[2023-06-07 22:40:04,170] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:40:04,172] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:40:04,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fc300dc-2516-42dc-924a-7c512d656a7a/dqc_reference
[2023-06-07 22:40:05,449] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:40:05,450] [INFO] Task started: Prodigal
[2023-06-07 22:40:05,450] [INFO] Running command: gunzip -c /var/lib/cwl/stg555d3210-8cb1-4144-a153-2aa7bd2168d0/GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna.gz | prodigal -d GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/cds.fna -a GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:40:08,111] [INFO] Task succeeded: Prodigal
[2023-06-07 22:40:08,112] [INFO] Task started: HMMsearch
[2023-06-07 22:40:08,112] [INFO] Running command: hmmsearch --tblout GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fc300dc-2516-42dc-924a-7c512d656a7a/dqc_reference/reference_markers.hmm GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:40:08,349] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:40:08,351] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg555d3210-8cb1-4144-a153-2aa7bd2168d0/GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna.gz]
[2023-06-07 22:40:08,369] [INFO] Query marker FASTA was written to GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/markers.fasta
[2023-06-07 22:40:08,370] [INFO] Task started: Blastn
[2023-06-07 22:40:08,370] [INFO] Running command: blastn -query GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fc300dc-2516-42dc-924a-7c512d656a7a/dqc_reference/reference_markers.fasta -out GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:40:08,950] [INFO] Task succeeded: Blastn
[2023-06-07 22:40:08,954] [INFO] Selected 8 target genomes.
[2023-06-07 22:40:08,955] [INFO] Target genome list was writen to GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/target_genomes.txt
[2023-06-07 22:40:08,957] [INFO] Task started: fastANI
[2023-06-07 22:40:08,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg555d3210-8cb1-4144-a153-2aa7bd2168d0/GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna.gz --refList GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/target_genomes.txt --output GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 22:40:11,324] [INFO] Task succeeded: fastANI
[2023-06-07 22:40:11,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fc300dc-2516-42dc-924a-7c512d656a7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 22:40:11,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fc300dc-2516-42dc-924a-7c512d656a7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 22:40:11,341] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2023-06-07 22:40:11,342] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-07 22:40:11,342] [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=ATCC 9812	GCA_000187265.1	1335	1335	type	True	96.5735	294	328	95	conclusive
Streptococcus equinus	strain=NCTC12969	GCA_900459295.1	1335	1335	type	True	96.5055	295	328	95	conclusive
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	88.3446	281	328	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1158	GCA_016725165.1	150055	150055	type	True	88.22	285	328	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1018	GCA_016403165.1	150055	150055	type	True	88.1805	284	328	95	below_threshold
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	87.4639	276	328	95	below_threshold
Streptococcus infantarius	strain=FDAARGOS_1019	GCA_016127275.1	102684	102684	type	True	87.4489	282	328	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	87.4236	283	328	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 22:40:11,344] [INFO] DFAST Taxonomy check result was written to GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/tc_result.tsv
[2023-06-07 22:40:11,345] [INFO] ===== Taxonomy check completed =====
[2023-06-07 22:40:11,345] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:40:11,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fc300dc-2516-42dc-924a-7c512d656a7a/dqc_reference/checkm_data
[2023-06-07 22:40:11,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:40:11,364] [INFO] Task started: CheckM
[2023-06-07 22:40:11,364] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/checkm_input GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/checkm_result
[2023-06-07 22:40:28,012] [INFO] Task succeeded: CheckM
[2023-06-07 22:40:28,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 22:40:28,033] [INFO] ===== Completeness check finished =====
[2023-06-07 22:40:28,033] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:40:28,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/markers.fasta)
[2023-06-07 22:40:28,034] [INFO] Task started: Blastn
[2023-06-07 22:40:28,034] [INFO] Running command: blastn -query GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fc300dc-2516-42dc-924a-7c512d656a7a/dqc_reference/reference_markers_gtdb.fasta -out GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:40:28,768] [INFO] Task succeeded: Blastn
[2023-06-07 22:40:28,772] [INFO] Selected 9 target genomes.
[2023-06-07 22:40:28,772] [INFO] Target genome list was writen to GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:40:28,777] [INFO] Task started: fastANI
[2023-06-07 22:40:28,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg555d3210-8cb1-4144-a153-2aa7bd2168d0/GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna.gz --refList GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/target_genomes_gtdb.txt --output GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:40:32,210] [INFO] Task succeeded: fastANI
[2023-06-07 22:40:32,220] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 22:40:32,220] [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	96.5735	294	328	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	88.3446	281	328	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	87.6193	296	328	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	87.4639	276	328	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	86.8655	291	328	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	86.776	295	328	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000985.1	s__Streptococcus gallolyticus	84.0783	276	328	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	84.0425	260	328	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.1304	99.06	98.58	0.89	0.84	22	-
--------------------------------------------------------------------------------
[2023-06-07 22:40:32,222] [INFO] GTDB search result was written to GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/result_gtdb.tsv
[2023-06-07 22:40:32,223] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:40:32,226] [INFO] DFAST_QC result json was written to GCA_902779655.1_Rumen_uncultured_genome_RUG12492_genomic.fna/dqc_result.json
[2023-06-07 22:40:32,226] [INFO] DFAST_QC completed!
[2023-06-07 22:40:32,226] [INFO] Total running time: 0h0m28s