[2024-01-24 13:41:40,854] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,856] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,856] [INFO] DQC Reference Directory: /var/lib/cwl/stgce7d812b-f10e-4302-9fcc-343705ee7a7f/dqc_reference
[2024-01-24 13:41:42,118] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,119] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,119] [INFO] Running command: gunzip -c /var/lib/cwl/stg85102f82-560c-44c1-b1e6-aedff2548282/GCF_001021975.1_ASM102197v1_genomic.fna.gz | prodigal -d GCF_001021975.1_ASM102197v1_genomic.fna/cds.fna -a GCF_001021975.1_ASM102197v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:59,541] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:59,542] [INFO] Task started: HMMsearch
[2024-01-24 13:41:59,542] [INFO] Running command: hmmsearch --tblout GCF_001021975.1_ASM102197v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce7d812b-f10e-4302-9fcc-343705ee7a7f/dqc_reference/reference_markers.hmm GCF_001021975.1_ASM102197v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:59,817] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:59,818] [INFO] Found 6/6 markers.
[2024-01-24 13:41:59,862] [INFO] Query marker FASTA was written to GCF_001021975.1_ASM102197v1_genomic.fna/markers.fasta
[2024-01-24 13:41:59,862] [INFO] Task started: Blastn
[2024-01-24 13:41:59,862] [INFO] Running command: blastn -query GCF_001021975.1_ASM102197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce7d812b-f10e-4302-9fcc-343705ee7a7f/dqc_reference/reference_markers.fasta -out GCF_001021975.1_ASM102197v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:00,513] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:00,517] [INFO] Selected 22 target genomes.
[2024-01-24 13:42:00,518] [INFO] Target genome list was writen to GCF_001021975.1_ASM102197v1_genomic.fna/target_genomes.txt
[2024-01-24 13:42:00,527] [INFO] Task started: fastANI
[2024-01-24 13:42:00,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg85102f82-560c-44c1-b1e6-aedff2548282/GCF_001021975.1_ASM102197v1_genomic.fna.gz --refList GCF_001021975.1_ASM102197v1_genomic.fna/target_genomes.txt --output GCF_001021975.1_ASM102197v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:22,951] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:22,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce7d812b-f10e-4302-9fcc-343705ee7a7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:22,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce7d812b-f10e-4302-9fcc-343705ee7a7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:22,972] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:22,972] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:22,972] [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 gallinarum	strain=DSM 27622	GCA_001021975.1	1324352	1324352	type	True	100.0	1543	1544	95	conclusive
Chryseobacterium contaminans	strain=C-26	GCA_001684955.1	1423959	1423959	type	True	83.0885	884	1544	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	83.0834	974	1544	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	82.6727	946	1544	95	below_threshold
Chryseobacterium arthrosphaerae	strain=CC-VM-7	GCA_001684965.1	651561	651561	type	True	82.6247	992	1544	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	82.5299	960	1544	95	below_threshold
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	82.5253	980	1544	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	82.5122	960	1544	95	below_threshold
Chryseobacterium panacisoli	strain=Gsoil 183	GCA_008274625.1	1807141	1807141	type	True	82.5028	969	1544	95	below_threshold
Chryseobacterium candidae	strain=JC507	GCA_004916905.1	1978493	1978493	type	True	82.4306	918	1544	95	below_threshold
Chryseobacterium nakagawai	strain=NCTC13529	GCA_900637665.1	1241982	1241982	type	True	82.3934	995	1544	95	below_threshold
Chryseobacterium lactis	strain=NCTC11390	GCA_002899875.1	1241981	1241981	type	True	82.3045	1021	1544	95	below_threshold
Chryseobacterium viscerum	strain=687B-08	GCA_002899945.2	1037377	1037377	type	True	82.2678	977	1544	95	below_threshold
Chryseobacterium flavum	strain=KCTC 12877	GCA_003385595.1	415851	415851	type	True	82.2342	926	1544	95	below_threshold
Chryseobacterium aureum	strain=17S1E7	GCA_003971235.1	2497456	2497456	type	True	82.1729	956	1544	95	below_threshold
Chryseobacterium rhizosphaerae	strain=KCTC 22548	GCA_003385455.1	395937	395937	type	True	82.0818	981	1544	95	below_threshold
Chryseobacterium rhizosphaerae	strain=NBRC 105248	GCA_007991415.1	395937	395937	type	True	82.06	980	1544	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.2835	643	1544	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	79.9439	676	1544	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.0439	510	1544	95	below_threshold
Kaistella palustris	strain=DSM 21579	GCA_000422265.1	493376	493376	type	True	77.2161	91	1544	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	77.1473	158	1544	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:22,974] [INFO] DFAST Taxonomy check result was written to GCF_001021975.1_ASM102197v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:22,977] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:22,977] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:22,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce7d812b-f10e-4302-9fcc-343705ee7a7f/dqc_reference/checkm_data
[2024-01-24 13:42:22,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:23,028] [INFO] Task started: CheckM
[2024-01-24 13:42:23,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001021975.1_ASM102197v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001021975.1_ASM102197v1_genomic.fna/checkm_input GCF_001021975.1_ASM102197v1_genomic.fna/checkm_result
[2024-01-24 13:43:16,062] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:16,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:16,085] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:16,085] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:16,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001021975.1_ASM102197v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:16,086] [INFO] Task started: Blastn
[2024-01-24 13:43:16,086] [INFO] Running command: blastn -query GCF_001021975.1_ASM102197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce7d812b-f10e-4302-9fcc-343705ee7a7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001021975.1_ASM102197v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:16,936] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:16,941] [INFO] Selected 20 target genomes.
[2024-01-24 13:43:16,941] [INFO] Target genome list was writen to GCF_001021975.1_ASM102197v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:17,039] [INFO] Task started: fastANI
[2024-01-24 13:43:17,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg85102f82-560c-44c1-b1e6-aedff2548282/GCF_001021975.1_ASM102197v1_genomic.fna.gz --refList GCF_001021975.1_ASM102197v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001021975.1_ASM102197v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:40,525] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:40,556] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:40,557] [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_001021975.1	s__Chryseobacterium gallinarum	100.0	1541	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.61	98.27	0.91	0.91	3	conclusive
GCF_003729935.1	s__Chryseobacterium sp003729935	86.2289	1137	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835665.1	s__Chryseobacterium sp002835665	83.4246	873	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001684955.1	s__Chryseobacterium contaminans	83.0793	887	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003815975.1	s__Chryseobacterium bernardetii_A	82.7394	1000	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.62	98.62	0.90	0.90	2	-
GCA_019203745.1	s__Chryseobacterium sp019203745	82.6843	984	1544	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	82.6754	945	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.62	96.62	0.92	0.92	2	-
GCF_003347605.1	s__Chryseobacterium sp003347605	82.6716	965	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001684965.1	s__Chryseobacterium arthrosphaerae	82.625	993	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.97	97.80	0.92	0.90	5	-
GCF_900636535.1	s__Chryseobacterium gleum	82.5677	984	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.52	97.29	0.95	0.89	6	-
GCF_016775705.1	s__Chryseobacterium sp003182335	82.5669	959	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.03	95.49	0.90	0.89	5	-
GCF_003815715.1	s__Chryseobacterium sp003815715	82.5639	991	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799235.1	s__Chryseobacterium sp000799235	82.5451	978	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182655.1	s__Chryseobacterium rhizoplanae	82.5319	960	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.47	95.07	0.88	0.87	3	-
GCF_001013295.1	s__Chryseobacterium indologenes_B	82.5189	985	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.53	97.53	0.94	0.90	6	-
GCF_002979755.1	s__Chryseobacterium culicis_A	82.4882	965	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.05	96.10	0.96	0.92	3	-
GCF_900078205.2	s__Chryseobacterium timonianum	82.4458	1017	1544	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	82.4303	956	1544	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	82.3784	994	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003385455.1	s__Chryseobacterium rhizosphaerae	82.0866	980	1544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.95	95.13	0.92	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:40,583] [INFO] GTDB search result was written to GCF_001021975.1_ASM102197v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:40,584] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:40,592] [INFO] DFAST_QC result json was written to GCF_001021975.1_ASM102197v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:40,593] [INFO] DFAST_QC completed!
[2024-01-24 13:43:40,593] [INFO] Total running time: 0h1m60s