[2024-01-24 11:34:55,089] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:55,092] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:55,092] [INFO] DQC Reference Directory: /var/lib/cwl/stg35d5d9b6-1418-4715-8971-43d829a2d16d/dqc_reference
[2024-01-24 11:34:56,578] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,579] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,579] [INFO] Running command: gunzip -c /var/lib/cwl/stg34eaa139-b1b8-46ec-9e8a-ec9ba534b511/GCF_900475715.1_44927_A02_genomic.fna.gz | prodigal -d GCF_900475715.1_44927_A02_genomic.fna/cds.fna -a GCF_900475715.1_44927_A02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:02,392] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:02,392] [INFO] Task started: HMMsearch
[2024-01-24 11:35:02,393] [INFO] Running command: hmmsearch --tblout GCF_900475715.1_44927_A02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35d5d9b6-1418-4715-8971-43d829a2d16d/dqc_reference/reference_markers.hmm GCF_900475715.1_44927_A02_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:02,668] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:02,669] [INFO] Found 6/6 markers.
[2024-01-24 11:35:02,693] [INFO] Query marker FASTA was written to GCF_900475715.1_44927_A02_genomic.fna/markers.fasta
[2024-01-24 11:35:02,693] [INFO] Task started: Blastn
[2024-01-24 11:35:02,693] [INFO] Running command: blastn -query GCF_900475715.1_44927_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg35d5d9b6-1418-4715-8971-43d829a2d16d/dqc_reference/reference_markers.fasta -out GCF_900475715.1_44927_A02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:03,304] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:03,307] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:03,307] [INFO] Target genome list was writen to GCF_900475715.1_44927_A02_genomic.fna/target_genomes.txt
[2024-01-24 11:35:03,312] [INFO] Task started: fastANI
[2024-01-24 11:35:03,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg34eaa139-b1b8-46ec-9e8a-ec9ba534b511/GCF_900475715.1_44927_A02_genomic.fna.gz --refList GCF_900475715.1_44927_A02_genomic.fna/target_genomes.txt --output GCF_900475715.1_44927_A02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:09,503] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:09,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35d5d9b6-1418-4715-8971-43d829a2d16d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:09,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35d5d9b6-1418-4715-8971-43d829a2d16d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:09,514] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:09,514] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:09,514] [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 gallolyticus	strain=NCTC13773	GCA_900475715.1	315405	315405	suspected-type	True	100.0	829	831	95	conclusive
Streptococcus gallolyticus subsp. gallolyticus	strain=DSM 16831	GCA_002000985.1	53354	315405	type	True	99.9996	826	831	95	conclusive
Streptococcus infantarius	strain=FDAARGOS_1019	GCA_016127275.1	102684	102684	type	True	85.254	470	831	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	85.1496	487	831	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	85.1156	470	831	95	below_threshold
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	84.9383	470	831	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1018	GCA_016403165.1	150055	150055	type	True	84.804	476	831	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1158	GCA_016725165.1	150055	150055	type	True	84.6319	465	831	95	below_threshold
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	84.5672	462	831	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.274	99	831	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:09,516] [INFO] DFAST Taxonomy check result was written to GCF_900475715.1_44927_A02_genomic.fna/tc_result.tsv
[2024-01-24 11:35:09,516] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:09,517] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:09,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35d5d9b6-1418-4715-8971-43d829a2d16d/dqc_reference/checkm_data
[2024-01-24 11:35:09,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:09,547] [INFO] Task started: CheckM
[2024-01-24 11:35:09,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900475715.1_44927_A02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900475715.1_44927_A02_genomic.fna/checkm_input GCF_900475715.1_44927_A02_genomic.fna/checkm_result
[2024-01-24 11:35:33,734] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:33,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:33,753] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:33,754] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:33,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900475715.1_44927_A02_genomic.fna/markers.fasta)
[2024-01-24 11:35:33,755] [INFO] Task started: Blastn
[2024-01-24 11:35:33,755] [INFO] Running command: blastn -query GCF_900475715.1_44927_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg35d5d9b6-1418-4715-8971-43d829a2d16d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900475715.1_44927_A02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:34,573] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:34,577] [INFO] Selected 8 target genomes.
[2024-01-24 11:35:34,577] [INFO] Target genome list was writen to GCF_900475715.1_44927_A02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:34,583] [INFO] Task started: fastANI
[2024-01-24 11:35:34,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg34eaa139-b1b8-46ec-9e8a-ec9ba534b511/GCF_900475715.1_44927_A02_genomic.fna.gz --refList GCF_900475715.1_44927_A02_genomic.fna/target_genomes_gtdb.txt --output GCF_900475715.1_44927_A02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:38,810] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:38,818] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:35:38,818] [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_002000985.1	s__Streptococcus gallolyticus	99.9996	828	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	98.04	96.86	0.89	0.79	22	inconclusive
GCA_000283635.1	s__Streptococcus macedonicus	96.1548	574	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	99.04	98.50	0.90	0.83	11	-
GCA_900478025.1	s__Streptococcus pasteurianus	95.9608	578	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.1304	99.06	98.58	0.89	0.84	22	-
GCF_003337175.1	s__Streptococcus gallolyticus_B	95.8278	526	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.6693	N/A	N/A	N/A	N/A	1	inconclusive
GCF_016461705.1	s__Streptococcus vicugnae	85.1496	487	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
GCF_000154985.1	s__Streptococcus infantarius	84.9383	470	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_900104225.1	s__Streptococcus equinus_D	84.4504	462	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101445.1	s__Streptococcus equinus_B	83.8832	493	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:38,820] [INFO] GTDB search result was written to GCF_900475715.1_44927_A02_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:38,820] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:38,823] [INFO] DFAST_QC result json was written to GCF_900475715.1_44927_A02_genomic.fna/dqc_result.json
[2024-01-24 11:35:38,823] [INFO] DFAST_QC completed!
[2024-01-24 11:35:38,823] [INFO] Total running time: 0h0m44s