[2023-06-28 12:18:03,578] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:18:03,580] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:18:03,581] [INFO] DQC Reference Directory: /var/lib/cwl/stgd10cd774-40c4-49f4-8f1e-09eda68b68d7/dqc_reference
[2023-06-28 12:18:04,897] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:18:04,898] [INFO] Task started: Prodigal
[2023-06-28 12:18:04,899] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1bf4d61-16a0-4719-818e-ffe96456ffaa/GCA_017307665.1_ASM1730766v1_genomic.fna.gz | prodigal -d GCA_017307665.1_ASM1730766v1_genomic.fna/cds.fna -a GCA_017307665.1_ASM1730766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:18:19,780] [INFO] Task succeeded: Prodigal
[2023-06-28 12:18:19,781] [INFO] Task started: HMMsearch
[2023-06-28 12:18:19,781] [INFO] Running command: hmmsearch --tblout GCA_017307665.1_ASM1730766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd10cd774-40c4-49f4-8f1e-09eda68b68d7/dqc_reference/reference_markers.hmm GCA_017307665.1_ASM1730766v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:18:20,047] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:18:20,048] [INFO] Found 6/6 markers.
[2023-06-28 12:18:20,081] [INFO] Query marker FASTA was written to GCA_017307665.1_ASM1730766v1_genomic.fna/markers.fasta
[2023-06-28 12:18:20,081] [INFO] Task started: Blastn
[2023-06-28 12:18:20,081] [INFO] Running command: blastn -query GCA_017307665.1_ASM1730766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd10cd774-40c4-49f4-8f1e-09eda68b68d7/dqc_reference/reference_markers.fasta -out GCA_017307665.1_ASM1730766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:18:20,756] [INFO] Task succeeded: Blastn
[2023-06-28 12:18:20,762] [INFO] Selected 25 target genomes.
[2023-06-28 12:18:20,763] [INFO] Target genome list was writen to GCA_017307665.1_ASM1730766v1_genomic.fna/target_genomes.txt
[2023-06-28 12:18:20,767] [INFO] Task started: fastANI
[2023-06-28 12:18:20,767] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1bf4d61-16a0-4719-818e-ffe96456ffaa/GCA_017307665.1_ASM1730766v1_genomic.fna.gz --refList GCA_017307665.1_ASM1730766v1_genomic.fna/target_genomes.txt --output GCA_017307665.1_ASM1730766v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:18:36,832] [INFO] Task succeeded: fastANI
[2023-06-28 12:18:36,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd10cd774-40c4-49f4-8f1e-09eda68b68d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:18:36,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd10cd774-40c4-49f4-8f1e-09eda68b68d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:18:36,861] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:18:36,861] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:18:36,861] [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 koreense	strain=CCUG 49689	GCA_001045435.1	232216	232216	type	True	78.4684	278	1009	95	below_threshold
Chryseobacterium koreense	strain=DSM 25209	GCA_014201785.1	232216	232216	type	True	78.3786	277	1009	95	below_threshold
Chryseobacterium nakagawai	strain=NCTC13529	GCA_900637665.1	1241982	1241982	type	True	78.3608	144	1009	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	77.9147	210	1009	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	77.8444	208	1009	95	below_threshold
Chryseobacterium taichungense	strain=DSM 17453	GCA_900109935.1	295069	295069	type	True	77.8215	155	1009	95	below_threshold
Chryseobacterium phocaeense	strain=6021061333	GCA_900169075.1	1816690	1816690	type	True	77.5967	129	1009	95	below_threshold
Kaistella chaponensis	strain=DSM 23145	GCA_900156725.1	713588	713588	type	True	77.5688	199	1009	95	below_threshold
Kaistella daneshvariae	strain=H3001	GCA_003860505.1	2487074	2487074	type	True	77.4977	174	1009	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	77.461	140	1009	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	77.3802	172	1009	95	below_threshold
Chryseobacterium glaciei	strain=IHBB 10212	GCA_001648155.1	1685010	1685010	type	True	77.3015	121	1009	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	77.2469	136	1009	95	below_threshold
Kaistella gelatinilytica	strain=G5-32	GCA_015679325.1	2787636	2787636	type	True	77.2342	187	1009	95	below_threshold
Kaistella jeonii	strain=NCTC13459	GCA_900638245.1	266749	266749	type	True	77.1655	196	1009	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_000812865.1	266749	266749	type	True	77.1554	195	1009	95	below_threshold
Chryseobacterium kwangjuense	strain=KJ1R5	GCA_001563495.1	267125	267125	type	True	77.1489	126	1009	95	below_threshold
Riemerella columbina	strain=DSM 16469	GCA_000374405.1	103810	103810	type	True	77.1438	67	1009	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_900112115.1	266749	266749	type	True	77.1315	198	1009	95	below_threshold
Chryseobacterium polytrichastri	strain=DSM 26899	GCA_900142445.1	1302687	1302687	type	True	77.0656	120	1009	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:18:36,865] [INFO] DFAST Taxonomy check result was written to GCA_017307665.1_ASM1730766v1_genomic.fna/tc_result.tsv
[2023-06-28 12:18:36,865] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:18:36,866] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:18:36,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd10cd774-40c4-49f4-8f1e-09eda68b68d7/dqc_reference/checkm_data
[2023-06-28 12:18:36,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:18:36,901] [INFO] Task started: CheckM
[2023-06-28 12:18:36,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017307665.1_ASM1730766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017307665.1_ASM1730766v1_genomic.fna/checkm_input GCA_017307665.1_ASM1730766v1_genomic.fna/checkm_result
[2023-06-28 12:19:23,607] [INFO] Task succeeded: CheckM
[2023-06-28 12:19:23,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:19:23,633] [INFO] ===== Completeness check finished =====
[2023-06-28 12:19:23,634] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:19:23,634] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017307665.1_ASM1730766v1_genomic.fna/markers.fasta)
[2023-06-28 12:19:23,634] [INFO] Task started: Blastn
[2023-06-28 12:19:23,635] [INFO] Running command: blastn -query GCA_017307665.1_ASM1730766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd10cd774-40c4-49f4-8f1e-09eda68b68d7/dqc_reference/reference_markers_gtdb.fasta -out GCA_017307665.1_ASM1730766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:19:24,544] [INFO] Task succeeded: Blastn
[2023-06-28 12:19:24,550] [INFO] Selected 21 target genomes.
[2023-06-28 12:19:24,550] [INFO] Target genome list was writen to GCA_017307665.1_ASM1730766v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:19:24,564] [INFO] Task started: fastANI
[2023-06-28 12:19:24,565] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1bf4d61-16a0-4719-818e-ffe96456ffaa/GCA_017307665.1_ASM1730766v1_genomic.fna.gz --refList GCA_017307665.1_ASM1730766v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017307665.1_ASM1730766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:19:38,926] [INFO] Task succeeded: fastANI
[2023-06-28 12:19:38,942] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:19:38,942] [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
GCA_001898255.1	s__Kaistella sp001898255	99.9449	985	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	99.97	99.97	0.99	0.99	2	conclusive
GCF_000735695.2	s__Kaistella haifensis	79.1971	258	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.72	96.43	0.83	0.82	4	-
GCF_001403755.1	s__Kaistella senegalense	78.8428	241	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002453895.1	s__Kaistella sp002453895	78.7143	206	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001045435.1	s__Kaistella koreensis	78.5063	274	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	99.98	99.98	0.99	0.99	2	-
GCA_002426785.1	s__Kaistella sp002426785	78.0181	240	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	98.19	97.96	0.88	0.84	4	-
GCF_019195395.1	s__Kaistella sp019195395	77.8599	207	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109935.1	s__Chryseobacterium taichungense	77.8215	155	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002205795.1	s__Kaistella sp002205795	77.6676	225	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	95.66	95.02	0.89	0.88	3	-
GCA_002197835.1	s__Kaistella sp002197835	77.6618	226	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	97.62	97.62	0.94	0.94	2	-
GCF_003860505.1	s__Kaistella daneshvariae	77.5169	172	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.86	96.86	0.91	0.91	2	-
GCA_015999765.1	s__Kaistella sp015999765	77.5059	181	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	0.96	0.96	2	-
GCF_900156735.1	s__Chryseobacterium ureilyticum	77.4863	138	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018902795.1	s__Kaistella sp018902795	77.3922	233	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003860585.1	s__Kaistella carnis	77.3802	172	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.86	96.44	0.91	0.90	4	-
GCF_001648155.1	s__Chryseobacterium glaciei	77.3238	120	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014837035.1	s__Kaistella sp014837035	77.2547	141	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015191005.1	s__Kaistella flava	77.161	191	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001563495.1	s__Chryseobacterium kwangjuense	77.1472	126	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142445.1	s__Chryseobacterium polytrichastri	77.0677	119	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799255.1	s__Chryseobacterium sp000799255	76.9642	117	1009	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.94	98.94	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-28 12:19:38,944] [INFO] GTDB search result was written to GCA_017307665.1_ASM1730766v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:19:38,945] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:19:38,949] [INFO] DFAST_QC result json was written to GCA_017307665.1_ASM1730766v1_genomic.fna/dqc_result.json
[2023-06-28 12:19:38,950] [INFO] DFAST_QC completed!
[2023-06-28 12:19:38,950] [INFO] Total running time: 0h1m35s