[2024-01-25 20:06:35,896] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:06:35,899] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:06:35,899] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2261339-6ebe-4899-9a0c-224a4b695dc0/dqc_reference
[2024-01-25 20:06:37,065] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:06:37,066] [INFO] Task started: Prodigal
[2024-01-25 20:06:37,066] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f8eeb3f-9227-4f72-9381-23db191d9ee7/GCF_003143695.2_ASM314369v2_genomic.fna.gz | prodigal -d GCF_003143695.2_ASM314369v2_genomic.fna/cds.fna -a GCF_003143695.2_ASM314369v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:06:40,960] [INFO] Task succeeded: Prodigal
[2024-01-25 20:06:40,960] [INFO] Task started: HMMsearch
[2024-01-25 20:06:40,961] [INFO] Running command: hmmsearch --tblout GCF_003143695.2_ASM314369v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2261339-6ebe-4899-9a0c-224a4b695dc0/dqc_reference/reference_markers.hmm GCF_003143695.2_ASM314369v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:06:41,241] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:06:41,242] [INFO] Found 6/6 markers.
[2024-01-25 20:06:41,260] [INFO] Query marker FASTA was written to GCF_003143695.2_ASM314369v2_genomic.fna/markers.fasta
[2024-01-25 20:06:41,260] [INFO] Task started: Blastn
[2024-01-25 20:06:41,260] [INFO] Running command: blastn -query GCF_003143695.2_ASM314369v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2261339-6ebe-4899-9a0c-224a4b695dc0/dqc_reference/reference_markers.fasta -out GCF_003143695.2_ASM314369v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:41,809] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:41,812] [INFO] Selected 14 target genomes.
[2024-01-25 20:06:41,812] [INFO] Target genome list was writen to GCF_003143695.2_ASM314369v2_genomic.fna/target_genomes.txt
[2024-01-25 20:06:41,823] [INFO] Task started: fastANI
[2024-01-25 20:06:41,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f8eeb3f-9227-4f72-9381-23db191d9ee7/GCF_003143695.2_ASM314369v2_genomic.fna.gz --refList GCF_003143695.2_ASM314369v2_genomic.fna/target_genomes.txt --output GCF_003143695.2_ASM314369v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:47,895] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:47,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2261339-6ebe-4899-9a0c-224a4b695dc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:47,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2261339-6ebe-4899-9a0c-224a4b695dc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:47,906] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:06:47,906] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:06:47,906] [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 halitosis	strain=VT-4	GCA_003143695.2	2172545	2172545	type	True	100.0	621	622	95	conclusive
Streptococcus oralis	strain=FDAARGOS_1020	GCA_016127555.1	1303	1303	type	True	93.3362	518	622	95	below_threshold
Streptococcus oralis	strain=CCUG 13229	GCA_002014885.1	1303	1303	type	True	93.3246	518	622	95	below_threshold
Streptococcus oralis	strain=CCUG 24891	GCA_001639375.1	1303	1303	type	True	93.3038	521	622	95	below_threshold
Streptococcus oralis	strain=ATCC 35037	GCA_000164095.1	1303	1303	type	True	93.2686	517	622	95	below_threshold
Streptococcus oralis	strain=ATCC 35037	GCA_000148565.2	1303	1303	type	True	93.1865	522	622	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	92.0072	512	622	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	87.0474	455	622	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	86.9997	461	622	95	below_threshold
Streptococcus infantis	strain=ATCC 700779	GCA_000187465.1	68892	68892	suspected-type	True	83.4686	384	622	95	below_threshold
Streptococcus infantis	strain=ATCC 700779	GCA_000260755.1	68892	68892	suspected-type	True	83.3557	371	622	95	below_threshold
Streptococcus peroris	strain=ATCC 700780	GCA_000187585.1	68891	68891	type	True	82.6605	360	622	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.0003	114	622	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.3205	95	622	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:47,908] [INFO] DFAST Taxonomy check result was written to GCF_003143695.2_ASM314369v2_genomic.fna/tc_result.tsv
[2024-01-25 20:06:47,908] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:47,908] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:47,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2261339-6ebe-4899-9a0c-224a4b695dc0/dqc_reference/checkm_data
[2024-01-25 20:06:47,909] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:47,933] [INFO] Task started: CheckM
[2024-01-25 20:06:47,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003143695.2_ASM314369v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003143695.2_ASM314369v2_genomic.fna/checkm_input GCF_003143695.2_ASM314369v2_genomic.fna/checkm_result
[2024-01-25 20:07:05,840] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:05,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:05,855] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:05,855] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:05,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003143695.2_ASM314369v2_genomic.fna/markers.fasta)
[2024-01-25 20:07:05,856] [INFO] Task started: Blastn
[2024-01-25 20:07:05,856] [INFO] Running command: blastn -query GCF_003143695.2_ASM314369v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2261339-6ebe-4899-9a0c-224a4b695dc0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003143695.2_ASM314369v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:06,738] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:06,741] [INFO] Selected 20 target genomes.
[2024-01-25 20:07:06,741] [INFO] Target genome list was writen to GCF_003143695.2_ASM314369v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:06,763] [INFO] Task started: fastANI
[2024-01-25 20:07:06,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f8eeb3f-9227-4f72-9381-23db191d9ee7/GCF_003143695.2_ASM314369v2_genomic.fna.gz --refList GCF_003143695.2_ASM314369v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003143695.2_ASM314369v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:15,529] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:15,541] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:15,541] [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_003143695.2	s__Streptococcus halitosis	100.0	621	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.61	95.24	0.91	0.88	11	conclusive
GCF_000257845.1	s__Streptococcus oralis_W	94.7764	544	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.64	95.02	0.95	0.90	8	-
GCA_905221355.1	s__Streptococcus sp905221355	94.5327	541	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018448765.1	s__Streptococcus oralis_BM	94.458	522	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000344275.1	s__Streptococcus oralis_E	94.2149	534	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.70	95.70	0.91	0.91	2	-
GCF_000287715.1	s__Streptococcus oralis_Y	94.1884	552	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.24	95.17	0.89	0.88	3	-
GCF_002356415.1	s__Streptococcus oralis_F	94.1142	537	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.57	95.26	0.91	0.90	6	-
GCA_905221415.1	s__Streptococcus sp905221415	94.1063	522	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003942795.1	s__Streptococcus mitis_BJ	94.0515	538	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.60	99.60	0.93	0.93	2	-
GCF_015561235.1	s__Streptococcus oralis_BK	93.7559	529	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.42	96.42	0.92	0.92	2	-
GCF_900637025.1	s__Streptococcus oralis	93.3777	519	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.04	95.11	0.90	0.80	39	-
GCF_002386345.1	s__Streptococcus oralis_S	93.2441	543	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.64	95.33	0.92	0.86	22	-
GCF_001579025.1	s__Streptococcus oralis_X	92.7364	520	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000253155.1	s__Streptococcus oralis_L	92.7042	530	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.38	95.38	0.91	0.91	2	-
GCA_905221385.1	s__Streptococcus sp905221385	92.6006	501	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.72	97.71	0.92	0.92	3	-
GCA_905221255.1	s__Streptococcus sp905221255	92.4834	510	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.55	97.53	0.94	0.94	3	-
GCF_002096685.1	s__Streptococcus oralis_AD	92.1037	514	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003943905.1	s__Streptococcus mitis_BC	92.0126	508	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.34	95.34	0.89	0.89	2	-
GCA_905221365.1	s__Streptococcus sp905221365	91.9321	497	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003942695.1	s__Streptococcus mitis_BD	91.8202	511	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:15,542] [INFO] GTDB search result was written to GCF_003143695.2_ASM314369v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:15,543] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:15,546] [INFO] DFAST_QC result json was written to GCF_003143695.2_ASM314369v2_genomic.fna/dqc_result.json
[2024-01-25 20:07:15,546] [INFO] DFAST_QC completed!
[2024-01-25 20:07:15,546] [INFO] Total running time: 0h0m40s