[2024-01-24 13:52:12,389] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:52:12,391] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:52:12,391] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7dde4e9-2798-42ce-a161-16036b762d8b/dqc_reference
[2024-01-24 13:52:13,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:52:13,635] [INFO] Task started: Prodigal
[2024-01-24 13:52:13,635] [INFO] Running command: gunzip -c /var/lib/cwl/stga1c70dad-677a-4d81-a746-861c69aecb64/GCF_900459475.1_46463_D01_genomic.fna.gz | prodigal -d GCF_900459475.1_46463_D01_genomic.fna/cds.fna -a GCF_900459475.1_46463_D01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:52:18,111] [INFO] Task succeeded: Prodigal
[2024-01-24 13:52:18,111] [INFO] Task started: HMMsearch
[2024-01-24 13:52:18,111] [INFO] Running command: hmmsearch --tblout GCF_900459475.1_46463_D01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7dde4e9-2798-42ce-a161-16036b762d8b/dqc_reference/reference_markers.hmm GCF_900459475.1_46463_D01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:52:18,403] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:52:18,404] [INFO] Found 6/6 markers.
[2024-01-24 13:52:18,429] [INFO] Query marker FASTA was written to GCF_900459475.1_46463_D01_genomic.fna/markers.fasta
[2024-01-24 13:52:18,430] [INFO] Task started: Blastn
[2024-01-24 13:52:18,430] [INFO] Running command: blastn -query GCF_900459475.1_46463_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7dde4e9-2798-42ce-a161-16036b762d8b/dqc_reference/reference_markers.fasta -out GCF_900459475.1_46463_D01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:19,016] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:19,020] [INFO] Selected 9 target genomes.
[2024-01-24 13:52:19,021] [INFO] Target genome list was writen to GCF_900459475.1_46463_D01_genomic.fna/target_genomes.txt
[2024-01-24 13:52:19,027] [INFO] Task started: fastANI
[2024-01-24 13:52:19,027] [INFO] Running command: fastANI --query /var/lib/cwl/stga1c70dad-677a-4d81-a746-861c69aecb64/GCF_900459475.1_46463_D01_genomic.fna.gz --refList GCF_900459475.1_46463_D01_genomic.fna/target_genomes.txt --output GCF_900459475.1_46463_D01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:23,858] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:23,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7dde4e9-2798-42ce-a161-16036b762d8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:23,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7dde4e9-2798-42ce-a161-16036b762d8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:23,869] [INFO] Found 8 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:52:23,869] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:52:23,869] [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 equi subsp. zooepidemicus	strain=NCTC4676	GCA_900459475.1	40041	1336	type	True	100.0	700	702	95	conclusive
Streptococcus equi	strain=DSM 20561	GCA_900110405.1	1336	1336	type	True	97.1101	567	702	95	conclusive
Streptococcus equi	strain=ATCC 33398	GCA_900156215.1	1336	1336	type	True	97.1029	574	702	95	conclusive
Streptococcus equi subsp. zooepidemicus	strain=NCTC7023	GCA_900460185.1	40041	1336	type	True	96.7305	629	702	95	conclusive
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	96.1086	573	702	95	conclusive
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	80.0357	63	702	95	below_threshold
Streptococcus porcinus	strain=NCTC10999	GCA_900475415.1	1340	1340	type	True	79.9741	139	702	95	below_threshold
Streptococcus pyogenes	strain=PartK-Spyogenes-RM8376	GCA_022869605.1	1314	1314	type	True	79.086	225	702	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:23,871] [INFO] DFAST Taxonomy check result was written to GCF_900459475.1_46463_D01_genomic.fna/tc_result.tsv
[2024-01-24 13:52:23,872] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:23,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:23,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7dde4e9-2798-42ce-a161-16036b762d8b/dqc_reference/checkm_data
[2024-01-24 13:52:23,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:23,899] [INFO] Task started: CheckM
[2024-01-24 13:52:23,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900459475.1_46463_D01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900459475.1_46463_D01_genomic.fna/checkm_input GCF_900459475.1_46463_D01_genomic.fna/checkm_result
[2024-01-24 13:52:44,624] [INFO] Task succeeded: CheckM
[2024-01-24 13:52:44,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:52:44,643] [INFO] ===== Completeness check finished =====
[2024-01-24 13:52:44,643] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:52:44,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900459475.1_46463_D01_genomic.fna/markers.fasta)
[2024-01-24 13:52:44,644] [INFO] Task started: Blastn
[2024-01-24 13:52:44,645] [INFO] Running command: blastn -query GCF_900459475.1_46463_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7dde4e9-2798-42ce-a161-16036b762d8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900459475.1_46463_D01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:45,416] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:45,421] [INFO] Selected 21 target genomes.
[2024-01-24 13:52:45,421] [INFO] Target genome list was writen to GCF_900459475.1_46463_D01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:45,456] [INFO] Task started: fastANI
[2024-01-24 13:52:45,456] [INFO] Running command: fastANI --query /var/lib/cwl/stga1c70dad-677a-4d81-a746-861c69aecb64/GCF_900459475.1_46463_D01_genomic.fna.gz --refList GCF_900459475.1_46463_D01_genomic.fna/target_genomes_gtdb.txt --output GCF_900459475.1_46463_D01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:53,050] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:53,069] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:53,070] [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
GCA_900637675.1	s__Streptococcus equi	97.0799	610	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.36	95.16	0.97	0.81	392	conclusive
GCF_000186445.1	s__Streptococcus agalactiae	80.4469	89	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.63	98.18	0.88	0.63	1516	-
GCF_900459225.1	s__Streptococcus dysgalactiae	80.1325	227	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.49	0.83	0.78	121	-
GCF_900475415.1	s__Streptococcus porcinus	80.0221	140	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.32	99.10	0.96	0.93	7	-
GCF_901542335.1	s__Streptococcus porcinus_A	79.8065	129	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.24	98.24	0.90	0.90	2	-
GCF_900636575.1	s__Streptococcus canis	79.5482	244	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.95	97.68	0.91	0.86	20	-
GCF_000222765.1	s__Streptococcus cristatus	79.4653	72	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.39	95.04	0.92	0.87	17	-
GCF_000188035.1	s__Streptococcus pseudoporcinus	79.3104	141	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.36	97.79	0.89	0.85	10	-
GCF_002055535.1	s__Streptococcus pyogenes	79.0739	222	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.85	98.36	0.95	0.87	2144	-
GCF_016908655.1	s__Streptococcus saliviloxodontae	79.0705	86	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908645.1	s__Streptococcus loxodontisalivarius	79.069	80	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380005.1	s__Streptococcus didelphis	79.0067	128	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003686955.1	s__Streptococcus sp003686955	78.9356	90	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729355.1	s__Streptococcus sp902729355	78.915	87	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.77	98.74	0.88	0.87	5	-
GCF_000188015.2	s__Streptococcus ictaluri	78.8857	206	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003943505.1	s__Streptococcus cristatus_E	78.8029	61	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425025.1	s__Streptococcus castoreus	78.6985	199	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001302265.1	s__Streptococcus phocae	78.5118	174	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.05	97.05	0.87	0.87	2	-
GCF_000380105.1	s__Streptococcus orisratti	78.1894	105	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570575.1	s__Streptococcus cuniculi_A	78.0909	67	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000286075.1	s__Streptococcus ratti	77.8533	87	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.59	98.38	0.97	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:53,071] [INFO] GTDB search result was written to GCF_900459475.1_46463_D01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:53,072] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:53,075] [INFO] DFAST_QC result json was written to GCF_900459475.1_46463_D01_genomic.fna/dqc_result.json
[2024-01-24 13:52:53,076] [INFO] DFAST_QC completed!
[2024-01-24 13:52:53,076] [INFO] Total running time: 0h0m41s