[2024-01-25 19:11:20,761] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:20,763] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:20,763] [INFO] DQC Reference Directory: /var/lib/cwl/stga5d775dd-1e94-42ad-84e2-c618cc1cf18d/dqc_reference
[2024-01-25 19:11:21,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:21,893] [INFO] Task started: Prodigal
[2024-01-25 19:11:21,893] [INFO] Running command: gunzip -c /var/lib/cwl/stg77a77077-deb6-43c9-a0b2-8b088561c86d/GCF_003385455.1_ASM338545v1_genomic.fna.gz | prodigal -d GCF_003385455.1_ASM338545v1_genomic.fna/cds.fna -a GCF_003385455.1_ASM338545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:37,724] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:37,724] [INFO] Task started: HMMsearch
[2024-01-25 19:11:37,725] [INFO] Running command: hmmsearch --tblout GCF_003385455.1_ASM338545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5d775dd-1e94-42ad-84e2-c618cc1cf18d/dqc_reference/reference_markers.hmm GCF_003385455.1_ASM338545v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:38,000] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:38,002] [INFO] Found 6/6 markers.
[2024-01-25 19:11:38,045] [INFO] Query marker FASTA was written to GCF_003385455.1_ASM338545v1_genomic.fna/markers.fasta
[2024-01-25 19:11:38,045] [INFO] Task started: Blastn
[2024-01-25 19:11:38,045] [INFO] Running command: blastn -query GCF_003385455.1_ASM338545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5d775dd-1e94-42ad-84e2-c618cc1cf18d/dqc_reference/reference_markers.fasta -out GCF_003385455.1_ASM338545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:38,671] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:38,674] [INFO] Selected 20 target genomes.
[2024-01-25 19:11:38,674] [INFO] Target genome list was writen to GCF_003385455.1_ASM338545v1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:38,689] [INFO] Task started: fastANI
[2024-01-25 19:11:38,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg77a77077-deb6-43c9-a0b2-8b088561c86d/GCF_003385455.1_ASM338545v1_genomic.fna.gz --refList GCF_003385455.1_ASM338545v1_genomic.fna/target_genomes.txt --output GCF_003385455.1_ASM338545v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:02,071] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:02,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5d775dd-1e94-42ad-84e2-c618cc1cf18d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:02,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5d775dd-1e94-42ad-84e2-c618cc1cf18d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:02,084] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:12:02,085] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:12:02,085] [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 rhizosphaerae	strain=KCTC 22548	GCA_003385455.1	395937	395937	type	True	100.0	1706	1712	95	conclusive
Chryseobacterium rhizosphaerae	strain=NBRC 105248	GCA_007991415.1	395937	395937	type	True	99.9657	1652	1712	95	conclusive
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	82.9692	1124	1712	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	82.9249	1116	1712	95	below_threshold
Chryseobacterium viscerum	strain=687B-08	GCA_002899945.2	1037377	1037377	type	True	82.8712	1130	1712	95	below_threshold
Chryseobacterium aurantiacum	strain=F30	GCA_003020585.1	2116499	2116499	type	True	82.8455	1056	1712	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	82.7958	1108	1712	95	below_threshold
Chryseobacterium panacisoli	strain=Gsoil 183	GCA_008274625.1	1807141	1807141	type	True	82.711	1142	1712	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	82.6841	1090	1712	95	below_threshold
Chryseobacterium lactis	strain=NCTC11390	GCA_002899875.1	1241981	1241981	type	True	82.6409	1142	1712	95	below_threshold
Chryseobacterium cucumeris	strain=GSE06	GCA_001593385.1	1813611	1813611	type	True	82.6379	1107	1712	95	below_threshold
Chryseobacterium flavum	strain=KCTC 12877	GCA_003385595.1	415851	415851	type	True	82.542	1050	1712	95	below_threshold
Chryseobacterium nakagawai	strain=NCTC13529	GCA_900637665.1	1241982	1241982	type	True	82.3048	1102	1712	95	below_threshold
Chryseobacterium aureum	strain=17S1E7	GCA_003971235.1	2497456	2497456	type	True	82.3041	1077	1712	95	below_threshold
Chryseobacterium soli	strain=DSM 19298	GCA_000737705.1	445961	445961	type	True	80.5384	842	1712	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.5199	668	1712	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.2176	721	1712	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.1548	728	1712	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.4459	497	1712	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.2719	597	1712	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:02,088] [INFO] DFAST Taxonomy check result was written to GCF_003385455.1_ASM338545v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:02,088] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:02,088] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:02,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5d775dd-1e94-42ad-84e2-c618cc1cf18d/dqc_reference/checkm_data
[2024-01-25 19:12:02,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:02,141] [INFO] Task started: CheckM
[2024-01-25 19:12:02,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385455.1_ASM338545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385455.1_ASM338545v1_genomic.fna/checkm_input GCF_003385455.1_ASM338545v1_genomic.fna/checkm_result
[2024-01-25 19:12:49,196] [INFO] Task succeeded: CheckM
[2024-01-25 19:12:49,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:12:49,215] [INFO] ===== Completeness check finished =====
[2024-01-25 19:12:49,215] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:12:49,216] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385455.1_ASM338545v1_genomic.fna/markers.fasta)
[2024-01-25 19:12:49,216] [INFO] Task started: Blastn
[2024-01-25 19:12:49,216] [INFO] Running command: blastn -query GCF_003385455.1_ASM338545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5d775dd-1e94-42ad-84e2-c618cc1cf18d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385455.1_ASM338545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:50,119] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:50,122] [INFO] Selected 21 target genomes.
[2024-01-25 19:12:50,122] [INFO] Target genome list was writen to GCF_003385455.1_ASM338545v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:12:50,152] [INFO] Task started: fastANI
[2024-01-25 19:12:50,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg77a77077-deb6-43c9-a0b2-8b088561c86d/GCF_003385455.1_ASM338545v1_genomic.fna.gz --refList GCF_003385455.1_ASM338545v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385455.1_ASM338545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:14,135] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:14,148] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:13:14,148] [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_003385455.1	s__Chryseobacterium rhizosphaerae	100.0	1706	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.95	95.13	0.92	0.87	6	conclusive
GCA_019236175.1	s__Chryseobacterium sp019236175	83.0388	1081	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903969135.1	s__Chryseobacterium sp900156935	83.0072	1139	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.11	99.11	0.93	0.93	2	-
GCF_000799335.1	s__Chryseobacterium sp000799335	82.9865	1135	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100075.1	s__Chryseobacterium jejuense	82.9741	1124	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900182655.1	s__Chryseobacterium rhizoplanae	82.9437	1114	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.47	95.07	0.88	0.87	3	-
GCF_002899945.2	s__Chryseobacterium viscerum	82.8589	1132	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.88	95.74	0.91	0.87	3	-
GCF_003020585.1	s__Chryseobacterium aurantiacum	82.8532	1055	1712	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	82.8108	1122	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.05	96.10	0.96	0.92	3	-
GCF_008386505.1	s__Chryseobacterium sediminis	82.7894	1109	1712	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	82.7376	1123	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274625.1	s__Chryseobacterium sp008274625	82.715	1142	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663845.1	s__Chryseobacterium sp003663845	82.6984	1073	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752975.1	s__Chryseobacterium sp011752975	82.6698	1037	1712	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	82.6474	1090	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001593385.1	s__Chryseobacterium cucumeris	82.6378	1107	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.67	98.29	0.93	0.90	5	-
GCF_003729935.1	s__Chryseobacterium sp003729935	82.6211	1013	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385595.1	s__Chryseobacterium flavum	82.542	1050	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.84	98.79	0.93	0.93	3	-
GCF_900637665.1	s__Chryseobacterium nakagawai	82.3108	1101	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003971235.1	s__Chryseobacterium aureum	82.3073	1076	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737705.1	s__Chryseobacterium soli	80.5272	844	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:14,150] [INFO] GTDB search result was written to GCF_003385455.1_ASM338545v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:14,150] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:14,155] [INFO] DFAST_QC result json was written to GCF_003385455.1_ASM338545v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:14,155] [INFO] DFAST_QC completed!
[2024-01-25 19:13:14,156] [INFO] Total running time: 0h1m53s