[2024-01-24 15:18:51,880] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:51,884] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:51,884] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdc05c02-87e5-4d2f-9ff9-2f9fe229ab82/dqc_reference
[2024-01-24 15:18:54,591] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:54,592] [INFO] Task started: Prodigal
[2024-01-24 15:18:54,593] [INFO] Running command: gunzip -c /var/lib/cwl/stg2df1997d-5cad-49aa-8b4a-4217de00f8eb/GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/cds.fna -a GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:11,265] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:11,265] [INFO] Task started: HMMsearch
[2024-01-24 15:19:11,266] [INFO] Running command: hmmsearch --tblout GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdc05c02-87e5-4d2f-9ff9-2f9fe229ab82/dqc_reference/reference_markers.hmm GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:11,564] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:11,565] [INFO] Found 6/6 markers.
[2024-01-24 15:19:11,617] [INFO] Query marker FASTA was written to GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:19:11,618] [INFO] Task started: Blastn
[2024-01-24 15:19:11,618] [INFO] Running command: blastn -query GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdc05c02-87e5-4d2f-9ff9-2f9fe229ab82/dqc_reference/reference_markers.fasta -out GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:12,327] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:12,333] [INFO] Selected 15 target genomes.
[2024-01-24 15:19:12,334] [INFO] Target genome list was writen to GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:19:12,356] [INFO] Task started: fastANI
[2024-01-24 15:19:12,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg2df1997d-5cad-49aa-8b4a-4217de00f8eb/GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna.gz --refList GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:28,280] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:28,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdc05c02-87e5-4d2f-9ff9-2f9fe229ab82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:28,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdc05c02-87e5-4d2f-9ff9-2f9fe229ab82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:28,296] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:28,296] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:28,296] [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 limigenitum	strain=SUR2	GCA_900114875.1	1612149	1612149	type	True	100.0	1533	1538	95	conclusive
Chryseobacterium glaciei	strain=IHBB 10212	GCA_001648155.1	1685010	1685010	type	True	91.4232	1158	1538	95	below_threshold
Chryseobacterium polytrichastri	strain=DSM 26899	GCA_900142445.1	1302687	1302687	type	True	86.6468	1037	1538	95	below_threshold
Chryseobacterium soldanellicola	strain=DSM 17072	GCA_900100115.1	311333	311333	type	True	83.467	928	1538	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	83.142	986	1538	95	below_threshold
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	82.1715	907	1538	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	81.7507	746	1538	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	81.4253	820	1538	95	below_threshold
Chryseobacterium soli	strain=DSM 19298	GCA_000737705.1	445961	445961	type	True	81.2628	869	1538	95	below_threshold
Chryseobacterium luteum	strain=DSM 18605	GCA_000737785.1	421531	421531	type	True	81.0619	732	1538	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	80.8697	752	1538	95	below_threshold
Chryseobacterium aquaticum subsp. greenlandense	strain=UMB34	GCA_001507325.1	345663	452084	type	True	80.5587	713	1538	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	80.4649	750	1538	95	below_threshold
Chryseobacterium artocarpi	strain=UTM-3	GCA_001684975.1	1414727	1414727	type	True	80.3997	754	1538	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	77.2052	181	1538	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:28,298] [INFO] DFAST Taxonomy check result was written to GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:19:28,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:28,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:28,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdc05c02-87e5-4d2f-9ff9-2f9fe229ab82/dqc_reference/checkm_data
[2024-01-24 15:19:28,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:28,346] [INFO] Task started: CheckM
[2024-01-24 15:19:28,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/checkm_input GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:20:17,860] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:17,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:17,880] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:17,881] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:17,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:20:17,881] [INFO] Task started: Blastn
[2024-01-24 15:20:17,882] [INFO] Running command: blastn -query GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdc05c02-87e5-4d2f-9ff9-2f9fe229ab82/dqc_reference/reference_markers_gtdb.fasta -out GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:18,839] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:18,842] [INFO] Selected 6 target genomes.
[2024-01-24 15:20:18,842] [INFO] Target genome list was writen to GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:18,847] [INFO] Task started: fastANI
[2024-01-24 15:20:18,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg2df1997d-5cad-49aa-8b4a-4217de00f8eb/GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna.gz --refList GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:26,890] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:26,899] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:26,899] [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_900114875.1	s__Chryseobacterium limigenitum	100.0	1533	1538	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_001648155.1	s__Chryseobacterium glaciei	91.4232	1158	1538	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	91.2876	1189	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142445.1	s__Chryseobacterium polytrichastri	86.5992	1042	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001297705.1	s__Chryseobacterium sp001297705	86.5309	1063	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100115.1	s__Chryseobacterium soldanellicola	83.4383	931	1538	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 15:20:26,901] [INFO] GTDB search result was written to GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:26,902] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:26,905] [INFO] DFAST_QC result json was written to GCF_900114875.1_IMG-taxon_2654587896_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:20:26,905] [INFO] DFAST_QC completed!
[2024-01-24 15:20:26,905] [INFO] Total running time: 0h1m35s