[2024-01-24 11:26:38,944] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,945] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,946] [INFO] DQC Reference Directory: /var/lib/cwl/stge590a235-a339-4192-b429-04718f57bb4c/dqc_reference
[2024-01-24 11:26:40,301] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,302] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,302] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a5f2295-c5db-49e2-9bd5-b262e369712d/GCF_030161715.1_ASM3016171v1_genomic.fna.gz | prodigal -d GCF_030161715.1_ASM3016171v1_genomic.fna/cds.fna -a GCF_030161715.1_ASM3016171v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:51,134] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:51,135] [INFO] Task started: HMMsearch
[2024-01-24 11:26:51,135] [INFO] Running command: hmmsearch --tblout GCF_030161715.1_ASM3016171v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge590a235-a339-4192-b429-04718f57bb4c/dqc_reference/reference_markers.hmm GCF_030161715.1_ASM3016171v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:51,378] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:51,380] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9a5f2295-c5db-49e2-9bd5-b262e369712d/GCF_030161715.1_ASM3016171v1_genomic.fna.gz]
[2024-01-24 11:26:51,413] [INFO] Query marker FASTA was written to GCF_030161715.1_ASM3016171v1_genomic.fna/markers.fasta
[2024-01-24 11:26:51,414] [INFO] Task started: Blastn
[2024-01-24 11:26:51,414] [INFO] Running command: blastn -query GCF_030161715.1_ASM3016171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge590a235-a339-4192-b429-04718f57bb4c/dqc_reference/reference_markers.fasta -out GCF_030161715.1_ASM3016171v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:52,048] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:52,052] [INFO] Selected 12 target genomes.
[2024-01-24 11:26:52,052] [INFO] Target genome list was writen to GCF_030161715.1_ASM3016171v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:52,058] [INFO] Task started: fastANI
[2024-01-24 11:26:52,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a5f2295-c5db-49e2-9bd5-b262e369712d/GCF_030161715.1_ASM3016171v1_genomic.fna.gz --refList GCF_030161715.1_ASM3016171v1_genomic.fna/target_genomes.txt --output GCF_030161715.1_ASM3016171v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:00,008] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:00,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge590a235-a339-4192-b429-04718f57bb4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:00,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge590a235-a339-4192-b429-04718f57bb4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:00,017] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:00,018] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:00,018] [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 sacchari	strain=DSM 17974	GCA_004366795.1	392010	392010	type	True	99.8488	942	1059	95	conclusive
Alicyclobacillus hesperidum	strain=DSM 12489	GCA_900107035.1	89784	89784	type	True	83.827	735	1059	95	below_threshold
Alicyclobacillus vulcanalis	strain=DSM 16176	GCA_900156755.1	252246	252246	type	True	78.839	141	1059	95	below_threshold
Alicyclobacillus sendaiensis	strain=NBRC 100866	GCA_001552675.1	192387	192387	type	True	77.1269	113	1059	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:00,020] [INFO] DFAST Taxonomy check result was written to GCF_030161715.1_ASM3016171v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:00,020] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:00,020] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:00,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge590a235-a339-4192-b429-04718f57bb4c/dqc_reference/checkm_data
[2024-01-24 11:27:00,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:00,054] [INFO] Task started: CheckM
[2024-01-24 11:27:00,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161715.1_ASM3016171v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161715.1_ASM3016171v1_genomic.fna/checkm_input GCF_030161715.1_ASM3016171v1_genomic.fna/checkm_result
[2024-01-24 11:27:35,345] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:35,346] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:35,366] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:35,366] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:35,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161715.1_ASM3016171v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:35,367] [INFO] Task started: Blastn
[2024-01-24 11:27:35,368] [INFO] Running command: blastn -query GCF_030161715.1_ASM3016171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge590a235-a339-4192-b429-04718f57bb4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161715.1_ASM3016171v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:36,272] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:36,276] [INFO] Selected 9 target genomes.
[2024-01-24 11:27:36,276] [INFO] Target genome list was writen to GCF_030161715.1_ASM3016171v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:36,332] [INFO] Task started: fastANI
[2024-01-24 11:27:36,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a5f2295-c5db-49e2-9bd5-b262e369712d/GCF_030161715.1_ASM3016171v1_genomic.fna.gz --refList GCF_030161715.1_ASM3016171v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161715.1_ASM3016171v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:41,556] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:41,571] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:41,571] [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_004366795.1	s__Alicyclobacillus sacchari	99.8488	942	1059	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_900107035.1	s__Alicyclobacillus hesperidum	83.8179	736	1059	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.6061	98.78	98.78	0.94	0.94	2	-
GCF_001447355.1	s__Alicyclobacillus tengchongensis	83.6859	735	1059	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.6061	N/A	N/A	N/A	N/A	1	-
GCF_000173835.1	s__Alicyclobacillus acidocaldarius_B	79.6407	143	1059	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156755.1	s__Alicyclobacillus vulcanalis	78.8845	139	1059	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	78.3799	140	1059	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	77.1269	113	1059	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 11:27:41,574] [INFO] GTDB search result was written to GCF_030161715.1_ASM3016171v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:41,575] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:41,578] [INFO] DFAST_QC result json was written to GCF_030161715.1_ASM3016171v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:41,578] [INFO] DFAST_QC completed!
[2024-01-24 11:27:41,578] [INFO] Total running time: 0h1m3s