[2024-01-24 14:06:07,242] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:07,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:07,244] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf6b0dd2-c311-43a2-879c-1a7d4102a402/dqc_reference
[2024-01-24 14:06:08,596] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,597] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,597] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ef1433a-73bc-4260-82b0-91631bb850eb/GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/cds.fna -a GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:11,502] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:11,503] [INFO] Task started: HMMsearch
[2024-01-24 14:06:11,503] [INFO] Running command: hmmsearch --tblout GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf6b0dd2-c311-43a2-879c-1a7d4102a402/dqc_reference/reference_markers.hmm GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:11,760] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:11,762] [INFO] Found 6/6 markers.
[2024-01-24 14:06:11,788] [INFO] Query marker FASTA was written to GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:06:11,789] [INFO] Task started: Blastn
[2024-01-24 14:06:11,789] [INFO] Running command: blastn -query GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf6b0dd2-c311-43a2-879c-1a7d4102a402/dqc_reference/reference_markers.fasta -out GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:12,397] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:12,400] [INFO] Selected 13 target genomes.
[2024-01-24 14:06:12,400] [INFO] Target genome list was writen to GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:06:12,423] [INFO] Task started: fastANI
[2024-01-24 14:06:12,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ef1433a-73bc-4260-82b0-91631bb850eb/GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna.gz --refList GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:17,059] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:17,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf6b0dd2-c311-43a2-879c-1a7d4102a402/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:17,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf6b0dd2-c311-43a2-879c-1a7d4102a402/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:17,067] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:06:17,067] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:17,067] [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 lindneri	strain=DSM 20690	GCA_900167245.1	53444	53444	type	True	100.0	459	460	95	conclusive
Fructilactobacillus lindneri	strain=DSM 20690	GCA_001438685.1	53444	53444	type	True	99.976	454	460	95	conclusive
Fructilactobacillus lindneri	strain=TMW 1.88	GCA_002907375.1	53444	53444	type	True	99.9425	455	460	95	conclusive
Fructilactobacillus sanfranciscensis	strain=TMW 1.53	GCA_002907365.1	1625	1625	type	True	79.3259	193	460	95	below_threshold
Fructilactobacillus sanfranciscensis	strain=JCM 5668	GCA_003369815.1	1625	1625	type	True	79.188	201	460	95	below_threshold
Apilactobacillus micheneri	strain=Hlig3	GCA_002993975.1	1899430	1899430	type	True	77.3312	63	460	95	below_threshold
Apilactobacillus xinyiensis	strain=F575-4	GCA_019656235.1	2841032	2841032	type	True	77.1206	64	460	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:17,069] [INFO] DFAST Taxonomy check result was written to GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:06:17,070] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:17,070] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:17,070] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf6b0dd2-c311-43a2-879c-1a7d4102a402/dqc_reference/checkm_data
[2024-01-24 14:06:17,071] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:17,088] [INFO] Task started: CheckM
[2024-01-24 14:06:17,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/checkm_input GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:06:34,736] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:34,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:34,755] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:34,755] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:34,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:06:34,756] [INFO] Task started: Blastn
[2024-01-24 14:06:34,756] [INFO] Running command: blastn -query GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf6b0dd2-c311-43a2-879c-1a7d4102a402/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:35,576] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:35,580] [INFO] Selected 22 target genomes.
[2024-01-24 14:06:35,580] [INFO] Target genome list was writen to GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:35,599] [INFO] Task started: fastANI
[2024-01-24 14:06:35,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ef1433a-73bc-4260-82b0-91631bb850eb/GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna.gz --refList GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:41,847] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:41,854] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:41,855] [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_002907375.1	s__Fructilactobacillus lindneri	99.9425	455	460	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.90	99.78	0.98	0.96	12	conclusive
GCF_001436035.1	s__Fructilactobacillus sanfranciscensis	79.0298	190	460	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.31	98.98	0.96	0.90	32	-
GCF_002994005.1	s__Apilactobacillus quenuiae	77.4233	63	460	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436645.1	s__Fructilactobacillus florum	77.3506	70	460	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.34	99.05	0.97	0.97	4	-
GCF_002993975.1	s__Apilactobacillus micheneri	77.3312	63	460	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.16	96.49	0.93	0.89	21	-
GCF_002993965.1	s__Apilactobacillus timberlakei	77.3201	61	460	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.96	98.30	0.93	0.87	9	-
GCF_003864335.1	s__Lentilactobacillus curieae_A	76.7416	54	460	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:41,856] [INFO] GTDB search result was written to GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:41,857] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:41,861] [INFO] DFAST_QC result json was written to GCF_900167245.1_IMG-taxon_2568526012_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:06:41,861] [INFO] DFAST_QC completed!
[2024-01-24 14:06:41,861] [INFO] Total running time: 0h0m35s