[2023-06-28 21:51:17,438] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:51:17,440] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:51:17,440] [INFO] DQC Reference Directory: /var/lib/cwl/stg493306ff-39bb-44fd-922c-d5973884b621/dqc_reference
[2023-06-28 21:51:18,741] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:51:18,742] [INFO] Task started: Prodigal
[2023-06-28 21:51:18,743] [INFO] Running command: gunzip -c /var/lib/cwl/stgf68b61ce-fb25-4ebb-a336-ef818fe7f929/GCA_015059535.1_ASM1505953v1_genomic.fna.gz | prodigal -d GCA_015059535.1_ASM1505953v1_genomic.fna/cds.fna -a GCA_015059535.1_ASM1505953v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:51:22,999] [INFO] Task succeeded: Prodigal
[2023-06-28 21:51:23,000] [INFO] Task started: HMMsearch
[2023-06-28 21:51:23,000] [INFO] Running command: hmmsearch --tblout GCA_015059535.1_ASM1505953v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg493306ff-39bb-44fd-922c-d5973884b621/dqc_reference/reference_markers.hmm GCA_015059535.1_ASM1505953v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:51:23,241] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:51:23,243] [INFO] Found 6/6 markers.
[2023-06-28 21:51:23,264] [INFO] Query marker FASTA was written to GCA_015059535.1_ASM1505953v1_genomic.fna/markers.fasta
[2023-06-28 21:51:23,264] [INFO] Task started: Blastn
[2023-06-28 21:51:23,264] [INFO] Running command: blastn -query GCA_015059535.1_ASM1505953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg493306ff-39bb-44fd-922c-d5973884b621/dqc_reference/reference_markers.fasta -out GCA_015059535.1_ASM1505953v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:51:23,895] [INFO] Task succeeded: Blastn
[2023-06-28 21:51:23,899] [INFO] Selected 14 target genomes.
[2023-06-28 21:51:23,900] [INFO] Target genome list was writen to GCA_015059535.1_ASM1505953v1_genomic.fna/target_genomes.txt
[2023-06-28 21:51:23,903] [INFO] Task started: fastANI
[2023-06-28 21:51:23,903] [INFO] Running command: fastANI --query /var/lib/cwl/stgf68b61ce-fb25-4ebb-a336-ef818fe7f929/GCA_015059535.1_ASM1505953v1_genomic.fna.gz --refList GCA_015059535.1_ASM1505953v1_genomic.fna/target_genomes.txt --output GCA_015059535.1_ASM1505953v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:51:29,672] [INFO] Task succeeded: fastANI
[2023-06-28 21:51:29,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg493306ff-39bb-44fd-922c-d5973884b621/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:51:29,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg493306ff-39bb-44fd-922c-d5973884b621/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:51:29,687] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2023-06-28 21:51:29,687] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 21:51:29,687] [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 equinus	strain=NCTC12969	GCA_900459295.1	1335	1335	type	True	96.8184	504	615	95	conclusive
Streptococcus equinus	strain=ATCC 9812	GCA_000187265.1	1335	1335	type	True	96.8144	509	615	95	conclusive
Streptococcus lutetiensis	strain=FDAARGOS_1158	GCA_016725165.1	150055	150055	type	True	88.2964	477	615	95	below_threshold
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	88.2277	479	615	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1018	GCA_016403165.1	150055	150055	type	True	88.0078	484	615	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	87.2511	489	615	95	below_threshold
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	87.2335	485	615	95	below_threshold
Streptococcus infantarius	strain=FDAARGOS_1019	GCA_016127275.1	102684	102684	type	True	87.2258	497	615	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	86.9019	494	615	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 21:51:29,689] [INFO] DFAST Taxonomy check result was written to GCA_015059535.1_ASM1505953v1_genomic.fna/tc_result.tsv
[2023-06-28 21:51:29,690] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:51:29,690] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:51:29,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg493306ff-39bb-44fd-922c-d5973884b621/dqc_reference/checkm_data
[2023-06-28 21:51:29,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:51:29,719] [INFO] Task started: CheckM
[2023-06-28 21:51:29,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015059535.1_ASM1505953v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015059535.1_ASM1505953v1_genomic.fna/checkm_input GCA_015059535.1_ASM1505953v1_genomic.fna/checkm_result
[2023-06-28 21:51:50,588] [INFO] Task succeeded: CheckM
[2023-06-28 21:51:50,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:51:50,611] [INFO] ===== Completeness check finished =====
[2023-06-28 21:51:50,611] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:51:50,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015059535.1_ASM1505953v1_genomic.fna/markers.fasta)
[2023-06-28 21:51:50,612] [INFO] Task started: Blastn
[2023-06-28 21:51:50,612] [INFO] Running command: blastn -query GCA_015059535.1_ASM1505953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg493306ff-39bb-44fd-922c-d5973884b621/dqc_reference/reference_markers_gtdb.fasta -out GCA_015059535.1_ASM1505953v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:51:51,430] [INFO] Task succeeded: Blastn
[2023-06-28 21:51:51,434] [INFO] Selected 7 target genomes.
[2023-06-28 21:51:51,434] [INFO] Target genome list was writen to GCA_015059535.1_ASM1505953v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:51:51,439] [INFO] Task started: fastANI
[2023-06-28 21:51:51,439] [INFO] Running command: fastANI --query /var/lib/cwl/stgf68b61ce-fb25-4ebb-a336-ef818fe7f929/GCA_015059535.1_ASM1505953v1_genomic.fna.gz --refList GCA_015059535.1_ASM1505953v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015059535.1_ASM1505953v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:51:54,686] [INFO] Task succeeded: fastANI
[2023-06-28 21:51:54,696] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:51:54,697] [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_000187265.1	s__Streptococcus equinus	96.8144	509	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.03	95.86	0.90	0.87	42	conclusive
GCF_900475675.1	s__Streptococcus lutetiensis	88.2277	479	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	95.22	0.92	0.85	50	-
GCF_900101445.1	s__Streptococcus equinus_B	87.584	510	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_000154985.1	s__Streptococcus infantarius	87.2335	485	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_016461705.1	s__Streptococcus vicugnae	86.8768	495	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
GCF_900104225.1	s__Streptococcus equinus_D	86.7001	509	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:51:54,699] [INFO] GTDB search result was written to GCA_015059535.1_ASM1505953v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:51:54,699] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:51:54,702] [INFO] DFAST_QC result json was written to GCA_015059535.1_ASM1505953v1_genomic.fna/dqc_result.json
[2023-06-28 21:51:54,702] [INFO] DFAST_QC completed!
[2023-06-28 21:51:54,702] [INFO] Total running time: 0h0m37s