[2024-01-24 14:22:34,114] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:34,116] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:34,116] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dddca9e-1bb6-4c77-8b68-8d0d1ad7b759/dqc_reference
[2024-01-24 14:22:35,369] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:35,370] [INFO] Task started: Prodigal
[2024-01-24 14:22:35,370] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c85896f-ad92-443a-bb4f-127191f3d40d/GCF_006385165.1_ASM638516v1_genomic.fna.gz | prodigal -d GCF_006385165.1_ASM638516v1_genomic.fna/cds.fna -a GCF_006385165.1_ASM638516v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:40,452] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:40,453] [INFO] Task started: HMMsearch
[2024-01-24 14:22:40,453] [INFO] Running command: hmmsearch --tblout GCF_006385165.1_ASM638516v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dddca9e-1bb6-4c77-8b68-8d0d1ad7b759/dqc_reference/reference_markers.hmm GCF_006385165.1_ASM638516v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:40,768] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:40,770] [INFO] Found 6/6 markers.
[2024-01-24 14:22:40,794] [INFO] Query marker FASTA was written to GCF_006385165.1_ASM638516v1_genomic.fna/markers.fasta
[2024-01-24 14:22:40,794] [INFO] Task started: Blastn
[2024-01-24 14:22:40,795] [INFO] Running command: blastn -query GCF_006385165.1_ASM638516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dddca9e-1bb6-4c77-8b68-8d0d1ad7b759/dqc_reference/reference_markers.fasta -out GCF_006385165.1_ASM638516v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:41,606] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:41,610] [INFO] Selected 17 target genomes.
[2024-01-24 14:22:41,610] [INFO] Target genome list was writen to GCF_006385165.1_ASM638516v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:41,619] [INFO] Task started: fastANI
[2024-01-24 14:22:41,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c85896f-ad92-443a-bb4f-127191f3d40d/GCF_006385165.1_ASM638516v1_genomic.fna.gz --refList GCF_006385165.1_ASM638516v1_genomic.fna/target_genomes.txt --output GCF_006385165.1_ASM638516v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:50,431] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:50,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dddca9e-1bb6-4c77-8b68-8d0d1ad7b759/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:50,432] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dddca9e-1bb6-4c77-8b68-8d0d1ad7b759/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:50,448] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:50,448] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:50,448] [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
Streptococcus symci	strain=C17	GCA_006385165.1	2588991	2588991	type	True	100.0	680	728	95	conclusive
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	94.6526	548	728	95	below_threshold
Streptococcus gwangjuense	strain=ChDC B345	GCA_003627155.1	1433513	1433513	type	True	94.4831	535	728	95	below_threshold
Streptococcus chosunense	strain=ChDC B353	GCA_003626515.1	2707003	2707003	type	True	94.2279	539	728	95	below_threshold
Streptococcus mitis	strain=FDAARGOS 1456	GCA_019047825.1	28037	28037	suspected-type	True	93.3723	491	728	95	below_threshold
Streptococcus mitis	strain=NCTC 12261	GCA_000148585.3	28037	28037	suspected-type	True	93.3689	499	728	95	below_threshold
Streptococcus mitis	strain=NCTC12261	GCA_900459425.1	28037	28037	suspected-type	True	93.3303	503	728	95	below_threshold
Streptococcus mitis	strain=CCUG 31611	GCA_002014755.1	28037	28037	suspected-type	True	93.2633	497	728	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	93.06	508	728	95	below_threshold
Streptococcus shenyangsis	strain=D19	GCA_006385785.1	2589786	2589786	type	True	92.1094	504	728	95	below_threshold
Streptococcus pseudopneumoniae	strain=CCUG 49455	GCA_002087075.1	257758	257758	type	True	91.6628	474	728	95	below_threshold
Streptococcus pseudopneumoniae	strain=ATCC BAA-960	GCA_000257825.1	257758	257758	type	True	91.5994	421	728	95	below_threshold
Streptococcus pneumoniae	strain=CCUG 28588	GCA_001679535.1	1313	1313	type	True	91.3019	471	728	95	below_threshold
Streptococcus pneumoniae	strain=NCTC7465	GCA_001457635.1	1313	1313	type	True	91.2602	489	728	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	87.2744	483	728	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.3235	121	728	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.2663	106	728	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:50,450] [INFO] DFAST Taxonomy check result was written to GCF_006385165.1_ASM638516v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:50,450] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:50,451] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:50,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dddca9e-1bb6-4c77-8b68-8d0d1ad7b759/dqc_reference/checkm_data
[2024-01-24 14:22:50,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:50,476] [INFO] Task started: CheckM
[2024-01-24 14:22:50,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006385165.1_ASM638516v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006385165.1_ASM638516v1_genomic.fna/checkm_input GCF_006385165.1_ASM638516v1_genomic.fna/checkm_result
[2024-01-24 14:23:14,037] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:14,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 16.67%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:14,061] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:14,061] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:14,061] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006385165.1_ASM638516v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:14,062] [INFO] Task started: Blastn
[2024-01-24 14:23:14,062] [INFO] Running command: blastn -query GCF_006385165.1_ASM638516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dddca9e-1bb6-4c77-8b68-8d0d1ad7b759/dqc_reference/reference_markers_gtdb.fasta -out GCF_006385165.1_ASM638516v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:15,000] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:15,005] [INFO] Selected 23 target genomes.
[2024-01-24 14:23:15,005] [INFO] Target genome list was writen to GCF_006385165.1_ASM638516v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:15,040] [INFO] Task started: fastANI
[2024-01-24 14:23:15,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c85896f-ad92-443a-bb4f-127191f3d40d/GCF_006385165.1_ASM638516v1_genomic.fna.gz --refList GCF_006385165.1_ASM638516v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006385165.1_ASM638516v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:27,126] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:27,144] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:27,145] [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_006385165.1	s__Streptococcus symci	100.0	678	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.44	95.02	0.84	0.78	21	conclusive
GCF_003942765.1	s__Streptococcus mitis_BE	94.8652	556	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.27	95.27	0.86	0.84	3	-
GCF_016658865.1	s__Streptococcus mitis_BT	94.6892	563	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626515.1	s__Streptococcus chosunense	94.2279	539	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.51	95.33	0.92	0.89	3	-
GCF_002096815.1	s__Streptococcus mitis_AD	94.1718	543	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002096895.1	s__Streptococcus mitis_AH	93.9168	534	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905369855.1	s__Streptococcus oralis_BN	93.853	367	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013305725.1	s__Streptococcus mitis_BO	93.7427	531	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003942865.1	s__Streptococcus mitis_BI	93.6774	520	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221155.1	s__Streptococcus sp905221155	93.5803	505	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002096925.1	s__Streptococcus mitis_AF	93.4197	500	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000148585.2	s__Streptococcus mitis	93.3689	499	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.33	95.07	0.91	0.87	25	-
GCF_005144795.1	s__Streptococcus mitis_BB	93.2826	516	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.49	95.02	0.87	0.86	5	-
GCF_002096755.1	s__Streptococcus mitis_AC	93.1419	491	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.32	95.11	0.87	0.86	7	-
GCF_002096835.1	s__Streptococcus mitis_W	93.0968	480	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901542415.1	s__Streptococcus mitis_BL	92.9732	501	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860905.1	s__Streptococcus oralis_BA	92.8353	492	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.58	98.58	0.96	0.96	2	-
GCF_002860865.1	s__Streptococcus mitis_AT	92.5061	497	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.74	95.72	0.90	0.90	3	-
GCF_013276795.1	s__Streptococcus sp013276795	92.2245	478	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.33	95.34	0.95	0.89	5	-
GCA_905221235.1	s__Streptococcus sp905221235	91.9242	477	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221095.1	s__Streptococcus sp905221095	91.6941	481	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002087075.1	s__Streptococcus pseudopneumoniae	91.6628	474	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.77	96.15	0.92	0.85	120	-
GCF_001457635.1	s__Streptococcus pneumoniae	91.2623	488	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.62	97.54	0.92	0.81	8452	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:27,147] [INFO] GTDB search result was written to GCF_006385165.1_ASM638516v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:27,148] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:27,152] [INFO] DFAST_QC result json was written to GCF_006385165.1_ASM638516v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:27,152] [INFO] DFAST_QC completed!
[2024-01-24 14:23:27,152] [INFO] Total running time: 0h0m53s