[2024-01-24 12:30:52,739] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:52,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:52,742] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bf974be-7222-4c40-8b05-8434895e73f3/dqc_reference
[2024-01-24 12:30:54,040] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:54,103] [INFO] Task started: Prodigal
[2024-01-24 12:30:54,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg22696826-b5dc-451d-915b-3cea16cd1ebd/GCF_001436645.1_ASM143664v1_genomic.fna.gz | prodigal -d GCF_001436645.1_ASM143664v1_genomic.fna/cds.fna -a GCF_001436645.1_ASM143664v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:57,055] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:57,055] [INFO] Task started: HMMsearch
[2024-01-24 12:30:57,056] [INFO] Running command: hmmsearch --tblout GCF_001436645.1_ASM143664v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bf974be-7222-4c40-8b05-8434895e73f3/dqc_reference/reference_markers.hmm GCF_001436645.1_ASM143664v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:57,284] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:57,286] [INFO] Found 6/6 markers.
[2024-01-24 12:30:57,304] [INFO] Query marker FASTA was written to GCF_001436645.1_ASM143664v1_genomic.fna/markers.fasta
[2024-01-24 12:30:57,304] [INFO] Task started: Blastn
[2024-01-24 12:30:57,304] [INFO] Running command: blastn -query GCF_001436645.1_ASM143664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bf974be-7222-4c40-8b05-8434895e73f3/dqc_reference/reference_markers.fasta -out GCF_001436645.1_ASM143664v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:57,872] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:57,876] [INFO] Selected 21 target genomes.
[2024-01-24 12:30:57,876] [INFO] Target genome list was writen to GCF_001436645.1_ASM143664v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:57,906] [INFO] Task started: fastANI
[2024-01-24 12:30:57,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg22696826-b5dc-451d-915b-3cea16cd1ebd/GCF_001436645.1_ASM143664v1_genomic.fna.gz --refList GCF_001436645.1_ASM143664v1_genomic.fna/target_genomes.txt --output GCF_001436645.1_ASM143664v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:05,234] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:05,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bf974be-7222-4c40-8b05-8434895e73f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:05,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bf974be-7222-4c40-8b05-8434895e73f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:05,243] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:31:05,243] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:05,243] [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
Fructilactobacillus florum	strain=DSM 22689	GCA_001436645.1	640331	640331	type	True	100.0	429	430	95	conclusive
Fructilactobacillus florum	strain=JCM 16035	GCA_001311215.1	640331	640331	type	True	99.8568	418	430	95	conclusive
Fructilactobacillus ixorae	strain=Ru20-1	GCA_024029915.1	1750535	1750535	type	True	77.4958	53	430	95	below_threshold
Fructilactobacillus lindneri	strain=TMW 1.88	GCA_002907375.1	53444	53444	type	True	77.1456	83	430	95	below_threshold
Fructilactobacillus lindneri	strain=DSM 20690	GCA_001438685.1	53444	53444	type	True	77.1338	83	430	95	below_threshold
Fructilactobacillus lindneri	strain=DSM 20690	GCA_900167245.1	53444	53444	type	True	76.8764	83	430	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:05,245] [INFO] DFAST Taxonomy check result was written to GCF_001436645.1_ASM143664v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:05,247] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:05,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:05,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bf974be-7222-4c40-8b05-8434895e73f3/dqc_reference/checkm_data
[2024-01-24 12:31:05,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:05,268] [INFO] Task started: CheckM
[2024-01-24 12:31:05,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001436645.1_ASM143664v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001436645.1_ASM143664v1_genomic.fna/checkm_input GCF_001436645.1_ASM143664v1_genomic.fna/checkm_result
[2024-01-24 12:31:21,999] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:22,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:22,017] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:22,017] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:22,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001436645.1_ASM143664v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:22,018] [INFO] Task started: Blastn
[2024-01-24 12:31:22,018] [INFO] Running command: blastn -query GCF_001436645.1_ASM143664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bf974be-7222-4c40-8b05-8434895e73f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001436645.1_ASM143664v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:22,757] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:22,760] [INFO] Selected 26 target genomes.
[2024-01-24 12:31:22,760] [INFO] Target genome list was writen to GCF_001436645.1_ASM143664v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:22,797] [INFO] Task started: fastANI
[2024-01-24 12:31:22,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg22696826-b5dc-451d-915b-3cea16cd1ebd/GCF_001436645.1_ASM143664v1_genomic.fna.gz --refList GCF_001436645.1_ASM143664v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001436645.1_ASM143664v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:32,324] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:32,331] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:32,331] [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_001436645.1	s__Fructilactobacillus florum	100.0	429	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.34	99.05	0.97	0.97	4	conclusive
GCF_002907375.1	s__Fructilactobacillus lindneri	77.1456	83	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.90	99.78	0.98	0.96	12	-
GCF_001436035.1	s__Fructilactobacillus sanfranciscensis	77.0387	61	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.31	98.98	0.96	0.90	32	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:32,333] [INFO] GTDB search result was written to GCF_001436645.1_ASM143664v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:32,333] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:32,336] [INFO] DFAST_QC result json was written to GCF_001436645.1_ASM143664v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:32,337] [INFO] DFAST_QC completed!
[2024-01-24 12:31:32,337] [INFO] Total running time: 0h0m40s