[2024-01-24 12:31:34,692] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,696] [INFO] DQC Reference Directory: /var/lib/cwl/stg267aeb69-13fc-479f-8294-38230a03757a/dqc_reference
[2024-01-24 12:31:36,008] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:36,008] [INFO] Task started: Prodigal
[2024-01-24 12:31:36,009] [INFO] Running command: gunzip -c /var/lib/cwl/stg173ba813-98e4-4352-9a8b-f5dc34142e0a/GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/cds.fna -a GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:45,844] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:45,845] [INFO] Task started: HMMsearch
[2024-01-24 12:31:45,845] [INFO] Running command: hmmsearch --tblout GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg267aeb69-13fc-479f-8294-38230a03757a/dqc_reference/reference_markers.hmm GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:46,117] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:46,119] [INFO] Found 6/6 markers.
[2024-01-24 12:31:46,150] [INFO] Query marker FASTA was written to GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:31:46,151] [INFO] Task started: Blastn
[2024-01-24 12:31:46,151] [INFO] Running command: blastn -query GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg267aeb69-13fc-479f-8294-38230a03757a/dqc_reference/reference_markers.fasta -out GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:46,744] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:46,748] [INFO] Selected 14 target genomes.
[2024-01-24 12:31:46,748] [INFO] Target genome list was writen to GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:31:46,752] [INFO] Task started: fastANI
[2024-01-24 12:31:46,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg173ba813-98e4-4352-9a8b-f5dc34142e0a/GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna.gz --refList GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:54,739] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:54,740] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg267aeb69-13fc-479f-8294-38230a03757a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:54,740] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg267aeb69-13fc-479f-8294-38230a03757a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:54,748] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:54,748] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:54,748] [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
Alicyclobacillus hesperidum	strain=DSM 12489	GCA_900107035.1	89784	89784	type	True	100.0	919	922	95	conclusive
Alicyclobacillus sacchari	strain=DSM 17974	GCA_004366795.1	392010	392010	type	True	83.7348	736	922	95	below_threshold
Alicyclobacillus acidocaldarius subsp. acidocaldarius	strain=DSM 446	GCA_000024285.1	1388	405212	type	True	78.2492	130	922	95	below_threshold
Alicyclobacillus mali	strain=FSL-W10-0018	GCA_017329565.1	1123961	1123961	type	True	76.9088	111	922	95	below_threshold
Alicyclobacillus sendaiensis	strain=NBRC 100866	GCA_001552675.1	192387	192387	type	True	76.8392	101	922	95	below_threshold
Alicyclobacillus fructus	strain=FSL-W10-0059	GCA_017329605.1	2816082	2816082	type	True	76.7141	113	922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:54,750] [INFO] DFAST Taxonomy check result was written to GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:31:54,751] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:54,751] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:54,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg267aeb69-13fc-479f-8294-38230a03757a/dqc_reference/checkm_data
[2024-01-24 12:31:54,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:54,788] [INFO] Task started: CheckM
[2024-01-24 12:31:54,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/checkm_input GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:32:27,380] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:27,382] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:27,403] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:27,403] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:27,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:32:27,404] [INFO] Task started: Blastn
[2024-01-24 12:32:27,404] [INFO] Running command: blastn -query GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg267aeb69-13fc-479f-8294-38230a03757a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:28,238] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:28,243] [INFO] Selected 14 target genomes.
[2024-01-24 12:32:28,243] [INFO] Target genome list was writen to GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:28,251] [INFO] Task started: fastANI
[2024-01-24 12:32:28,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg173ba813-98e4-4352-9a8b-f5dc34142e0a/GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna.gz --refList GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:36,419] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:36,430] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:36,431] [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_900107035.1	s__Alicyclobacillus hesperidum	100.0	919	922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.6061	98.78	98.78	0.94	0.94	2	conclusive
GCF_001447355.1	s__Alicyclobacillus tengchongensis	95.537	814	922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.6061	N/A	N/A	N/A	N/A	1	-
GCF_004366795.1	s__Alicyclobacillus sacchari	83.7302	736	922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024285.1	s__Alicyclobacillus acidocaldarius	78.223	131	922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000219875.1	s__Alicyclobacillus acidocaldarius_A	77.3423	114	922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552675.1	s__Alicyclobacillus sendaiensis	76.8193	102	922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017329635.1	s__Alicyclobacillus sp017329635	76.6573	112	922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001570745.1	s__Alicyclobacillus mali	76.6156	106	922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	98.73	98.27	0.95	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:36,432] [INFO] GTDB search result was written to GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:36,432] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:36,435] [INFO] DFAST_QC result json was written to GCF_900107035.1_IMG-taxon_2634166329_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:32:36,435] [INFO] DFAST_QC completed!
[2024-01-24 12:32:36,435] [INFO] Total running time: 0h1m2s