[2024-01-24 11:35:11,534] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,537] [INFO] DQC Reference Directory: /var/lib/cwl/stg415d3d8d-fc9a-45a4-9f46-e6f8b4552cf6/dqc_reference
[2024-01-24 11:35:12,823] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:12,824] [INFO] Task started: Prodigal
[2024-01-24 11:35:12,824] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9f627d8-e2fa-44bd-a135-7a55ba9a2269/GCF_002899825.2_ASM289982v2_genomic.fna.gz | prodigal -d GCF_002899825.2_ASM289982v2_genomic.fna/cds.fna -a GCF_002899825.2_ASM289982v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:32,879] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:32,880] [INFO] Task started: HMMsearch
[2024-01-24 11:35:32,880] [INFO] Running command: hmmsearch --tblout GCF_002899825.2_ASM289982v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg415d3d8d-fc9a-45a4-9f46-e6f8b4552cf6/dqc_reference/reference_markers.hmm GCF_002899825.2_ASM289982v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:33,187] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:33,189] [INFO] Found 6/6 markers.
[2024-01-24 11:35:33,237] [INFO] Query marker FASTA was written to GCF_002899825.2_ASM289982v2_genomic.fna/markers.fasta
[2024-01-24 11:35:33,237] [INFO] Task started: Blastn
[2024-01-24 11:35:33,237] [INFO] Running command: blastn -query GCF_002899825.2_ASM289982v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg415d3d8d-fc9a-45a4-9f46-e6f8b4552cf6/dqc_reference/reference_markers.fasta -out GCF_002899825.2_ASM289982v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:33,922] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:33,926] [INFO] Selected 16 target genomes.
[2024-01-24 11:35:33,926] [INFO] Target genome list was writen to GCF_002899825.2_ASM289982v2_genomic.fna/target_genomes.txt
[2024-01-24 11:35:33,937] [INFO] Task started: fastANI
[2024-01-24 11:35:33,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9f627d8-e2fa-44bd-a135-7a55ba9a2269/GCF_002899825.2_ASM289982v2_genomic.fna.gz --refList GCF_002899825.2_ASM289982v2_genomic.fna/target_genomes.txt --output GCF_002899825.2_ASM289982v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:50,849] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:50,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg415d3d8d-fc9a-45a4-9f46-e6f8b4552cf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:50,850] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg415d3d8d-fc9a-45a4-9f46-e6f8b4552cf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:50,864] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:50,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:50,864] [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 phosphatilyticum	strain=ISE14	GCA_002899825.2	475075	475075	type	True	100.0	1713	1714	95	conclusive
Chryseobacterium indologenes	strain=NCTC10796	GCA_900460995.1	253	253	type	True	85.5779	1293	1714	95	below_threshold
Chryseobacterium indologenes	strain=DSM 16777	GCA_900113975.1	253	253	type	True	85.5667	1312	1714	95	below_threshold
Chryseobacterium indologenes	strain=NBRC 14944	GCA_000520835.1	253	253	type	True	85.5649	1285	1714	95	below_threshold
Chryseobacterium lactis	strain=NCTC11390	GCA_002899875.1	1241981	1241981	type	True	84.1348	1284	1714	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	83.0935	1102	1714	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	83.046	1087	1714	95	below_threshold
Chryseobacterium panacisoli	strain=Gsoil 183	GCA_008274625.1	1807141	1807141	type	True	82.8604	1109	1714	95	below_threshold
Chryseobacterium artocarpi	strain=UTM-3	GCA_001684975.1	1414727	1414727	type	True	82.6745	1052	1714	95	below_threshold
Chryseobacterium nakagawai	strain=NCTC13529	GCA_900637665.1	1241982	1241982	type	True	82.6742	1094	1714	95	below_threshold
Chryseobacterium aurantiacum	strain=F30	GCA_003020585.1	2116499	2116499	type	True	82.5962	1023	1714	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.2755	682	1714	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.1389	713	1714	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	79.9004	710	1714	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.0853	591	1714	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	77.2874	145	1714	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:50,866] [INFO] DFAST Taxonomy check result was written to GCF_002899825.2_ASM289982v2_genomic.fna/tc_result.tsv
[2024-01-24 11:35:50,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:50,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:50,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg415d3d8d-fc9a-45a4-9f46-e6f8b4552cf6/dqc_reference/checkm_data
[2024-01-24 11:35:50,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:50,922] [INFO] Task started: CheckM
[2024-01-24 11:35:50,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002899825.2_ASM289982v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002899825.2_ASM289982v2_genomic.fna/checkm_input GCF_002899825.2_ASM289982v2_genomic.fna/checkm_result
[2024-01-24 11:36:51,134] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:51,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:51,159] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:51,159] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:51,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002899825.2_ASM289982v2_genomic.fna/markers.fasta)
[2024-01-24 11:36:51,160] [INFO] Task started: Blastn
[2024-01-24 11:36:51,160] [INFO] Running command: blastn -query GCF_002899825.2_ASM289982v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg415d3d8d-fc9a-45a4-9f46-e6f8b4552cf6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002899825.2_ASM289982v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:52,081] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:52,086] [INFO] Selected 21 target genomes.
[2024-01-24 11:36:52,086] [INFO] Target genome list was writen to GCF_002899825.2_ASM289982v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:52,122] [INFO] Task started: fastANI
[2024-01-24 11:36:52,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9f627d8-e2fa-44bd-a135-7a55ba9a2269/GCF_002899825.2_ASM289982v2_genomic.fna.gz --refList GCF_002899825.2_ASM289982v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002899825.2_ASM289982v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:15,773] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:15,793] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:15,793] [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_002899825.2	s__Chryseobacterium phosphatilyticum	100.0	1713	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016025055.1	s__Chryseobacterium indologenes	85.4821	1305	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.10	98.65	0.93	0.89	60	-
GCF_003815875.1	s__Chryseobacterium lactis	84.0616	1300	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900182655.1	s__Chryseobacterium rhizoplanae	83.0894	1103	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.47	95.07	0.88	0.87	3	-
GCF_000799235.1	s__Chryseobacterium sp000799235	83.0563	1110	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386505.1	s__Chryseobacterium sediminis	83.0341	1088	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.62	96.62	0.92	0.92	2	-
GCF_000745535.1	s__Chryseobacterium sp000745535	82.9908	1126	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979755.1	s__Chryseobacterium culicis_A	82.889	1115	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.05	96.10	0.96	0.92	3	-
GCF_008274625.1	s__Chryseobacterium sp008274625	82.8678	1108	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979455.1	s__Chryseobacterium sp002979455	82.819	1092	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815715.1	s__Chryseobacterium sp003815715	82.7877	1105	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004119445.1	s__Chryseobacterium sp004119445	82.7773	1069	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156735.1	s__Chryseobacterium ureilyticum	82.7716	1047	1714	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	82.6837	1092	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001684975.1	s__Chryseobacterium artocarpi	82.6706	1053	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002899945.2	s__Chryseobacterium viscerum	82.6516	1135	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.88	95.74	0.91	0.87	3	-
GCF_003385515.1	s__Chryseobacterium sp003385515	82.6201	1111	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.92	97.92	0.86	0.86	2	-
GCF_003020585.1	s__Chryseobacterium aurantiacum	82.6051	1023	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877355.1	s__Chryseobacterium jejuense_A	82.5952	1075	1714	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	82.5407	1093	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006829085.1	s__Chryseobacterium sp006829085	82.5046	1065	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.29	97.29	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:15,795] [INFO] GTDB search result was written to GCF_002899825.2_ASM289982v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:15,796] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:15,800] [INFO] DFAST_QC result json was written to GCF_002899825.2_ASM289982v2_genomic.fna/dqc_result.json
[2024-01-24 11:37:15,800] [INFO] DFAST_QC completed!
[2024-01-24 11:37:15,800] [INFO] Total running time: 0h2m4s