[2024-01-24 11:05:23,847] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:23,849] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:23,849] [INFO] DQC Reference Directory: /var/lib/cwl/stg97879858-269d-4e35-8032-ef6b39a5e395/dqc_reference
[2024-01-24 11:05:25,537] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:25,540] [INFO] Task started: Prodigal
[2024-01-24 11:05:25,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg3414f023-b718-48fc-b299-03c5bd800b6b/GCF_019218685.1_ASM1921868v1_genomic.fna.gz | prodigal -d GCF_019218685.1_ASM1921868v1_genomic.fna/cds.fna -a GCF_019218685.1_ASM1921868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:30,074] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:30,074] [INFO] Task started: HMMsearch
[2024-01-24 11:05:30,074] [INFO] Running command: hmmsearch --tblout GCF_019218685.1_ASM1921868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97879858-269d-4e35-8032-ef6b39a5e395/dqc_reference/reference_markers.hmm GCF_019218685.1_ASM1921868v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:30,367] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:30,368] [INFO] Found 6/6 markers.
[2024-01-24 11:05:30,392] [INFO] Query marker FASTA was written to GCF_019218685.1_ASM1921868v1_genomic.fna/markers.fasta
[2024-01-24 11:05:30,393] [INFO] Task started: Blastn
[2024-01-24 11:05:30,393] [INFO] Running command: blastn -query GCF_019218685.1_ASM1921868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97879858-269d-4e35-8032-ef6b39a5e395/dqc_reference/reference_markers.fasta -out GCF_019218685.1_ASM1921868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:31,648] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:31,655] [INFO] Selected 16 target genomes.
[2024-01-24 11:05:31,655] [INFO] Target genome list was writen to GCF_019218685.1_ASM1921868v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:32,087] [INFO] Task started: fastANI
[2024-01-24 11:05:32,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg3414f023-b718-48fc-b299-03c5bd800b6b/GCF_019218685.1_ASM1921868v1_genomic.fna.gz --refList GCF_019218685.1_ASM1921868v1_genomic.fna/target_genomes.txt --output GCF_019218685.1_ASM1921868v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:39,534] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:39,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97879858-269d-4e35-8032-ef6b39a5e395/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:39,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97879858-269d-4e35-8032-ef6b39a5e395/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:39,549] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:39,549] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:39,549] [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 vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	100.0	637	637	95	conclusive
Streptococcus gwangjuense	strain=ChDC B345	GCA_003627155.1	1433513	1433513	type	True	94.5945	544	637	95	below_threshold
Streptococcus chosunense	strain=ChDC B353	GCA_003626515.1	2707003	2707003	type	True	94.5028	549	637	95	below_threshold
Streptococcus mitis	strain=NCTC 12261	GCA_000148585.3	28037	28037	suspected-type	True	93.895	503	637	95	below_threshold
Streptococcus mitis	strain=FDAARGOS 1456	GCA_019047825.1	28037	28037	suspected-type	True	93.8946	500	637	95	below_threshold
Streptococcus mitis	strain=NCTC12261	GCA_900459425.1	28037	28037	suspected-type	True	93.8928	502	637	95	below_threshold
Streptococcus mitis	strain=CCUG 31611	GCA_002014755.1	28037	28037	suspected-type	True	93.8154	503	637	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	93.2426	495	637	95	below_threshold
Streptococcus shenyangsis	strain=D19	GCA_006385785.1	2589786	2589786	type	True	92.3604	511	637	95	below_threshold
Streptococcus pseudopneumoniae	strain=ATCC BAA-960	GCA_000257825.1	257758	257758	type	True	92.0007	408	637	95	below_threshold
Streptococcus pseudopneumoniae	strain=CCUG 49455	GCA_002087075.1	257758	257758	type	True	91.8622	469	637	95	below_threshold
Streptococcus pneumoniae	strain=NCTC7465	GCA_001457635.1	1313	1313	type	True	91.4466	488	637	95	below_threshold
Streptococcus pneumoniae	strain=CCUG 28588	GCA_001679535.1	1313	1313	type	True	91.4025	468	637	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	87.1672	473	637	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.2057	105	637	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	78.3655	87	637	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:39,551] [INFO] DFAST Taxonomy check result was written to GCF_019218685.1_ASM1921868v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:39,551] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:39,551] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:39,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97879858-269d-4e35-8032-ef6b39a5e395/dqc_reference/checkm_data
[2024-01-24 11:05:39,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:39,582] [INFO] Task started: CheckM
[2024-01-24 11:05:39,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019218685.1_ASM1921868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019218685.1_ASM1921868v1_genomic.fna/checkm_input GCF_019218685.1_ASM1921868v1_genomic.fna/checkm_result
[2024-01-24 11:06:00,524] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:00,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:00,546] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:00,546] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:00,547] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019218685.1_ASM1921868v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:00,548] [INFO] Task started: Blastn
[2024-01-24 11:06:00,548] [INFO] Running command: blastn -query GCF_019218685.1_ASM1921868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97879858-269d-4e35-8032-ef6b39a5e395/dqc_reference/reference_markers_gtdb.fasta -out GCF_019218685.1_ASM1921868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:01,481] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:01,486] [INFO] Selected 25 target genomes.
[2024-01-24 11:06:01,486] [INFO] Target genome list was writen to GCF_019218685.1_ASM1921868v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:01,524] [INFO] Task started: fastANI
[2024-01-24 11:06:01,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg3414f023-b718-48fc-b299-03c5bd800b6b/GCF_019218685.1_ASM1921868v1_genomic.fna.gz --refList GCF_019218685.1_ASM1921868v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019218685.1_ASM1921868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:13,437] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:13,460] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:13,460] [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_001579665.1	s__Streptococcus mitis_S	95.7303	559	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.64	95.33	0.87	0.85	4	conclusive
GCF_001650315.1	s__Streptococcus sp001650315	94.8966	535	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.60	97.60	0.91	0.91	2	-
GCF_003627155.1	s__Streptococcus gwangjuense	94.5945	544	637	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	94.5028	549	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.51	95.33	0.92	0.89	3	-
GCF_003942765.1	s__Streptococcus mitis_BE	94.4351	563	637	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	94.3634	563	637	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	94.2629	535	637	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	93.895	503	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.33	95.07	0.91	0.87	25	-
GCA_905221165.1	s__Streptococcus sp905221165	93.7598	516	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.98	95.98	0.92	0.92	2	-
GCA_905221155.1	s__Streptococcus sp905221155	93.584	509	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220045.1	s__Streptococcus mitis_AP	93.5578	490	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002096835.1	s__Streptococcus mitis_W	93.5549	491	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905187535.1	s__Streptococcus mitis_BS	93.537	503	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001076775.1	s__Streptococcus pseudopneumoniae_G	93.5215	495	637	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	93.3029	496	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001810785.1	s__Streptococcus sp001810785	92.9765	493	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009496165.1	s__Streptococcus mitis_BM	92.775	501	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.49	95.44	0.98	0.88	26	-
GCA_905221085.1	s__Streptococcus sp905221085	92.617	496	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009496155.1	s__Streptococcus mitis_BQ	92.6081	501	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013276795.1	s__Streptococcus sp013276795	92.4791	479	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.33	95.34	0.95	0.89	5	-
GCF_001579045.1	s__Streptococcus mitis_D	92.4075	478	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221105.1	s__Streptococcus sp905221105	92.2241	468	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000257905.1	s__Streptococcus mitis_L	92.1291	488	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221065.1	s__Streptococcus sp905221065	91.932	486	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCA_905221505.1	s__Streptococcus sp905221505	91.9015	472	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	0.98	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:13,462] [INFO] GTDB search result was written to GCF_019218685.1_ASM1921868v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:13,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:13,468] [INFO] DFAST_QC result json was written to GCF_019218685.1_ASM1921868v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:13,469] [INFO] DFAST_QC completed!
[2024-01-24 11:06:13,469] [INFO] Total running time: 0h0m50s