[2024-01-24 15:18:05,220] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:05,222] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:05,222] [INFO] DQC Reference Directory: /var/lib/cwl/stg43120265-157b-4ea9-b85f-a5846c52b52b/dqc_reference
[2024-01-24 15:18:07,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:07,532] [INFO] Task started: Prodigal
[2024-01-24 15:18:07,532] [INFO] Running command: gunzip -c /var/lib/cwl/stgf515d807-5f7e-4fd6-99fd-a1e55a63a3de/GCF_948472335.1_Marseille-Q6994_genomic.fna.gz | prodigal -d GCF_948472335.1_Marseille-Q6994_genomic.fna/cds.fna -a GCF_948472335.1_Marseille-Q6994_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:16,054] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:16,055] [INFO] Task started: HMMsearch
[2024-01-24 15:18:16,055] [INFO] Running command: hmmsearch --tblout GCF_948472335.1_Marseille-Q6994_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43120265-157b-4ea9-b85f-a5846c52b52b/dqc_reference/reference_markers.hmm GCF_948472335.1_Marseille-Q6994_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:16,443] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:16,445] [INFO] Found 6/6 markers.
[2024-01-24 15:18:16,488] [INFO] Query marker FASTA was written to GCF_948472335.1_Marseille-Q6994_genomic.fna/markers.fasta
[2024-01-24 15:18:16,489] [INFO] Task started: Blastn
[2024-01-24 15:18:16,489] [INFO] Running command: blastn -query GCF_948472335.1_Marseille-Q6994_genomic.fna/markers.fasta -db /var/lib/cwl/stg43120265-157b-4ea9-b85f-a5846c52b52b/dqc_reference/reference_markers.fasta -out GCF_948472335.1_Marseille-Q6994_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:17,153] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:17,157] [INFO] Selected 19 target genomes.
[2024-01-24 15:18:17,157] [INFO] Target genome list was writen to GCF_948472335.1_Marseille-Q6994_genomic.fna/target_genomes.txt
[2024-01-24 15:18:17,178] [INFO] Task started: fastANI
[2024-01-24 15:18:17,178] [INFO] Running command: fastANI --query /var/lib/cwl/stgf515d807-5f7e-4fd6-99fd-a1e55a63a3de/GCF_948472335.1_Marseille-Q6994_genomic.fna.gz --refList GCF_948472335.1_Marseille-Q6994_genomic.fna/target_genomes.txt --output GCF_948472335.1_Marseille-Q6994_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:30,128] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:30,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43120265-157b-4ea9-b85f-a5846c52b52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:30,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43120265-157b-4ea9-b85f-a5846c52b52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:30,149] [INFO] Found 18 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 15:18:30,149] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:18:30,149] [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 pseudopneumoniae	strain=CCUG 49455	GCA_002087075.1	257758	257758	type	True	96.4399	628	1235	95	inconclusive
Streptococcus pseudopneumoniae	strain=ATCC BAA-960	GCA_000257825.1	257758	257758	type	True	96.104	537	1235	95	inconclusive
Streptococcus mitis	strain=FDAARGOS 1456	GCA_019047825.1	28037	28037	suspected-type	True	95.3678	577	1235	95	inconclusive
Streptococcus mitis	strain=NCTC12261	GCA_900459425.1	28037	28037	suspected-type	True	95.3632	579	1235	95	inconclusive
Streptococcus mitis	strain=NCTC 12261	GCA_000148585.3	28037	28037	suspected-type	True	95.3486	576	1235	95	inconclusive
Streptococcus mitis	strain=CCUG 31611	GCA_002014755.1	28037	28037	suspected-type	True	95.3445	570	1235	95	inconclusive
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	94.3235	599	1235	95	below_threshold
Streptococcus pneumoniae	strain=NCTC7465	GCA_001457635.1	1313	1313	type	True	93.9561	585	1235	95	below_threshold
Streptococcus pneumoniae	strain=CCUG 28588	GCA_001679535.1	1313	1313	type	True	93.944	543	1235	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	93.8187	540	1235	95	below_threshold
Streptococcus gwangjuense	strain=ChDC B345	GCA_003627155.1	1433513	1433513	type	True	93.5686	549	1235	95	below_threshold
Streptococcus chosunense	strain=ChDC B353	GCA_003626515.1	2707003	2707003	type	True	93.5011	530	1235	95	below_threshold
Streptococcus symci	strain=C17	GCA_006385165.1	2588991	2588991	type	True	93.2147	559	1235	95	below_threshold
Streptococcus shenyangsis	strain=D19	GCA_006385785.1	2589786	2589786	type	True	93.098	558	1235	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	87.2749	512	1235	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	79.9748	178	1235	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.8832	169	1235	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.5411	141	1235	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:30,151] [INFO] DFAST Taxonomy check result was written to GCF_948472335.1_Marseille-Q6994_genomic.fna/tc_result.tsv
[2024-01-24 15:18:30,151] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:30,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:30,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43120265-157b-4ea9-b85f-a5846c52b52b/dqc_reference/checkm_data
[2024-01-24 15:18:30,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:30,198] [INFO] Task started: CheckM
[2024-01-24 15:18:30,199] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_948472335.1_Marseille-Q6994_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_948472335.1_Marseille-Q6994_genomic.fna/checkm_input GCF_948472335.1_Marseille-Q6994_genomic.fna/checkm_result
[2024-01-24 15:19:06,268] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:06,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 81.94%
Strain heterogeneity: 96.15%
--------------------------------------------------------------------------------
[2024-01-24 15:19:06,321] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:06,321] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:06,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_948472335.1_Marseille-Q6994_genomic.fna/markers.fasta)
[2024-01-24 15:19:06,322] [INFO] Task started: Blastn
[2024-01-24 15:19:06,323] [INFO] Running command: blastn -query GCF_948472335.1_Marseille-Q6994_genomic.fna/markers.fasta -db /var/lib/cwl/stg43120265-157b-4ea9-b85f-a5846c52b52b/dqc_reference/reference_markers_gtdb.fasta -out GCF_948472335.1_Marseille-Q6994_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:07,278] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:07,283] [INFO] Selected 35 target genomes.
[2024-01-24 15:19:07,284] [INFO] Target genome list was writen to GCF_948472335.1_Marseille-Q6994_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:07,305] [INFO] Task started: fastANI
[2024-01-24 15:19:07,305] [INFO] Running command: fastANI --query /var/lib/cwl/stgf515d807-5f7e-4fd6-99fd-a1e55a63a3de/GCF_948472335.1_Marseille-Q6994_genomic.fna.gz --refList GCF_948472335.1_Marseille-Q6994_genomic.fna/target_genomes_gtdb.txt --output GCF_948472335.1_Marseille-Q6994_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:33,281] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:33,314] [INFO] Found 35 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 15:19:33,315] [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_002087075.1	s__Streptococcus pseudopneumoniae	96.4399	628	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.77	96.15	0.92	0.85	120	inconclusive
GCF_000148585.2	s__Streptococcus mitis	95.3513	575	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.33	95.07	0.91	0.87	25	inconclusive
GCF_001810785.1	s__Streptococcus sp001810785	94.6452	576	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001070815.1	s__Streptococcus pseudopneumoniae_P	94.4213	549	1235	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	94.4026	577	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002096855.1	s__Streptococcus mitis_Y	94.2849	558	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.03	96.03	0.87	0.87	2	-
GCF_001650315.1	s__Streptococcus sp001650315	94.243	542	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.60	97.60	0.91	0.91	2	-
GCF_002096895.1	s__Streptococcus mitis_AH	94.1927	542	1235	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	94.0378	600	1235	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	94.0126	536	1235	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	93.966	541	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457635.1	s__Streptococcus pneumoniae	93.9249	585	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.62	97.54	0.92	0.81	8452	-
GCA_905369855.1	s__Streptococcus oralis_BN	93.923	398	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001347015.1	s__Streptococcus pneumoniae_E	93.8348	600	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002096815.1	s__Streptococcus mitis_AD	93.7339	546	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221225.1	s__Streptococcus sp905221225	93.699	538	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903645285.1	s__Streptococcus sp903645285	93.6665	574	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.16	95.16	0.86	0.86	2	-
GCF_013276795.1	s__Streptococcus sp013276795	93.6605	569	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.33	95.34	0.95	0.89	5	-
GCF_000220085.1	s__Streptococcus mitis_K	93.6556	541	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.14	95.10	0.87	0.86	3	-
GCF_013277515.1	s__Streptococcus sp013277515	93.6308	568	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001113365.1	s__Streptococcus pneumoniae_C	93.6129	617	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.29	95.29	0.90	0.90	2	-
GCF_900411395.1	s__Streptococcus mitis_BA	93.5982	592	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.49	95.11	0.89	0.86	15	-
GCF_001070715.1	s__Streptococcus pseudopneumoniae_H	93.5045	527	1235	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	93.5011	530	1235	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	93.4706	537	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.27	95.27	0.86	0.84	3	-
GCF_002096845.1	s__Streptococcus mitis_A	93.4331	563	1235	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	93.408	576	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001579035.1	s__Streptococcus mitis_J	93.3414	561	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860865.1	s__Streptococcus mitis_AT	93.3163	567	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.74	95.72	0.90	0.90	3	-
GCF_001579045.1	s__Streptococcus mitis_D	93.2629	597	1235	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	93.2351	530	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385165.1	s__Streptococcus symci	93.2096	558	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.44	95.02	0.84	0.78	21	-
GCA_905221115.1	s__Streptococcus sp905221115	93.1762	547	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144795.1	s__Streptococcus mitis_BB	92.7975	532	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.49	95.02	0.87	0.86	5	-
GCF_000722695.1	s__Streptococcus mitis_O	92.5982	583	1235	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.13	95.13	0.86	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:33,317] [INFO] GTDB search result was written to GCF_948472335.1_Marseille-Q6994_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:33,318] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:33,323] [INFO] DFAST_QC result json was written to GCF_948472335.1_Marseille-Q6994_genomic.fna/dqc_result.json
[2024-01-24 15:19:33,323] [INFO] DFAST_QC completed!
[2024-01-24 15:19:33,323] [INFO] Total running time: 0h1m28s