[2024-01-24 14:12:45,790] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:45,793] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:45,794] [INFO] DQC Reference Directory: /var/lib/cwl/stgda9ace46-644d-4a0e-97e1-e7cfbd59698e/dqc_reference
[2024-01-24 14:12:47,036] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:47,037] [INFO] Task started: Prodigal
[2024-01-24 14:12:47,038] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6f9576a-d034-443f-80c5-e5c289da4971/GCF_000024285.1_ASM2428v1_genomic.fna.gz | prodigal -d GCF_000024285.1_ASM2428v1_genomic.fna/cds.fna -a GCF_000024285.1_ASM2428v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:57,856] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:57,857] [INFO] Task started: HMMsearch
[2024-01-24 14:12:57,857] [INFO] Running command: hmmsearch --tblout GCF_000024285.1_ASM2428v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda9ace46-644d-4a0e-97e1-e7cfbd59698e/dqc_reference/reference_markers.hmm GCF_000024285.1_ASM2428v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:58,157] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:58,158] [INFO] Found 6/6 markers.
[2024-01-24 14:12:58,193] [INFO] Query marker FASTA was written to GCF_000024285.1_ASM2428v1_genomic.fna/markers.fasta
[2024-01-24 14:12:58,193] [INFO] Task started: Blastn
[2024-01-24 14:12:58,193] [INFO] Running command: blastn -query GCF_000024285.1_ASM2428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda9ace46-644d-4a0e-97e1-e7cfbd59698e/dqc_reference/reference_markers.fasta -out GCF_000024285.1_ASM2428v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:58,861] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:58,865] [INFO] Selected 5 target genomes.
[2024-01-24 14:12:58,865] [INFO] Target genome list was writen to GCF_000024285.1_ASM2428v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:58,868] [INFO] Task started: fastANI
[2024-01-24 14:12:58,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6f9576a-d034-443f-80c5-e5c289da4971/GCF_000024285.1_ASM2428v1_genomic.fna.gz --refList GCF_000024285.1_ASM2428v1_genomic.fna/target_genomes.txt --output GCF_000024285.1_ASM2428v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:02,935] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:02,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda9ace46-644d-4a0e-97e1-e7cfbd59698e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:02,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda9ace46-644d-4a0e-97e1-e7cfbd59698e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:02,949] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:02,950] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:02,950] [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 acidocaldarius subsp. acidocaldarius	strain=DSM 446	GCA_000024285.1	1388	405212	type	True	100.0	1066	1067	95	conclusive
Alicyclobacillus mali	strain=FSL-W10-0018	GCA_017329565.1	1123961	1123961	type	True	89.0107	794	1067	95	below_threshold
Alicyclobacillus sendaiensis	strain=NBRC 100866	GCA_001552675.1	192387	192387	type	True	88.3735	751	1067	95	below_threshold
Alicyclobacillus fructus	strain=FSL-W10-0059	GCA_017329605.1	2816082	2816082	type	True	85.7563	761	1067	95	below_threshold
Alicyclobacillus vulcanalis	strain=DSM 16176	GCA_900156755.1	252246	252246	type	True	83.2339	734	1067	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:02,952] [INFO] DFAST Taxonomy check result was written to GCF_000024285.1_ASM2428v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:02,953] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:02,953] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:02,953] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda9ace46-644d-4a0e-97e1-e7cfbd59698e/dqc_reference/checkm_data
[2024-01-24 14:13:02,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:02,987] [INFO] Task started: CheckM
[2024-01-24 14:13:02,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024285.1_ASM2428v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024285.1_ASM2428v1_genomic.fna/checkm_input GCF_000024285.1_ASM2428v1_genomic.fna/checkm_result
[2024-01-24 14:13:44,095] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:44,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:44,118] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:44,119] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:44,119] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024285.1_ASM2428v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:44,120] [INFO] Task started: Blastn
[2024-01-24 14:13:44,120] [INFO] Running command: blastn -query GCF_000024285.1_ASM2428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda9ace46-644d-4a0e-97e1-e7cfbd59698e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024285.1_ASM2428v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:45,115] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:45,119] [INFO] Selected 5 target genomes.
[2024-01-24 14:13:45,119] [INFO] Target genome list was writen to GCF_000024285.1_ASM2428v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:45,123] [INFO] Task started: fastANI
[2024-01-24 14:13:45,123] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6f9576a-d034-443f-80c5-e5c289da4971/GCF_000024285.1_ASM2428v1_genomic.fna.gz --refList GCF_000024285.1_ASM2428v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024285.1_ASM2428v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:49,373] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:49,384] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:49,385] [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_000024285.1	s__Alicyclobacillus acidocaldarius	100.0	1066	1067	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000173835.1	s__Alicyclobacillus acidocaldarius_B	94.0781	836	1067	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	91.3717	875	1067	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570745.1	s__Alicyclobacillus mali	89.2894	792	1067	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	98.73	98.27	0.95	0.93	4	-
GCF_001552675.1	s__Alicyclobacillus sendaiensis	88.3735	751	1067	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:49,386] [INFO] GTDB search result was written to GCF_000024285.1_ASM2428v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:49,387] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:49,391] [INFO] DFAST_QC result json was written to GCF_000024285.1_ASM2428v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:49,391] [INFO] DFAST_QC completed!
[2024-01-24 14:13:49,391] [INFO] Total running time: 0h1m4s