[2024-01-25 18:00:50,700] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:50,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:50,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg8222738d-dc8a-4253-bae8-7ba27cc5ae49/dqc_reference
[2024-01-25 18:00:51,845] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:51,846] [INFO] Task started: Prodigal
[2024-01-25 18:00:51,846] [INFO] Running command: gunzip -c /var/lib/cwl/stge17e1b6b-cc06-4aa9-b09c-f9d7fe350e25/GCF_943169825.2_ASM94316982v2_genomic.fna.gz | prodigal -d GCF_943169825.2_ASM94316982v2_genomic.fna/cds.fna -a GCF_943169825.2_ASM94316982v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:56,710] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:56,710] [INFO] Task started: HMMsearch
[2024-01-25 18:00:56,711] [INFO] Running command: hmmsearch --tblout GCF_943169825.2_ASM94316982v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8222738d-dc8a-4253-bae8-7ba27cc5ae49/dqc_reference/reference_markers.hmm GCF_943169825.2_ASM94316982v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:56,935] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:56,936] [INFO] Found 6/6 markers.
[2024-01-25 18:00:56,961] [INFO] Query marker FASTA was written to GCF_943169825.2_ASM94316982v2_genomic.fna/markers.fasta
[2024-01-25 18:00:56,962] [INFO] Task started: Blastn
[2024-01-25 18:00:56,962] [INFO] Running command: blastn -query GCF_943169825.2_ASM94316982v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8222738d-dc8a-4253-bae8-7ba27cc5ae49/dqc_reference/reference_markers.fasta -out GCF_943169825.2_ASM94316982v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:57,539] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:57,542] [INFO] Selected 5 target genomes.
[2024-01-25 18:00:57,543] [INFO] Target genome list was writen to GCF_943169825.2_ASM94316982v2_genomic.fna/target_genomes.txt
[2024-01-25 18:00:57,550] [INFO] Task started: fastANI
[2024-01-25 18:00:57,550] [INFO] Running command: fastANI --query /var/lib/cwl/stge17e1b6b-cc06-4aa9-b09c-f9d7fe350e25/GCF_943169825.2_ASM94316982v2_genomic.fna.gz --refList GCF_943169825.2_ASM94316982v2_genomic.fna/target_genomes.txt --output GCF_943169825.2_ASM94316982v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:00,715] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:00,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8222738d-dc8a-4253-bae8-7ba27cc5ae49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:00,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8222738d-dc8a-4253-bae8-7ba27cc5ae49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:00,720] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:01:00,721] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:01:00,721] [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	100.0	737	737	95	conclusive
Varibaculum massiliense	strain=Marseille-P2802	GCA_900106855.1	1852372	1852372	type	True	88.3414	625	737	95	below_threshold
Varibaculum cambriense	strain=DSM 15806	GCA_000420065.1	184870	184870	type	True	84.4126	525	737	95	below_threshold
Varibaculum vaginae	strain=Marseille-P5644	GCA_900604285.1	2364797	2364797	type	True	83.8686	532	737	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:00,722] [INFO] DFAST Taxonomy check result was written to GCF_943169825.2_ASM94316982v2_genomic.fna/tc_result.tsv
[2024-01-25 18:01:00,722] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:00,722] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:00,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8222738d-dc8a-4253-bae8-7ba27cc5ae49/dqc_reference/checkm_data
[2024-01-25 18:01:00,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:00,747] [INFO] Task started: CheckM
[2024-01-25 18:01:00,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_943169825.2_ASM94316982v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_943169825.2_ASM94316982v2_genomic.fna/checkm_input GCF_943169825.2_ASM94316982v2_genomic.fna/checkm_result
[2024-01-25 18:01:20,261] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:20,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:20,282] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:20,282] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:20,282] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_943169825.2_ASM94316982v2_genomic.fna/markers.fasta)
[2024-01-25 18:01:20,283] [INFO] Task started: Blastn
[2024-01-25 18:01:20,283] [INFO] Running command: blastn -query GCF_943169825.2_ASM94316982v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8222738d-dc8a-4253-bae8-7ba27cc5ae49/dqc_reference/reference_markers_gtdb.fasta -out GCF_943169825.2_ASM94316982v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:21,207] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:21,211] [INFO] Selected 8 target genomes.
[2024-01-25 18:01:21,211] [INFO] Target genome list was writen to GCF_943169825.2_ASM94316982v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:21,222] [INFO] Task started: fastANI
[2024-01-25 18:01:21,222] [INFO] Running command: fastANI --query /var/lib/cwl/stge17e1b6b-cc06-4aa9-b09c-f9d7fe350e25/GCF_943169825.2_ASM94316982v2_genomic.fna.gz --refList GCF_943169825.2_ASM94316982v2_genomic.fna/target_genomes_gtdb.txt --output GCF_943169825.2_ASM94316982v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:25,543] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:25,549] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:25,549] [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	100.0	737	737	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	88.3414	625	737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002848005.1	s__Varibaculum cambriense_B	84.8161	524	737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	97.10	95.33	0.92	0.87	3	-
GCF_000420065.1	s__Varibaculum cambriense	84.3867	524	737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	98.61	98.50	0.92	0.91	4	-
GCF_900604285.1	s__Varibaculum vaginae	83.8957	533	737	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	82.9819	472	737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	97.52	97.17	0.94	0.91	7	-
GCA_900120415.1	s__Varibaculum timonense_A	81.0545	353	737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	97.03	95.06	0.94	0.92	6	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:25,551] [INFO] GTDB search result was written to GCF_943169825.2_ASM94316982v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:25,551] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:25,553] [INFO] DFAST_QC result json was written to GCF_943169825.2_ASM94316982v2_genomic.fna/dqc_result.json
[2024-01-25 18:01:25,553] [INFO] DFAST_QC completed!
[2024-01-25 18:01:25,553] [INFO] Total running time: 0h0m35s