[2024-01-24 15:26:35,999] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:36,002] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:36,003] [INFO] DQC Reference Directory: /var/lib/cwl/stgefd18741-22de-4dbb-9427-49f7adff6d9f/dqc_reference
[2024-01-24 15:26:39,059] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:39,061] [INFO] Task started: Prodigal
[2024-01-24 15:26:39,062] [INFO] Running command: gunzip -c /var/lib/cwl/stg3787f98a-378e-43fd-8126-a36187b3aaa7/GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/cds.fna -a GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:42,764] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:42,765] [INFO] Task started: HMMsearch
[2024-01-24 15:26:42,765] [INFO] Running command: hmmsearch --tblout GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefd18741-22de-4dbb-9427-49f7adff6d9f/dqc_reference/reference_markers.hmm GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:43,196] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:43,198] [INFO] Found 6/6 markers.
[2024-01-24 15:26:43,220] [INFO] Query marker FASTA was written to GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:26:43,223] [INFO] Task started: Blastn
[2024-01-24 15:26:43,223] [INFO] Running command: blastn -query GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgefd18741-22de-4dbb-9427-49f7adff6d9f/dqc_reference/reference_markers.fasta -out GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:46,782] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:46,786] [INFO] Selected 28 target genomes.
[2024-01-24 15:26:46,786] [INFO] Target genome list was writen to GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:26:46,822] [INFO] Task started: fastANI
[2024-01-24 15:26:46,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg3787f98a-378e-43fd-8126-a36187b3aaa7/GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna.gz --refList GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:57,164] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:57,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefd18741-22de-4dbb-9427-49f7adff6d9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:57,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefd18741-22de-4dbb-9427-49f7adff6d9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:57,176] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:57,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:57,176] [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
Granulicatella balaenopterae	strain=DSM 15827	GCA_900111135.1	137733	137733	type	True	100.0	662	665	95	conclusive
Granulicatella adiacens	strain=ATCC 49175	GCA_000160675.1	46124	46124	type	True	78.8898	90	665	95	below_threshold
Granulicatella adiacens	strain=FDAARGOS_1477	GCA_019931005.1	46124	46124	type	True	78.7771	95	665	95	below_threshold
Granulicatella adiacens	strain=ATCC 49175	GCA_025150565.1	46124	46124	type	True	78.7575	93	665	95	below_threshold
Vagococcus fluvialis	strain=DSM 5731	GCA_003337315.1	2738	2738	type	True	77.2968	59	665	95	below_threshold
Carnobacterium inhibens subsp. gilichinskyi	strain=WN1359	GCA_000493735.1	1266845	147709	type	True	77.1033	51	665	95	below_threshold
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	77.0133	68	665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:57,179] [INFO] DFAST Taxonomy check result was written to GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:26:57,180] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:57,180] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:57,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefd18741-22de-4dbb-9427-49f7adff6d9f/dqc_reference/checkm_data
[2024-01-24 15:26:57,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:57,208] [INFO] Task started: CheckM
[2024-01-24 15:26:57,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/checkm_input GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:27:16,560] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:16,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:16,579] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:16,579] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:16,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:27:16,580] [INFO] Task started: Blastn
[2024-01-24 15:27:16,580] [INFO] Running command: blastn -query GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgefd18741-22de-4dbb-9427-49f7adff6d9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:17,384] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:17,389] [INFO] Selected 23 target genomes.
[2024-01-24 15:27:17,389] [INFO] Target genome list was writen to GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:17,409] [INFO] Task started: fastANI
[2024-01-24 15:27:17,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg3787f98a-378e-43fd-8126-a36187b3aaa7/GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna.gz --refList GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:27,781] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:27,790] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:27,791] [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_900111135.1	s__Granulicatella balaenopterae	100.0	662	665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000162475.2	s__Granulicatella elegans	79.3281	123	665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001071995.1	s__Granulicatella sp001071995	79.2343	86	665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018364485.1	s__Granulicatella adiacens_A	78.9491	73	665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905371865.1	s__Granulicatella sp905371865	78.4884	61	665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551535.1	s__Granulicatella sp900551535	77.9028	69	665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015264885.1	s__Granulicatella sp015264885	77.8269	52	665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	95.15	95.15	0.88	0.88	2	-
GCF_000746825.1	s__Carnobacterium_A inhibens	77.1753	50	665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.16	98.07	0.90	0.88	3	-
GCA_013874835.1	s__WM01 sp013874835	77.0094	64	665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__WM01	95.0	99.19	98.77	0.92	0.86	4	-
GCF_900163795.1	s__Vagococcus fluvialis_A	76.5685	62	665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:27,792] [INFO] GTDB search result was written to GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:27,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:27,796] [INFO] DFAST_QC result json was written to GCF_900111135.1_IMG-taxon_2684622850_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:27:27,796] [INFO] DFAST_QC completed!
[2024-01-24 15:27:27,797] [INFO] Total running time: 0h0m52s