[2024-01-25 19:47:36,354] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:36,355] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:36,355] [INFO] DQC Reference Directory: /var/lib/cwl/stg46d70eb5-8bc0-492d-b9e9-ce9f92ac8681/dqc_reference
[2024-01-25 19:47:37,477] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:37,478] [INFO] Task started: Prodigal
[2024-01-25 19:47:37,478] [INFO] Running command: gunzip -c /var/lib/cwl/stg10888d84-30be-4bab-80f2-d0e9b204be38/GCF_014202755.1_ASM1420275v1_genomic.fna.gz | prodigal -d GCF_014202755.1_ASM1420275v1_genomic.fna/cds.fna -a GCF_014202755.1_ASM1420275v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:42,375] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:42,375] [INFO] Task started: HMMsearch
[2024-01-25 19:47:42,375] [INFO] Running command: hmmsearch --tblout GCF_014202755.1_ASM1420275v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46d70eb5-8bc0-492d-b9e9-ce9f92ac8681/dqc_reference/reference_markers.hmm GCF_014202755.1_ASM1420275v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:42,559] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:42,560] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg10888d84-30be-4bab-80f2-d0e9b204be38/GCF_014202755.1_ASM1420275v1_genomic.fna.gz]
[2024-01-25 19:47:42,580] [INFO] Query marker FASTA was written to GCF_014202755.1_ASM1420275v1_genomic.fna/markers.fasta
[2024-01-25 19:47:42,580] [INFO] Task started: Blastn
[2024-01-25 19:47:42,580] [INFO] Running command: blastn -query GCF_014202755.1_ASM1420275v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46d70eb5-8bc0-492d-b9e9-ce9f92ac8681/dqc_reference/reference_markers.fasta -out GCF_014202755.1_ASM1420275v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:43,149] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:43,154] [INFO] Selected 22 target genomes.
[2024-01-25 19:47:43,155] [INFO] Target genome list was writen to GCF_014202755.1_ASM1420275v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:43,184] [INFO] Task started: fastANI
[2024-01-25 19:47:43,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg10888d84-30be-4bab-80f2-d0e9b204be38/GCF_014202755.1_ASM1420275v1_genomic.fna.gz --refList GCF_014202755.1_ASM1420275v1_genomic.fna/target_genomes.txt --output GCF_014202755.1_ASM1420275v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:56,986] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:56,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46d70eb5-8bc0-492d-b9e9-ce9f92ac8681/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:56,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46d70eb5-8bc0-492d-b9e9-ce9f92ac8681/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:56,990] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:56,991] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:56,991] [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
Catenisphaera adipataccumulans	strain=DSM 25799	GCA_014202755.1	700500	700500	type	True	100.0	659	660	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 19:47:56,992] [INFO] DFAST Taxonomy check result was written to GCF_014202755.1_ASM1420275v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:56,992] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:56,993] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:56,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46d70eb5-8bc0-492d-b9e9-ce9f92ac8681/dqc_reference/checkm_data
[2024-01-25 19:47:56,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:57,017] [INFO] Task started: CheckM
[2024-01-25 19:47:57,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202755.1_ASM1420275v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202755.1_ASM1420275v1_genomic.fna/checkm_input GCF_014202755.1_ASM1420275v1_genomic.fna/checkm_result
[2024-01-25 19:48:17,012] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:17,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.50%
Contamintation: 3.12%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-25 19:48:17,029] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:17,030] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:17,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202755.1_ASM1420275v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:17,031] [INFO] Task started: Blastn
[2024-01-25 19:48:17,031] [INFO] Running command: blastn -query GCF_014202755.1_ASM1420275v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46d70eb5-8bc0-492d-b9e9-ce9f92ac8681/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202755.1_ASM1420275v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:17,844] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:17,846] [INFO] Selected 21 target genomes.
[2024-01-25 19:48:17,847] [INFO] Target genome list was writen to GCF_014202755.1_ASM1420275v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:17,870] [INFO] Task started: fastANI
[2024-01-25 19:48:17,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg10888d84-30be-4bab-80f2-d0e9b204be38/GCF_014202755.1_ASM1420275v1_genomic.fna.gz --refList GCF_014202755.1_ASM1420275v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202755.1_ASM1420275v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:26,640] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:26,643] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:26,643] [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_014202755.1	s__Catenisphaera adipataccumulans	100.0	659	660	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Catenisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-25 19:48:26,645] [INFO] GTDB search result was written to GCF_014202755.1_ASM1420275v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:26,646] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:26,647] [INFO] DFAST_QC result json was written to GCF_014202755.1_ASM1420275v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:26,648] [INFO] DFAST_QC completed!
[2024-01-25 19:48:26,648] [INFO] Total running time: 0h0m50s