[2024-01-24 13:25:58,050] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:58,053] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:58,053] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3f75c35-8579-43cc-aab7-89282a1b0414/dqc_reference
[2024-01-24 13:26:00,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:00,377] [INFO] Task started: Prodigal
[2024-01-24 13:26:00,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg882529ae-aacb-4c50-a283-8153a0876382/GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna.gz | prodigal -d GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/cds.fna -a GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:14,491] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:14,491] [INFO] Task started: HMMsearch
[2024-01-24 13:26:14,492] [INFO] Running command: hmmsearch --tblout GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3f75c35-8579-43cc-aab7-89282a1b0414/dqc_reference/reference_markers.hmm GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:14,817] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:14,818] [INFO] Found 6/6 markers.
[2024-01-24 13:26:14,856] [INFO] Query marker FASTA was written to GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/markers.fasta
[2024-01-24 13:26:14,856] [INFO] Task started: Blastn
[2024-01-24 13:26:14,856] [INFO] Running command: blastn -query GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3f75c35-8579-43cc-aab7-89282a1b0414/dqc_reference/reference_markers.fasta -out GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:15,586] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:15,591] [INFO] Selected 26 target genomes.
[2024-01-24 13:26:15,591] [INFO] Target genome list was writen to GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 13:26:15,616] [INFO] Task started: fastANI
[2024-01-24 13:26:15,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg882529ae-aacb-4c50-a283-8153a0876382/GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna.gz --refList GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/target_genomes.txt --output GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:34,859] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:34,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3f75c35-8579-43cc-aab7-89282a1b0414/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:34,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3f75c35-8579-43cc-aab7-89282a1b0414/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:34,881] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:26:34,882] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:26:34,882] [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 fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	93.4796	1022	1385	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	79.3863	535	1385	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	79.3635	527	1385	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	79.3517	544	1385	95	below_threshold
Chryseobacterium gleum	strain=FDAARGOS_1103	GCA_016766875.1	250	250	type	True	79.3013	532	1385	95	below_threshold
Chryseobacterium piperi	strain=CTM	GCA_000737775.1	558152	558152	type	True	79.2842	540	1385	95	below_threshold
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	79.2504	572	1385	95	below_threshold
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	79.2493	531	1385	95	below_threshold
Chryseobacterium gleum	strain=NCTC11432	GCA_900636535.1	250	250	type	True	79.2452	521	1385	95	below_threshold
Chryseobacterium geocarposphaerae	strain=DSM 27617	GCA_002797535.1	1416776	1416776	type	True	79.2437	539	1385	95	below_threshold
Chryseobacterium piperi	strain=ATCC BAA-1782	GCA_002285635.2	558152	558152	type	True	79.2071	546	1385	95	below_threshold
Chryseobacterium defluvii	strain=DSM 14219	GCA_003634775.1	160396	160396	type	True	79.1877	492	1385	95	below_threshold
Chryseobacterium flavum	strain=KCTC 12877	GCA_003385595.1	415851	415851	type	True	79.1847	492	1385	95	below_threshold
Chryseobacterium populi	strain=CF314	GCA_000282115.1	1144316	1144316	type	True	79.0984	524	1385	95	below_threshold
Chryseobacterium takakiae	strain=DSM 26898	GCA_900129385.1	1302685	1302685	type	True	79.0929	469	1385	95	below_threshold
Chryseobacterium paridis	strain=YIM B02567	GCA_016595215.1	2800328	2800328	type	True	79.0896	543	1385	95	below_threshold
Chryseobacterium soli	strain=DSM 19298	GCA_000737705.1	445961	445961	type	True	79.0264	502	1385	95	below_threshold
Chryseobacterium formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	78.5045	460	1385	95	below_threshold
Riemerella columbina	strain=DSM 16469	GCA_000374405.1	103810	103810	type	True	76.5678	100	1385	95	below_threshold
Chishuiella changwenlii	strain=DSM 27989	GCA_900142565.1	1434701	1434701	type	True	75.6087	58	1385	95	below_threshold
Chishuiella changwenlii	strain=CGMCC 1.12707	GCA_014638465.1	1434701	1434701	type	True	75.3013	57	1385	95	below_threshold
Flavobacterium gelidilacus	strain=DSM 15343	GCA_000422685.1	206041	206041	type	True	75.2345	63	1385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:34,884] [INFO] DFAST Taxonomy check result was written to GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 13:26:34,884] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:34,884] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:34,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3f75c35-8579-43cc-aab7-89282a1b0414/dqc_reference/checkm_data
[2024-01-24 13:26:34,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:34,938] [INFO] Task started: CheckM
[2024-01-24 13:26:34,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/checkm_input GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/checkm_result
[2024-01-24 13:27:18,600] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:18,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:18,628] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:18,629] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:18,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/markers.fasta)
[2024-01-24 13:27:18,630] [INFO] Task started: Blastn
[2024-01-24 13:27:18,630] [INFO] Running command: blastn -query GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3f75c35-8579-43cc-aab7-89282a1b0414/dqc_reference/reference_markers_gtdb.fasta -out GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:19,519] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:19,524] [INFO] Selected 26 target genomes.
[2024-01-24 13:27:19,524] [INFO] Target genome list was writen to GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:19,558] [INFO] Task started: fastANI
[2024-01-24 13:27:19,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg882529ae-aacb-4c50-a283-8153a0876382/GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna.gz --refList GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:39,363] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:39,387] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:39,387] [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_003709475.1	s__Chryseobacterium nematophagum_A	95.8308	1183	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.82	95.82	0.85	0.85	2	conclusive
GCF_003710065.1	s__Chryseobacterium nematophagum_B	94.3156	1195	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.50	95.50	0.87	0.87	2	-
GCF_001045455.1	s__Chryseobacterium sp001045455	79.5479	594	1385	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	79.477	544	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799195.1	s__Chryseobacterium sp000799195	79.3842	571	1385	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	79.3446	555	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900636535.1	s__Chryseobacterium gleum	79.2361	522	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.52	97.29	0.95	0.89	6	-
GCF_002797535.1	s__Chryseobacterium geocarposphaerae	79.2349	540	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.65	95.65	0.87	0.87	2	-
GCF_002285635.2	s__Chryseobacterium piperi	79.2133	546	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003385595.1	s__Chryseobacterium flavum	79.1847	492	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.84	98.79	0.93	0.93	3	-
GCF_003634775.1	s__Chryseobacterium defluvii	79.178	493	1385	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	79.1397	535	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.05	96.10	0.96	0.92	3	-
GCF_000282115.1	s__Chryseobacterium populi	79.0984	524	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900129385.1	s__Chryseobacterium takakiae	79.0929	469	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595215.1	s__Chryseobacterium sp016595215	79.0737	542	1385	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	79.013	504	1385	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	78.9924	493	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.29	97.29	0.93	0.93	2	-
GCF_003815975.1	s__Chryseobacterium bernardetii_A	78.8771	526	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.62	98.62	0.90	0.90	2	-
GCF_900116415.1	s__Chryseobacterium formosense	78.499	460	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.74	97.50	0.90	0.80	3	-
GCA_002862805.1	s__Flavobacterium sp002862805	75.1831	53	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:39,389] [INFO] GTDB search result was written to GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:39,390] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:39,394] [INFO] DFAST_QC result json was written to GCF_902728265.1_Chryseobacterium_CECT9293_SPAdes_Prokka_genomic.fna/dqc_result.json
[2024-01-24 13:27:39,395] [INFO] DFAST_QC completed!
[2024-01-24 13:27:39,395] [INFO] Total running time: 0h1m41s