[2024-01-24 14:19:16,581] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:16,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:16,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg9636add3-c67c-4837-a62a-a24d414024a8/dqc_reference
[2024-01-24 14:19:17,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:17,878] [INFO] Task started: Prodigal
[2024-01-24 14:19:17,878] [INFO] Running command: gunzip -c /var/lib/cwl/stg6544f30f-7546-44c2-9790-0718a9f9e809/GCF_000420065.1_ASM42006v1_genomic.fna.gz | prodigal -d GCF_000420065.1_ASM42006v1_genomic.fna/cds.fna -a GCF_000420065.1_ASM42006v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:23,114] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:23,114] [INFO] Task started: HMMsearch
[2024-01-24 14:19:23,114] [INFO] Running command: hmmsearch --tblout GCF_000420065.1_ASM42006v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9636add3-c67c-4837-a62a-a24d414024a8/dqc_reference/reference_markers.hmm GCF_000420065.1_ASM42006v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:23,386] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:23,388] [INFO] Found 6/6 markers.
[2024-01-24 14:19:23,425] [INFO] Query marker FASTA was written to GCF_000420065.1_ASM42006v1_genomic.fna/markers.fasta
[2024-01-24 14:19:23,426] [INFO] Task started: Blastn
[2024-01-24 14:19:23,426] [INFO] Running command: blastn -query GCF_000420065.1_ASM42006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9636add3-c67c-4837-a62a-a24d414024a8/dqc_reference/reference_markers.fasta -out GCF_000420065.1_ASM42006v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:24,199] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:24,202] [INFO] Selected 10 target genomes.
[2024-01-24 14:19:24,203] [INFO] Target genome list was writen to GCF_000420065.1_ASM42006v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:24,209] [INFO] Task started: fastANI
[2024-01-24 14:19:24,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg6544f30f-7546-44c2-9790-0718a9f9e809/GCF_000420065.1_ASM42006v1_genomic.fna.gz --refList GCF_000420065.1_ASM42006v1_genomic.fna/target_genomes.txt --output GCF_000420065.1_ASM42006v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:29,153] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:29,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9636add3-c67c-4837-a62a-a24d414024a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:29,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9636add3-c67c-4837-a62a-a24d414024a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:29,160] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:29,160] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:29,160] [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 cambriense	strain=DSM 15806	GCA_000420065.1	184870	184870	type	True	100.0	669	670	95	conclusive
Varibaculum massiliense	strain=Marseille-P2802	GCA_900106855.1	1852372	1852372	type	True	85.83	507	670	95	below_threshold
Varibaculum prostatecancerukia	strain=EMRHCC_39	GCA_943169825.1	2811781	2811781	type	True	84.5624	523	670	95	below_threshold
Varibaculum vaginae	strain=Marseille-P5644	GCA_900604285.1	2364797	2364797	type	True	83.5179	451	670	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:29,162] [INFO] DFAST Taxonomy check result was written to GCF_000420065.1_ASM42006v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:29,163] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:29,163] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:29,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9636add3-c67c-4837-a62a-a24d414024a8/dqc_reference/checkm_data
[2024-01-24 14:19:29,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:29,189] [INFO] Task started: CheckM
[2024-01-24 14:19:29,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000420065.1_ASM42006v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000420065.1_ASM42006v1_genomic.fna/checkm_input GCF_000420065.1_ASM42006v1_genomic.fna/checkm_result
[2024-01-24 14:19:51,467] [INFO] Task succeeded: CheckM
[2024-01-24 14:19:51,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:19:51,489] [INFO] ===== Completeness check finished =====
[2024-01-24 14:19:51,489] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:19:51,490] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000420065.1_ASM42006v1_genomic.fna/markers.fasta)
[2024-01-24 14:19:51,490] [INFO] Task started: Blastn
[2024-01-24 14:19:51,491] [INFO] Running command: blastn -query GCF_000420065.1_ASM42006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9636add3-c67c-4837-a62a-a24d414024a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000420065.1_ASM42006v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:52,412] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:52,417] [INFO] Selected 8 target genomes.
[2024-01-24 14:19:52,417] [INFO] Target genome list was writen to GCF_000420065.1_ASM42006v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:19:52,453] [INFO] Task started: fastANI
[2024-01-24 14:19:52,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg6544f30f-7546-44c2-9790-0718a9f9e809/GCF_000420065.1_ASM42006v1_genomic.fna.gz --refList GCF_000420065.1_ASM42006v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000420065.1_ASM42006v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:19:56,349] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:56,357] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:19:56,357] [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_000420065.1	s__Varibaculum cambriense	100.0	669	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	98.61	98.50	0.92	0.91	4	conclusive
GCF_002848005.1	s__Varibaculum cambriense_B	92.0463	584	670	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	87.5489	578	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	97.52	97.17	0.94	0.91	7	-
GCF_900106855.1	s__Varibaculum massiliense	85.8073	506	670	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	84.6819	504	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900604285.1	s__Varibaculum vaginae	83.5188	451	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:19:56,359] [INFO] GTDB search result was written to GCF_000420065.1_ASM42006v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:19:56,360] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:19:56,362] [INFO] DFAST_QC result json was written to GCF_000420065.1_ASM42006v1_genomic.fna/dqc_result.json
[2024-01-24 14:19:56,362] [INFO] DFAST_QC completed!
[2024-01-24 14:19:56,363] [INFO] Total running time: 0h0m40s