[2024-01-24 14:14:06,043] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:06,045] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:06,046] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfdae589-3687-46d0-9a52-9660c188b97d/dqc_reference
[2024-01-24 14:14:07,458] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:07,459] [INFO] Task started: Prodigal
[2024-01-24 14:14:07,459] [INFO] Running command: gunzip -c /var/lib/cwl/stgbea930d6-e01f-4593-a260-be6d49f6b82e/GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/cds.fna -a GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:25,464] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:25,464] [INFO] Task started: HMMsearch
[2024-01-24 14:14:25,464] [INFO] Running command: hmmsearch --tblout GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfdae589-3687-46d0-9a52-9660c188b97d/dqc_reference/reference_markers.hmm GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:25,765] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:25,767] [INFO] Found 6/6 markers.
[2024-01-24 14:14:25,809] [INFO] Query marker FASTA was written to GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:14:25,810] [INFO] Task started: Blastn
[2024-01-24 14:14:25,810] [INFO] Running command: blastn -query GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfdae589-3687-46d0-9a52-9660c188b97d/dqc_reference/reference_markers.fasta -out GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:26,452] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:26,457] [INFO] Selected 15 target genomes.
[2024-01-24 14:14:26,457] [INFO] Target genome list was writen to GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:14:26,475] [INFO] Task started: fastANI
[2024-01-24 14:14:26,476] [INFO] Running command: fastANI --query /var/lib/cwl/stgbea930d6-e01f-4593-a260-be6d49f6b82e/GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna.gz --refList GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:42,147] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:42,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfdae589-3687-46d0-9a52-9660c188b97d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:42,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfdae589-3687-46d0-9a52-9660c188b97d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:42,168] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:42,168] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:42,168] [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 polytrichastri	strain=DSM 26899	GCA_900142445.1	1302687	1302687	type	True	100.0	1661	1667	95	conclusive
Chryseobacterium glaciei	strain=IHBB 10212	GCA_001648155.1	1685010	1685010	type	True	86.932	1168	1667	95	below_threshold
Chryseobacterium limigenitum	strain=SUR2	GCA_900114875.1	1612149	1612149	type	True	86.5034	1065	1667	95	below_threshold
Chryseobacterium soldanellicola	strain=DSM 17072	GCA_900100115.1	311333	311333	type	True	81.9086	846	1667	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	81.8765	943	1667	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	81.0089	750	1667	95	below_threshold
Chryseobacterium soli	strain=DSM 19298	GCA_000737705.1	445961	445961	type	True	80.9522	891	1667	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.8429	821	1667	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	80.4545	739	1667	95	below_threshold
Chryseobacterium paridis	strain=YIM B02567	GCA_016595215.1	2800328	2800328	type	True	80.3497	829	1667	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	80.3258	802	1667	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	80.1895	793	1667	95	below_threshold
Chryseobacterium artocarpi	strain=UTM-3	GCA_001684975.1	1414727	1414727	type	True	80.1843	781	1667	95	below_threshold
Chryseobacterium elymi	strain=KCTC 22547	GCA_003385495.1	395936	395936	type	True	80.0965	728	1667	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.1036	586	1667	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:42,170] [INFO] DFAST Taxonomy check result was written to GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:14:42,171] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:42,171] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:42,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfdae589-3687-46d0-9a52-9660c188b97d/dqc_reference/checkm_data
[2024-01-24 14:14:42,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:42,227] [INFO] Task started: CheckM
[2024-01-24 14:14:42,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/checkm_input GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:15:34,418] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:34,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:34,437] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:34,437] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:34,438] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:15:34,438] [INFO] Task started: Blastn
[2024-01-24 14:15:34,439] [INFO] Running command: blastn -query GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfdae589-3687-46d0-9a52-9660c188b97d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:35,533] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:35,536] [INFO] Selected 6 target genomes.
[2024-01-24 14:15:35,537] [INFO] Target genome list was writen to GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:35,544] [INFO] Task started: fastANI
[2024-01-24 14:15:35,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgbea930d6-e01f-4593-a260-be6d49f6b82e/GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna.gz --refList GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:43,261] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:43,268] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:43,268] [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_900142445.1	s__Chryseobacterium polytrichastri	100.0	1661	1667	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_001297705.1	s__Chryseobacterium sp001297705	92.2861	1401	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648155.1	s__Chryseobacterium glaciei	86.9617	1165	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114875.1	s__Chryseobacterium limigenitum	86.5111	1064	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815655.1	s__Chryseobacterium sp003815655	86.2422	1120	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385495.1	s__Chryseobacterium elymi	80.1052	726	1667	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 14:15:43,269] [INFO] GTDB search result was written to GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:43,270] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:43,274] [INFO] DFAST_QC result json was written to GCF_900142445.1_IMG-taxon_2700988715_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:15:43,274] [INFO] DFAST_QC completed!
[2024-01-24 14:15:43,274] [INFO] Total running time: 0h1m37s