[2024-01-24 13:18:45,644] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:45,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:45,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg98c160e6-52bd-4fc0-8765-b1bf90e9d0cf/dqc_reference
[2024-01-24 13:18:46,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:46,957] [INFO] Task started: Prodigal
[2024-01-24 13:18:46,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg3189d1bf-eb9c-401c-a0f3-e5de7e8831f0/GCF_004342905.1_ASM434290v1_genomic.fna.gz | prodigal -d GCF_004342905.1_ASM434290v1_genomic.fna/cds.fna -a GCF_004342905.1_ASM434290v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:53,894] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:53,894] [INFO] Task started: HMMsearch
[2024-01-24 13:18:53,894] [INFO] Running command: hmmsearch --tblout GCF_004342905.1_ASM434290v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98c160e6-52bd-4fc0-8765-b1bf90e9d0cf/dqc_reference/reference_markers.hmm GCF_004342905.1_ASM434290v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:54,166] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:54,167] [INFO] Found 6/6 markers.
[2024-01-24 13:18:54,199] [INFO] Query marker FASTA was written to GCF_004342905.1_ASM434290v1_genomic.fna/markers.fasta
[2024-01-24 13:18:54,200] [INFO] Task started: Blastn
[2024-01-24 13:18:54,200] [INFO] Running command: blastn -query GCF_004342905.1_ASM434290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98c160e6-52bd-4fc0-8765-b1bf90e9d0cf/dqc_reference/reference_markers.fasta -out GCF_004342905.1_ASM434290v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:54,785] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:54,791] [INFO] Selected 26 target genomes.
[2024-01-24 13:18:54,792] [INFO] Target genome list was writen to GCF_004342905.1_ASM434290v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:54,826] [INFO] Task started: fastANI
[2024-01-24 13:18:54,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg3189d1bf-eb9c-401c-a0f3-e5de7e8831f0/GCF_004342905.1_ASM434290v1_genomic.fna.gz --refList GCF_004342905.1_ASM434290v1_genomic.fna/target_genomes.txt --output GCF_004342905.1_ASM434290v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:10,213] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:10,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98c160e6-52bd-4fc0-8765-b1bf90e9d0cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:10,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98c160e6-52bd-4fc0-8765-b1bf90e9d0cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:10,218] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:10,219] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:10,219] [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
Melghiribacillus thermohalophilus	strain=DSM 25894	GCA_004342905.1	1324956	1324956	type	True	100.0	976	982	95	conclusive
Salinibacillus kushneri	strain=CGMCC 1.3566	GCA_900111405.1	237682	237682	type	True	76.7452	54	982	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:10,220] [INFO] DFAST Taxonomy check result was written to GCF_004342905.1_ASM434290v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:10,221] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:10,221] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:10,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98c160e6-52bd-4fc0-8765-b1bf90e9d0cf/dqc_reference/checkm_data
[2024-01-24 13:19:10,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:10,254] [INFO] Task started: CheckM
[2024-01-24 13:19:10,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342905.1_ASM434290v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342905.1_ASM434290v1_genomic.fna/checkm_input GCF_004342905.1_ASM434290v1_genomic.fna/checkm_result
[2024-01-24 13:19:37,892] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:37,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:37,911] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:37,911] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:37,912] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342905.1_ASM434290v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:37,912] [INFO] Task started: Blastn
[2024-01-24 13:19:37,912] [INFO] Running command: blastn -query GCF_004342905.1_ASM434290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98c160e6-52bd-4fc0-8765-b1bf90e9d0cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342905.1_ASM434290v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:38,646] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:38,650] [INFO] Selected 27 target genomes.
[2024-01-24 13:19:38,650] [INFO] Target genome list was writen to GCF_004342905.1_ASM434290v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:38,668] [INFO] Task started: fastANI
[2024-01-24 13:19:38,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg3189d1bf-eb9c-401c-a0f3-e5de7e8831f0/GCF_004342905.1_ASM434290v1_genomic.fna.gz --refList GCF_004342905.1_ASM434290v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342905.1_ASM434290v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:55,133] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:55,139] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:55,139] [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_004342905.1	s__Melghiribacillus thermohalophilus	100.0	976	982	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Melghiribacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010092505.1	s__Salinibacillus sp010092505	77.1066	66	982	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111405.1	s__Salinibacillus kushneri	76.7452	54	982	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:55,145] [INFO] GTDB search result was written to GCF_004342905.1_ASM434290v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:55,146] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:55,149] [INFO] DFAST_QC result json was written to GCF_004342905.1_ASM434290v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:55,150] [INFO] DFAST_QC completed!
[2024-01-24 13:19:55,150] [INFO] Total running time: 0h1m10s