[2024-01-24 14:11:46,267] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,269] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,269] [INFO] DQC Reference Directory: /var/lib/cwl/stg10c60670-ac33-44a0-a0b4-839dd0dc407f/dqc_reference
[2024-01-24 14:11:48,876] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:48,878] [INFO] Task started: Prodigal
[2024-01-24 14:11:48,878] [INFO] Running command: gunzip -c /var/lib/cwl/stgbcb46372-8d80-48cc-acff-99d74118189d/GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/cds.fna -a GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:05,714] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:05,714] [INFO] Task started: HMMsearch
[2024-01-24 14:12:05,715] [INFO] Running command: hmmsearch --tblout GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10c60670-ac33-44a0-a0b4-839dd0dc407f/dqc_reference/reference_markers.hmm GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:06,147] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:06,148] [INFO] Found 6/6 markers.
[2024-01-24 14:12:06,189] [INFO] Query marker FASTA was written to GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:12:06,190] [INFO] Task started: Blastn
[2024-01-24 14:12:06,190] [INFO] Running command: blastn -query GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg10c60670-ac33-44a0-a0b4-839dd0dc407f/dqc_reference/reference_markers.fasta -out GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:06,977] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:06,988] [INFO] Selected 17 target genomes.
[2024-01-24 14:12:06,988] [INFO] Target genome list was writen to GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:12:06,994] [INFO] Task started: fastANI
[2024-01-24 14:12:06,994] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcb46372-8d80-48cc-acff-99d74118189d/GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna.gz --refList GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:24,478] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:24,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10c60670-ac33-44a0-a0b4-839dd0dc407f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:24,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10c60670-ac33-44a0-a0b4-839dd0dc407f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:24,497] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:24,497] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:24,497] [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 formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	100.0	1471	1471	95	conclusive
Chryseobacterium scophthalmum	strain=DSM 16779	GCA_900143185.1	59733	59733	type	True	83.9195	955	1471	95	below_threshold
Chryseobacterium mulctrae	strain=CA10	GCA_006175945.1	2576777	2576777	type	True	83.8947	977	1471	95	below_threshold
Chryseobacterium piscium	strain=CCUG 51923	GCA_003385415.1	333702	333702	type	True	83.3264	919	1471	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	83.2897	922	1471	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_003815915.1	254	254	type	True	83.2508	927	1471	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_900156145.1	254	254	type	True	83.2355	925	1471	95	below_threshold
Chryseobacterium arachidis	strain=DSM 27619	GCA_900129245.1	1416778	1416778	type	True	81.5986	819	1471	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	81.2637	676	1471	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	81.2056	822	1471	95	below_threshold
Chryseobacterium limigenitum	strain=SUR2	GCA_900114875.1	1612149	1612149	type	True	81.0863	734	1471	95	below_threshold
Chryseobacterium aquaticum subsp. greenlandense	strain=UMB34	GCA_001507325.1	345663	452084	type	True	81.0774	771	1471	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.8978	744	1471	95	below_threshold
Chryseobacterium nakagawai	strain=NCTC13529	GCA_900637665.1	1241982	1241982	type	True	79.8079	593	1471	95	below_threshold
Chryseobacterium shigense	strain=DSM 17126	GCA_900156575.1	297244	297244	type	True	79.4806	584	1471	95	below_threshold
Chryseobacterium shigense	strain=DSM 17126	GCA_002943655.1	297244	297244	type	True	79.4327	588	1471	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	78.9037	463	1471	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:24,500] [INFO] DFAST Taxonomy check result was written to GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:12:24,501] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:24,501] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:24,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10c60670-ac33-44a0-a0b4-839dd0dc407f/dqc_reference/checkm_data
[2024-01-24 14:12:24,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:24,565] [INFO] Task started: CheckM
[2024-01-24 14:12:24,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/checkm_input GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:13:17,731] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:17,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:17,757] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:17,757] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:17,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:13:17,758] [INFO] Task started: Blastn
[2024-01-24 14:13:17,759] [INFO] Running command: blastn -query GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg10c60670-ac33-44a0-a0b4-839dd0dc407f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:18,799] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:18,804] [INFO] Selected 15 target genomes.
[2024-01-24 14:13:18,804] [INFO] Target genome list was writen to GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:18,816] [INFO] Task started: fastANI
[2024-01-24 14:13:18,816] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcb46372-8d80-48cc-acff-99d74118189d/GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna.gz --refList GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:33,982] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:34,061] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:34,062] [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_900116415.1	s__Chryseobacterium formosense	100.0	1471	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.74	97.50	0.90	0.80	3	conclusive
GCF_000799515.1	s__Chryseobacterium sp000799515	93.668	1061	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143185.1	s__Chryseobacterium scophthalmum	83.9378	953	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.42	95.16	0.86	0.85	5	-
GCF_006175945.1	s__Chryseobacterium mulctrae	83.8767	979	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385415.1	s__Chryseobacterium piscium	83.3322	918	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.69	96.60	0.88	0.87	3	-
GCF_903166575.1	s__Chryseobacterium sp903166575	83.2831	923	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815915.1	s__Chryseobacterium indoltheticum	83.2217	930	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.91	96.48	0.91	0.84	6	-
GCF_014779605.1	s__Chryseobacterium sp014779605	83.1498	948	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.70	96.70	0.87	0.87	2	-
GCF_000799195.1	s__Chryseobacterium sp000799195	81.679	813	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129245.1	s__Chryseobacterium arachidis	81.5933	820	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799455.1	s__Chryseobacterium sp000799455	81.1456	763	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507325.1	s__Chryseobacterium greenlandense	81.0637	773	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.6446	N/A	N/A	N/A	N/A	1	-
GCF_001425355.1	s__Chryseobacterium sp001425355	81.0474	776	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813825.1	s__Chryseobacterium taiwanense	80.9659	731	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156575.1	s__Chryseobacterium shigense	79.4862	583	1471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:34,064] [INFO] GTDB search result was written to GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:34,066] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:34,076] [INFO] DFAST_QC result json was written to GCF_900116415.1_IMG-taxon_2684622901_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:13:34,076] [INFO] DFAST_QC completed!
[2024-01-24 14:13:34,076] [INFO] Total running time: 0h1m48s