[2024-01-25 19:08:05,654] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:08:05,655] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:08:05,655] [INFO] DQC Reference Directory: /var/lib/cwl/stgaff0de4d-5ddf-4678-bc54-882d18e04ee4/dqc_reference
[2024-01-25 19:08:06,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:08:06,841] [INFO] Task started: Prodigal
[2024-01-25 19:08:06,842] [INFO] Running command: gunzip -c /var/lib/cwl/stg408a4533-f009-4f47-9281-193de5f9f2f2/GCF_016461705.1_ASM1646170v1_genomic.fna.gz | prodigal -d GCF_016461705.1_ASM1646170v1_genomic.fna/cds.fna -a GCF_016461705.1_ASM1646170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:08:10,531] [INFO] Task succeeded: Prodigal
[2024-01-25 19:08:10,531] [INFO] Task started: HMMsearch
[2024-01-25 19:08:10,531] [INFO] Running command: hmmsearch --tblout GCF_016461705.1_ASM1646170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaff0de4d-5ddf-4678-bc54-882d18e04ee4/dqc_reference/reference_markers.hmm GCF_016461705.1_ASM1646170v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:08:10,788] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:08:10,789] [INFO] Found 6/6 markers.
[2024-01-25 19:08:10,814] [INFO] Query marker FASTA was written to GCF_016461705.1_ASM1646170v1_genomic.fna/markers.fasta
[2024-01-25 19:08:10,814] [INFO] Task started: Blastn
[2024-01-25 19:08:10,814] [INFO] Running command: blastn -query GCF_016461705.1_ASM1646170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaff0de4d-5ddf-4678-bc54-882d18e04ee4/dqc_reference/reference_markers.fasta -out GCF_016461705.1_ASM1646170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:11,403] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:11,408] [INFO] Selected 14 target genomes.
[2024-01-25 19:08:11,408] [INFO] Target genome list was writen to GCF_016461705.1_ASM1646170v1_genomic.fna/target_genomes.txt
[2024-01-25 19:08:11,417] [INFO] Task started: fastANI
[2024-01-25 19:08:11,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg408a4533-f009-4f47-9281-193de5f9f2f2/GCF_016461705.1_ASM1646170v1_genomic.fna.gz --refList GCF_016461705.1_ASM1646170v1_genomic.fna/target_genomes.txt --output GCF_016461705.1_ASM1646170v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:16,779] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:16,779] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaff0de4d-5ddf-4678-bc54-882d18e04ee4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:16,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaff0de4d-5ddf-4678-bc54-882d18e04ee4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:16,788] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:08:16,788] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:08:16,788] [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 vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	100.0	627	629	95	conclusive
Streptococcus infantarius	strain=FDAARGOS_1019	GCA_016127275.1	102684	102684	type	True	90.2979	515	629	95	below_threshold
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	90.2912	509	629	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	90.2879	514	629	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1158	GCA_016725165.1	150055	150055	type	True	88.8395	490	629	95	below_threshold
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	88.7634	487	629	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1018	GCA_016403165.1	150055	150055	type	True	88.6981	502	629	95	below_threshold
Streptococcus equinus	strain=ATCC 9812	GCA_000187265.1	1335	1335	type	True	86.7952	480	629	95	below_threshold
Streptococcus gallolyticus subsp. gallolyticus	strain=DSM 16831	GCA_002000985.1	53354	315405	type	True	85.3604	484	629	95	below_threshold
Streptococcus gordonii	strain=FDAARGOS 1454	GCA_019046945.1	1302	1302	suspected-type	True	79.1382	93	629	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	78.8566	63	629	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:16,789] [INFO] DFAST Taxonomy check result was written to GCF_016461705.1_ASM1646170v1_genomic.fna/tc_result.tsv
[2024-01-25 19:08:16,790] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:16,790] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:16,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaff0de4d-5ddf-4678-bc54-882d18e04ee4/dqc_reference/checkm_data
[2024-01-25 19:08:16,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:16,814] [INFO] Task started: CheckM
[2024-01-25 19:08:16,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016461705.1_ASM1646170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016461705.1_ASM1646170v1_genomic.fna/checkm_input GCF_016461705.1_ASM1646170v1_genomic.fna/checkm_result
[2024-01-25 19:08:34,155] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:34,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:34,170] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:34,170] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:34,170] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016461705.1_ASM1646170v1_genomic.fna/markers.fasta)
[2024-01-25 19:08:34,170] [INFO] Task started: Blastn
[2024-01-25 19:08:34,170] [INFO] Running command: blastn -query GCF_016461705.1_ASM1646170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaff0de4d-5ddf-4678-bc54-882d18e04ee4/dqc_reference/reference_markers_gtdb.fasta -out GCF_016461705.1_ASM1646170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:35,023] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:35,027] [INFO] Selected 9 target genomes.
[2024-01-25 19:08:35,027] [INFO] Target genome list was writen to GCF_016461705.1_ASM1646170v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:35,035] [INFO] Task started: fastANI
[2024-01-25 19:08:35,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg408a4533-f009-4f47-9281-193de5f9f2f2/GCF_016461705.1_ASM1646170v1_genomic.fna.gz --refList GCF_016461705.1_ASM1646170v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016461705.1_ASM1646170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:08:39,209] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:39,216] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:08:39,216] [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_016461705.1	s__Streptococcus vicugnae	100.0	627	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	conclusive
GCF_900104225.1	s__Streptococcus equinus_D	94.9643	542	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154985.1	s__Streptococcus infantarius	90.2912	509	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_900101445.1	s__Streptococcus equinus_B	89.5232	525	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_900475675.1	s__Streptococcus lutetiensis	88.7634	487	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	95.22	0.92	0.85	50	-
GCF_000187265.1	s__Streptococcus equinus	86.7952	480	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.03	95.86	0.90	0.87	42	-
GCF_002000985.1	s__Streptococcus gallolyticus	85.3604	484	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	98.04	96.86	0.89	0.79	22	-
GCA_900478025.1	s__Streptococcus pasteurianus	84.716	455	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.1304	99.06	98.58	0.89	0.84	22	-
GCA_000283635.1	s__Streptococcus macedonicus	84.5785	467	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	99.04	98.50	0.90	0.83	11	-
--------------------------------------------------------------------------------
[2024-01-25 19:08:39,217] [INFO] GTDB search result was written to GCF_016461705.1_ASM1646170v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:08:39,218] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:08:39,222] [INFO] DFAST_QC result json was written to GCF_016461705.1_ASM1646170v1_genomic.fna/dqc_result.json
[2024-01-25 19:08:39,222] [INFO] DFAST_QC completed!
[2024-01-25 19:08:39,222] [INFO] Total running time: 0h0m34s