[2024-01-24 11:22:49,401] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,402] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,403] [INFO] DQC Reference Directory: /var/lib/cwl/stgd259464c-d0ea-45ef-aed5-22ce5abc6a30/dqc_reference
[2024-01-24 11:22:50,615] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,616] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,616] [INFO] Running command: gunzip -c /var/lib/cwl/stgca9bdf69-4c6c-447a-bd2a-11ef9de67ced/GCF_900451365.1_50569_C01_genomic.fna.gz | prodigal -d GCF_900451365.1_50569_C01_genomic.fna/cds.fna -a GCF_900451365.1_50569_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:22:58,540] [INFO] Task succeeded: Prodigal
[2024-01-24 11:22:58,540] [INFO] Task started: HMMsearch
[2024-01-24 11:22:58,541] [INFO] Running command: hmmsearch --tblout GCF_900451365.1_50569_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd259464c-d0ea-45ef-aed5-22ce5abc6a30/dqc_reference/reference_markers.hmm GCF_900451365.1_50569_C01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:22:58,778] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:22:58,780] [INFO] Found 6/6 markers.
[2024-01-24 11:22:58,859] [INFO] Query marker FASTA was written to GCF_900451365.1_50569_C01_genomic.fna/markers.fasta
[2024-01-24 11:22:58,860] [INFO] Task started: Blastn
[2024-01-24 11:22:58,860] [INFO] Running command: blastn -query GCF_900451365.1_50569_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd259464c-d0ea-45ef-aed5-22ce5abc6a30/dqc_reference/reference_markers.fasta -out GCF_900451365.1_50569_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:59,595] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:59,599] [INFO] Selected 18 target genomes.
[2024-01-24 11:22:59,599] [INFO] Target genome list was writen to GCF_900451365.1_50569_C01_genomic.fna/target_genomes.txt
[2024-01-24 11:23:00,201] [INFO] Task started: fastANI
[2024-01-24 11:23:00,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgca9bdf69-4c6c-447a-bd2a-11ef9de67ced/GCF_900451365.1_50569_C01_genomic.fna.gz --refList GCF_900451365.1_50569_C01_genomic.fna/target_genomes.txt --output GCF_900451365.1_50569_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:12,575] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:12,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd259464c-d0ea-45ef-aed5-22ce5abc6a30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:12,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd259464c-d0ea-45ef-aed5-22ce5abc6a30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:12,601] [INFO] Found 18 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:23:12,601] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:23:12,602] [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
Kingella denitrificans	strain=NCTC10995	GCA_900451365.1	502	502	type	True	100.0	744	747	95	conclusive
Kingella denitrificans	strain=FDAARGOS_1060	GCA_016127355.1	502	502	type	True	99.9958	739	747	95	conclusive
Kingella denitrificans	strain=ATCC 33394	GCA_000190695.1	502	502	type	True	99.9179	732	747	95	conclusive
Eikenella halliae	strain=NML130454	GCA_001648475.1	1795832	1795832	type	True	82.1724	296	747	95	below_threshold
Neisseria elongata subsp. glycolytica	strain=ATCC 29315	GCA_000818035.1	88719	495	type	True	81.3933	268	747	95	below_threshold
Neisseria elongata subsp. glycolytica	strain=NCTC11050	GCA_900475815.1	88719	495	type	True	81.3687	271	747	95	below_threshold
Eikenella exigua	strain=PXX	GCA_008805035.1	2528037	2528037	type	True	80.7632	219	747	95	below_threshold
Kingella bonacorsii	strain=Marseille-Q4569	GCA_016623605.1	2796361	2796361	type	True	79.7685	326	747	95	below_threshold
Kingella oralis	strain=DSM 18271	GCA_014054985.1	505	505	type	True	79.6654	310	747	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	79.0574	246	747	95	below_threshold
Kingella potus	strain=3/SID/1128	GCA_022870985.1	265175	265175	type	True	78.9318	255	747	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	78.6813	231	747	95	below_threshold
Kingella kingae	strain=NCTC10529	GCA_900475905.1	504	504	type	True	78.5757	280	747	95	below_threshold
Kingella kingae	strain=4177/66	GCA_022871005.1	504	504	type	True	78.4972	277	747	95	below_threshold
Conchiformibius steedae	strain=DSM 2580	GCA_014054725.1	153493	153493	type	True	78.2932	209	747	95	below_threshold
Kingella kingae	strain=ATCC 23330	GCA_000213535.1	504	504	type	True	78.1595	275	747	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	78.0085	253	747	95	below_threshold
Conchiformibius steedae	strain=DSM 2580	GCA_000620925.1	153493	153493	type	True	77.9311	211	747	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:12,609] [INFO] DFAST Taxonomy check result was written to GCF_900451365.1_50569_C01_genomic.fna/tc_result.tsv
[2024-01-24 11:23:12,610] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:12,610] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:12,611] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd259464c-d0ea-45ef-aed5-22ce5abc6a30/dqc_reference/checkm_data
[2024-01-24 11:23:12,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:12,640] [INFO] Task started: CheckM
[2024-01-24 11:23:12,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900451365.1_50569_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900451365.1_50569_C01_genomic.fna/checkm_input GCF_900451365.1_50569_C01_genomic.fna/checkm_result
[2024-01-24 11:23:39,838] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:39,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:39,860] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:39,860] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:39,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900451365.1_50569_C01_genomic.fna/markers.fasta)
[2024-01-24 11:23:39,861] [INFO] Task started: Blastn
[2024-01-24 11:23:39,861] [INFO] Running command: blastn -query GCF_900451365.1_50569_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd259464c-d0ea-45ef-aed5-22ce5abc6a30/dqc_reference/reference_markers_gtdb.fasta -out GCF_900451365.1_50569_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:41,106] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:41,110] [INFO] Selected 20 target genomes.
[2024-01-24 11:23:41,110] [INFO] Target genome list was writen to GCF_900451365.1_50569_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:41,128] [INFO] Task started: fastANI
[2024-01-24 11:23:41,128] [INFO] Running command: fastANI --query /var/lib/cwl/stgca9bdf69-4c6c-447a-bd2a-11ef9de67ced/GCF_900451365.1_50569_C01_genomic.fna.gz --refList GCF_900451365.1_50569_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900451365.1_50569_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:23:53,486] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:53,509] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:23:53,509] [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_000190695.1	s__Kingella_A denitrificans	99.9179	732	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_A	95.0	98.63	96.04	0.97	0.93	4	conclusive
GCF_001648475.1	s__Eikenella halliae	82.2682	292	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990355.1	s__Eikenella corrodens_B	82.0453	291	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187105.1	s__Eikenella corrodens	81.5375	269	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.96	95.30	0.90	0.87	23	-
GCF_900113545.1	s__Neisseria elongata	81.1993	284	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	96.68	96.06	0.91	0.86	20	-
GCA_000220865.1	s__Neisseria macacae	81.0106	270	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.509	99.99	99.99	0.98	0.98	2	-
GCF_008805035.1	s__Eikenella exigua	80.7905	219	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.49	95.37	0.95	0.91	11	-
GCA_001067655.1	s__Neisseria lactamica_B	80.3228	235	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_005886145.1	s__Neisseria sp000090875	80.1846	260	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_003044565.1	s__Neisseria sicca_A	80.1508	253	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.01	95.27	0.94	0.92	3	-
GCF_014054985.1	s__Kingella_B oralis	79.7499	312	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B	95.0	98.22	96.45	0.95	0.91	3	-
GCA_905373195.1	s__Kingella_B oralis_A	79.5874	168	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016025525.2	s__Eikenella sp016025525	79.5874	246	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014055005.1	s__Neisseria dentiae	79.1798	299	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCF_014054525.1	s__Alysiella filiformis	78.4283	236	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000226875.1	s__Eikenella shayeganii	78.4157	234	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.47	96.47	0.85	0.85	2	-
GCF_014054725.1	s__Conchiformibius steedae	78.2769	212	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Conchiformibius	95.0	98.09	96.18	0.94	0.87	3	-
GCF_900111845.1	s__Kingella kingae	78.0697	281	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	98.43	98.16	0.96	0.94	37	-
GCF_000751855.1	s__Kingella negevensis	77.7862	181	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	99.09	98.48	0.96	0.94	3	-
GCF_000745955.1	s__Alysiella crassa	77.781	203	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.94	99.94	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:23:53,511] [INFO] GTDB search result was written to GCF_900451365.1_50569_C01_genomic.fna/result_gtdb.tsv
[2024-01-24 11:23:53,511] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:23:53,516] [INFO] DFAST_QC result json was written to GCF_900451365.1_50569_C01_genomic.fna/dqc_result.json
[2024-01-24 11:23:53,516] [INFO] DFAST_QC completed!
[2024-01-24 11:23:53,516] [INFO] Total running time: 0h1m4s