[2023-06-30 09:37:05,751] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:37:05,754] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:37:05,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg48d8b0b9-b0ef-4472-8f9e-4ceeb149309b/dqc_reference
[2023-06-30 09:37:07,122] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:37:07,123] [INFO] Task started: Prodigal
[2023-06-30 09:37:07,123] [INFO] Running command: gunzip -c /var/lib/cwl/stg8032f66d-dc0b-4e4f-bf9c-48bded178892/GCA_900756255.1_ERS473392_7_genomic.fna.gz | prodigal -d GCA_900756255.1_ERS473392_7_genomic.fna/cds.fna -a GCA_900756255.1_ERS473392_7_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 09:37:10,313] [INFO] Task succeeded: Prodigal
[2023-06-30 09:37:10,314] [INFO] Task started: HMMsearch
[2023-06-30 09:37:10,314] [INFO] Running command: hmmsearch --tblout GCA_900756255.1_ERS473392_7_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48d8b0b9-b0ef-4472-8f9e-4ceeb149309b/dqc_reference/reference_markers.hmm GCA_900756255.1_ERS473392_7_genomic.fna/protein.faa > /dev/null
[2023-06-30 09:37:10,547] [INFO] Task succeeded: HMMsearch
[2023-06-30 09:37:10,548] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8032f66d-dc0b-4e4f-bf9c-48bded178892/GCA_900756255.1_ERS473392_7_genomic.fna.gz]
[2023-06-30 09:37:10,595] [INFO] Query marker FASTA was written to GCA_900756255.1_ERS473392_7_genomic.fna/markers.fasta
[2023-06-30 09:37:10,596] [INFO] Task started: Blastn
[2023-06-30 09:37:10,596] [INFO] Running command: blastn -query GCA_900756255.1_ERS473392_7_genomic.fna/markers.fasta -db /var/lib/cwl/stg48d8b0b9-b0ef-4472-8f9e-4ceeb149309b/dqc_reference/reference_markers.fasta -out GCA_900756255.1_ERS473392_7_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:37:11,303] [INFO] Task succeeded: Blastn
[2023-06-30 09:37:11,307] [INFO] Selected 7 target genomes.
[2023-06-30 09:37:11,307] [INFO] Target genome list was writen to GCA_900756255.1_ERS473392_7_genomic.fna/target_genomes.txt
[2023-06-30 09:37:11,310] [INFO] Task started: fastANI
[2023-06-30 09:37:11,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg8032f66d-dc0b-4e4f-bf9c-48bded178892/GCA_900756255.1_ERS473392_7_genomic.fna.gz --refList GCA_900756255.1_ERS473392_7_genomic.fna/target_genomes.txt --output GCA_900756255.1_ERS473392_7_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 09:37:14,505] [INFO] Task succeeded: fastANI
[2023-06-30 09:37:14,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48d8b0b9-b0ef-4472-8f9e-4ceeb149309b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 09:37:14,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48d8b0b9-b0ef-4472-8f9e-4ceeb149309b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 09:37:14,511] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 09:37:14,511] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 09:37:14,512] [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
Varibaculum prostatecancerukia	strain=EMRHCC_39	GCA_943169825.1	2811781	2811781	type	True	87.7024	112	148	95	below_threshold
Varibaculum cambriense	strain=DSM 15806	GCA_000420065.1	184870	184870	type	True	86.2995	111	148	95	below_threshold
Varibaculum massiliense	strain=Marseille-P2802	GCA_900106855.1	1852372	1852372	type	True	85.7425	106	148	95	below_threshold
Varibaculum vaginae	strain=Marseille-P5644	GCA_900604285.1	2364797	2364797	type	True	82.8648	101	148	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 09:37:14,514] [INFO] DFAST Taxonomy check result was written to GCA_900756255.1_ERS473392_7_genomic.fna/tc_result.tsv
[2023-06-30 09:37:14,514] [INFO] ===== Taxonomy check completed =====
[2023-06-30 09:37:14,514] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 09:37:14,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48d8b0b9-b0ef-4472-8f9e-4ceeb149309b/dqc_reference/checkm_data
[2023-06-30 09:37:14,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 09:37:14,539] [INFO] Task started: CheckM
[2023-06-30 09:37:14,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900756255.1_ERS473392_7_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900756255.1_ERS473392_7_genomic.fna/checkm_input GCA_900756255.1_ERS473392_7_genomic.fna/checkm_result
[2023-06-30 09:37:31,913] [INFO] Task succeeded: CheckM
[2023-06-30 09:37:31,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 09:37:31,935] [INFO] ===== Completeness check finished =====
[2023-06-30 09:37:31,935] [INFO] ===== Start GTDB Search =====
[2023-06-30 09:37:31,935] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900756255.1_ERS473392_7_genomic.fna/markers.fasta)
[2023-06-30 09:37:31,936] [INFO] Task started: Blastn
[2023-06-30 09:37:31,936] [INFO] Running command: blastn -query GCA_900756255.1_ERS473392_7_genomic.fna/markers.fasta -db /var/lib/cwl/stg48d8b0b9-b0ef-4472-8f9e-4ceeb149309b/dqc_reference/reference_markers_gtdb.fasta -out GCA_900756255.1_ERS473392_7_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:37:32,938] [INFO] Task succeeded: Blastn
[2023-06-30 09:37:32,942] [INFO] Selected 6 target genomes.
[2023-06-30 09:37:32,942] [INFO] Target genome list was writen to GCA_900756255.1_ERS473392_7_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 09:37:32,971] [INFO] Task started: fastANI
[2023-06-30 09:37:32,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg8032f66d-dc0b-4e4f-bf9c-48bded178892/GCA_900756255.1_ERS473392_7_genomic.fna.gz --refList GCA_900756255.1_ERS473392_7_genomic.fna/target_genomes_gtdb.txt --output GCA_900756255.1_ERS473392_7_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 09:37:35,072] [INFO] Task succeeded: fastANI
[2023-06-30 09:37:35,078] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 09:37:35,079] [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
GCA_905332515.2	s__Varibaculum sp905332515	87.7603	111	148	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420065.1	s__Varibaculum cambriense	86.2995	111	148	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	98.61	98.50	0.92	0.91	4	-
GCF_002848005.1	s__Varibaculum cambriense_B	86.1129	129	148	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	97.10	95.33	0.92	0.87	3	-
GCF_900106855.1	s__Varibaculum massiliense	85.7425	106	148	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000508625.1	s__Varibaculum cambriense_A	83.762	104	148	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	97.52	97.17	0.94	0.91	7	-
GCF_900604285.1	s__Varibaculum vaginae	82.8648	101	148	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 09:37:35,082] [INFO] GTDB search result was written to GCA_900756255.1_ERS473392_7_genomic.fna/result_gtdb.tsv
[2023-06-30 09:37:35,083] [INFO] ===== GTDB Search completed =====
[2023-06-30 09:37:35,087] [INFO] DFAST_QC result json was written to GCA_900756255.1_ERS473392_7_genomic.fna/dqc_result.json
[2023-06-30 09:37:35,087] [INFO] DFAST_QC completed!
[2023-06-30 09:37:35,087] [INFO] Total running time: 0h0m29s