045445.1	s__Chryseobacterium sp001045445	90.8689	1234	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003290185.1	s__Chryseobacterium lathyri	85.9504	1152	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014207845.1	s__Chryseobacterium shigense_A	85.6385	1068	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003385495.1	s__Chryseobacterium elymi	85.2004	1083	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737785.1	s__Chryseobacterium luteum	84.7081	1023	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045465.1	s__Chryseobacterium angstadtii	84.2241	1083	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737715.1	s__Chryseobacterium sp000737715	84.0208	1081	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001563495.1	s__Chryseobacterium kwangjuense	83.7214	1046	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900169075.1	s__Chryseobacterium phocaeense	83.6051	1056	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:13,017] [INFO] GTDB search result was written to GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:13,018] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:13,023] [INFO] DFAST_QC result json was written to GCF_900129755.1_IMG-taxon_2684623028_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:21:13,024] [INFO] DFAST_QC completed!
[2024-01-24 14:21:13,024] [INFO] Total running time: 0h1m53s