[2024-01-24 14:47:08,560] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,562] [INFO] DQC Reference Directory: /var/lib/cwl/stga7979cdf-f49d-4ece-ba91-c59a5c609e0c/dqc_reference
[2024-01-24 14:47:09,957] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:09,958] [INFO] Task started: Prodigal
[2024-01-24 14:47:09,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg75a313b6-94a0-4960-94ee-c0bf7ea36a16/GCF_900604935.1_PRJEB23934_genomic.fna.gz | prodigal -d GCF_900604935.1_PRJEB23934_genomic.fna/cds.fna -a GCF_900604935.1_PRJEB23934_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:13,427] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:13,427] [INFO] Task started: HMMsearch
[2024-01-24 14:47:13,427] [INFO] Running command: hmmsearch --tblout GCF_900604935.1_PRJEB23934_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7979cdf-f49d-4ece-ba91-c59a5c609e0c/dqc_reference/reference_markers.hmm GCF_900604935.1_PRJEB23934_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:13,693] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:13,694] [INFO] Found 6/6 markers.
[2024-01-24 14:47:13,717] [INFO] Query marker FASTA was written to GCF_900604935.1_PRJEB23934_genomic.fna/markers.fasta
[2024-01-24 14:47:13,718] [INFO] Task started: Blastn
[2024-01-24 14:47:13,718] [INFO] Running command: blastn -query GCF_900604935.1_PRJEB23934_genomic.fna/markers.fasta -db /var/lib/cwl/stga7979cdf-f49d-4ece-ba91-c59a5c609e0c/dqc_reference/reference_markers.fasta -out GCF_900604935.1_PRJEB23934_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:14,288] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:14,294] [INFO] Selected 26 target genomes.
[2024-01-24 14:47:14,295] [INFO] Target genome list was writen to GCF_900604935.1_PRJEB23934_genomic.fna/target_genomes.txt
[2024-01-24 14:47:14,349] [INFO] Task started: fastANI
[2024-01-24 14:47:14,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg75a313b6-94a0-4960-94ee-c0bf7ea36a16/GCF_900604935.1_PRJEB23934_genomic.fna.gz --refList GCF_900604935.1_PRJEB23934_genomic.fna/target_genomes.txt --output GCF_900604935.1_PRJEB23934_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:24,518] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:24,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7979cdf-f49d-4ece-ba91-c59a5c609e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:24,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7979cdf-f49d-4ece-ba91-c59a5c609e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:24,524] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:24,524] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:24,524] [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
Vaginisenegalia massiliensis	strain=Marseille-P5643	GCA_900604935.1	2058294	2058294	type	True	100.0	575	575	95	conclusive
Globicatella sanguinis	strain=NBRC 15551	GCA_001552295.1	13076	13076	type	True	79.9409	52	575	95	below_threshold
Globicatella sulfidifaciens	strain=DSM 15739	GCA_900167405.1	136093	136093	type	True	79.5004	59	575	95	below_threshold
Fundicoccus ignavus	strain=DSM 109652	GCA_009659375.1	2664442	2664442	type	True	78.21	54	575	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:24,525] [INFO] DFAST Taxonomy check result was written to GCF_900604935.1_PRJEB23934_genomic.fna/tc_result.tsv
[2024-01-24 14:47:24,526] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:24,526] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:24,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7979cdf-f49d-4ece-ba91-c59a5c609e0c/dqc_reference/checkm_data
[2024-01-24 14:47:24,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:24,563] [INFO] Task started: CheckM
[2024-01-24 14:47:24,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900604935.1_PRJEB23934_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900604935.1_PRJEB23934_genomic.fna/checkm_input GCF_900604935.1_PRJEB23934_genomic.fna/checkm_result
[2024-01-24 14:47:43,894] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:43,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:43,915] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:43,915] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:43,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900604935.1_PRJEB23934_genomic.fna/markers.fasta)
[2024-01-24 14:47:43,916] [INFO] Task started: Blastn
[2024-01-24 14:47:43,916] [INFO] Running command: blastn -query GCF_900604935.1_PRJEB23934_genomic.fna/markers.fasta -db /var/lib/cwl/stga7979cdf-f49d-4ece-ba91-c59a5c609e0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900604935.1_PRJEB23934_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:44,706] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:44,710] [INFO] Selected 24 target genomes.
[2024-01-24 14:47:44,711] [INFO] Target genome list was writen to GCF_900604935.1_PRJEB23934_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:44,729] [INFO] Task started: fastANI
[2024-01-24 14:47:44,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg75a313b6-94a0-4960-94ee-c0bf7ea36a16/GCF_900604935.1_PRJEB23934_genomic.fna.gz --refList GCF_900604935.1_PRJEB23934_genomic.fna/target_genomes_gtdb.txt --output GCF_900604935.1_PRJEB23934_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:54,339] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:54,346] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:54,346] [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_900604935.1	s__Abiotrophia massiliensis	100.0	575	575	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Abiotrophia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001552295.1	s__Globicatella sanguinis	79.9409	52	575	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Globicatella	95.0	97.13	96.22	0.85	0.84	3	-
GCF_900167405.1	s__Globicatella sulfidifaciens	79.5004	59	575	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Globicatella	95.0	97.81	97.81	0.71	0.71	2	-
GCF_009659375.1	s__Fundicoccus ignavus	78.21	54	575	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Fundicoccus	95.0	98.16	98.10	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:47:54,350] [INFO] GTDB search result was written to GCF_900604935.1_PRJEB23934_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:54,351] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:54,354] [INFO] DFAST_QC result json was written to GCF_900604935.1_PRJEB23934_genomic.fna/dqc_result.json
[2024-01-24 14:47:54,354] [INFO] DFAST_QC completed!
[2024-01-24 14:47:54,354] [INFO] Total running time: 0h0m46s