[2024-01-25 17:51:20,631] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:20,636] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:20,637] [INFO] DQC Reference Directory: /var/lib/cwl/stgc827faf2-098c-499e-98a3-1d1ca6bde11d/dqc_reference
[2024-01-25 17:51:21,753] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:21,755] [INFO] Task started: Prodigal
[2024-01-25 17:51:21,755] [INFO] Running command: gunzip -c /var/lib/cwl/stg3931139c-0293-4660-a3ac-311094d9dffd/GCF_900604285.1_PRJEB28802_genomic.fna.gz | prodigal -d GCF_900604285.1_PRJEB28802_genomic.fna/cds.fna -a GCF_900604285.1_PRJEB28802_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:26,026] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:26,026] [INFO] Task started: HMMsearch
[2024-01-25 17:51:26,026] [INFO] Running command: hmmsearch --tblout GCF_900604285.1_PRJEB28802_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc827faf2-098c-499e-98a3-1d1ca6bde11d/dqc_reference/reference_markers.hmm GCF_900604285.1_PRJEB28802_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:26,244] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:26,246] [INFO] Found 6/6 markers.
[2024-01-25 17:51:26,272] [INFO] Query marker FASTA was written to GCF_900604285.1_PRJEB28802_genomic.fna/markers.fasta
[2024-01-25 17:51:26,272] [INFO] Task started: Blastn
[2024-01-25 17:51:26,273] [INFO] Running command: blastn -query GCF_900604285.1_PRJEB28802_genomic.fna/markers.fasta -db /var/lib/cwl/stgc827faf2-098c-499e-98a3-1d1ca6bde11d/dqc_reference/reference_markers.fasta -out GCF_900604285.1_PRJEB28802_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:26,869] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:26,872] [INFO] Selected 5 target genomes.
[2024-01-25 17:51:26,872] [INFO] Target genome list was writen to GCF_900604285.1_PRJEB28802_genomic.fna/target_genomes.txt
[2024-01-25 17:51:26,875] [INFO] Task started: fastANI
[2024-01-25 17:51:26,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg3931139c-0293-4660-a3ac-311094d9dffd/GCF_900604285.1_PRJEB28802_genomic.fna.gz --refList GCF_900604285.1_PRJEB28802_genomic.fna/target_genomes.txt --output GCF_900604285.1_PRJEB28802_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:30,077] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:30,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc827faf2-098c-499e-98a3-1d1ca6bde11d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:30,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc827faf2-098c-499e-98a3-1d1ca6bde11d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:30,083] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:51:30,083] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:30,083] [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 vaginae	strain=Marseille-P5644	GCA_900604285.1	2364797	2364797	type	True	100.0	668	668	95	conclusive
Varibaculum massiliense	strain=Marseille-P2802	GCA_900106855.1	1852372	1852372	type	True	84.9338	558	668	95	below_threshold
Varibaculum prostatecancerukia	strain=EMRHCC_39	GCA_943169825.1	2811781	2811781	type	True	83.7909	563	668	95	below_threshold
Varibaculum cambriense	strain=DSM 15806	GCA_000420065.1	184870	184870	type	True	83.1818	454	668	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:30,085] [INFO] DFAST Taxonomy check result was written to GCF_900604285.1_PRJEB28802_genomic.fna/tc_result.tsv
[2024-01-25 17:51:30,085] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:30,085] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:30,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc827faf2-098c-499e-98a3-1d1ca6bde11d/dqc_reference/checkm_data
[2024-01-25 17:51:30,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:30,109] [INFO] Task started: CheckM
[2024-01-25 17:51:30,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900604285.1_PRJEB28802_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900604285.1_PRJEB28802_genomic.fna/checkm_input GCF_900604285.1_PRJEB28802_genomic.fna/checkm_result
[2024-01-25 17:51:48,173] [INFO] Task succeeded: CheckM
[2024-01-25 17:51:48,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:51:48,197] [INFO] ===== Completeness check finished =====
[2024-01-25 17:51:48,197] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:51:48,197] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900604285.1_PRJEB28802_genomic.fna/markers.fasta)
[2024-01-25 17:51:48,198] [INFO] Task started: Blastn
[2024-01-25 17:51:48,198] [INFO] Running command: blastn -query GCF_900604285.1_PRJEB28802_genomic.fna/markers.fasta -db /var/lib/cwl/stgc827faf2-098c-499e-98a3-1d1ca6bde11d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900604285.1_PRJEB28802_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:49,010] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:49,013] [INFO] Selected 10 target genomes.
[2024-01-25 17:51:49,013] [INFO] Target genome list was writen to GCF_900604285.1_PRJEB28802_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:49,029] [INFO] Task started: fastANI
[2024-01-25 17:51:49,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg3931139c-0293-4660-a3ac-311094d9dffd/GCF_900604285.1_PRJEB28802_genomic.fna.gz --refList GCF_900604285.1_PRJEB28802_genomic.fna/target_genomes_gtdb.txt --output GCF_900604285.1_PRJEB28802_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:53,662] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:53,668] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:53,668] [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_900604285.1	s__Varibaculum vaginae	100.0	668	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900106855.1	s__Varibaculum massiliense	84.9248	559	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905332515.2	s__Varibaculum sp905332515	83.8208	543	668	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	83.175	456	668	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	82.9922	455	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	97.10	95.33	0.92	0.87	3	-
GCA_000508625.1	s__Varibaculum cambriense_A	81.7374	417	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	97.52	97.17	0.94	0.91	7	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:53,669] [INFO] GTDB search result was written to GCF_900604285.1_PRJEB28802_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:53,670] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:53,674] [INFO] DFAST_QC result json was written to GCF_900604285.1_PRJEB28802_genomic.fna/dqc_result.json
[2024-01-25 17:51:53,674] [INFO] DFAST_QC completed!
[2024-01-25 17:51:53,674] [INFO] Total running time: 0h0m33s