[2024-01-24 12:46:34,789] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:34,792] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:34,793] [INFO] DQC Reference Directory: /var/lib/cwl/stg8620c42f-62b3-409b-b989-484826e3d346/dqc_reference
[2024-01-24 12:46:35,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:35,951] [INFO] Task started: Prodigal
[2024-01-24 12:46:35,951] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd9f3157-7f82-4073-9940-6f3ce2529e8a/GCF_000262045.1_KCTC_13613_01_genomic.fna.gz | prodigal -d GCF_000262045.1_KCTC_13613_01_genomic.fna/cds.fna -a GCF_000262045.1_KCTC_13613_01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:46:45,671] [INFO] Task succeeded: Prodigal
[2024-01-24 12:46:45,672] [INFO] Task started: HMMsearch
[2024-01-24 12:46:45,672] [INFO] Running command: hmmsearch --tblout GCF_000262045.1_KCTC_13613_01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8620c42f-62b3-409b-b989-484826e3d346/dqc_reference/reference_markers.hmm GCF_000262045.1_KCTC_13613_01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:46:45,897] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:46:45,898] [INFO] Found 6/6 markers.
[2024-01-24 12:46:45,932] [INFO] Query marker FASTA was written to GCF_000262045.1_KCTC_13613_01_genomic.fna/markers.fasta
[2024-01-24 12:46:45,932] [INFO] Task started: Blastn
[2024-01-24 12:46:45,933] [INFO] Running command: blastn -query GCF_000262045.1_KCTC_13613_01_genomic.fna/markers.fasta -db /var/lib/cwl/stg8620c42f-62b3-409b-b989-484826e3d346/dqc_reference/reference_markers.fasta -out GCF_000262045.1_KCTC_13613_01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:46,506] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:46,508] [INFO] Selected 13 target genomes.
[2024-01-24 12:46:46,509] [INFO] Target genome list was writen to GCF_000262045.1_KCTC_13613_01_genomic.fna/target_genomes.txt
[2024-01-24 12:46:46,513] [INFO] Task started: fastANI
[2024-01-24 12:46:46,514] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd9f3157-7f82-4073-9940-6f3ce2529e8a/GCF_000262045.1_KCTC_13613_01_genomic.fna.gz --refList GCF_000262045.1_KCTC_13613_01_genomic.fna/target_genomes.txt --output GCF_000262045.1_KCTC_13613_01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:56,606] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:56,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8620c42f-62b3-409b-b989-484826e3d346/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:56,607] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8620c42f-62b3-409b-b989-484826e3d346/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:56,617] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:46:56,617] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:46:56,617] [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
Bacillus siamensis	strain=KCTC 13613	GCA_000262045.1	659243	659243	type	True	100.0	1244	1246	95	conclusive
Bacillus velezensis	strain=KCTC 13012	GCA_001267695.1	492670	492670	type	True	94.2485	1162	1246	95	below_threshold
Bacillus velezensis	strain=NRRL B-41580	GCA_001461825.1	492670	492670	type	True	94.2372	1162	1246	95	below_threshold
Bacillus amyloliquefaciens	strain=DSM 7	GCA_000196735.1	1390	1390	suspected-type	True	93.6758	1137	1246	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	81.8457	593	1246	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	80.9918	646	1246	95	below_threshold
Bacillus halotolerans	strain=FJAT-2398	GCA_001637525.1	260554	260554	type	True	80.938	720	1246	95	below_threshold
Bacillus mojavensis	strain=RO-H-1 = KCTC 3706	GCA_000507105.1	72360	72360	type	True	80.7285	669	1246	95	below_threshold
Bacillus atrophaeus	strain=NRRL NRS 213	GCA_001584335.1	1452	1452	type	True	80.5244	704	1246	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	80.349	590	1246	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	77.0196	86	1246	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.7918	55	1246	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:56,619] [INFO] DFAST Taxonomy check result was written to GCF_000262045.1_KCTC_13613_01_genomic.fna/tc_result.tsv
[2024-01-24 12:46:56,619] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:56,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:56,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8620c42f-62b3-409b-b989-484826e3d346/dqc_reference/checkm_data
[2024-01-24 12:46:56,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:56,658] [INFO] Task started: CheckM
[2024-01-24 12:46:56,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000262045.1_KCTC_13613_01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000262045.1_KCTC_13613_01_genomic.fna/checkm_input GCF_000262045.1_KCTC_13613_01_genomic.fna/checkm_result
[2024-01-24 12:47:30,968] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:30,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:30,986] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:30,986] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:30,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000262045.1_KCTC_13613_01_genomic.fna/markers.fasta)
[2024-01-24 12:47:30,986] [INFO] Task started: Blastn
[2024-01-24 12:47:30,986] [INFO] Running command: blastn -query GCF_000262045.1_KCTC_13613_01_genomic.fna/markers.fasta -db /var/lib/cwl/stg8620c42f-62b3-409b-b989-484826e3d346/dqc_reference/reference_markers_gtdb.fasta -out GCF_000262045.1_KCTC_13613_01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:31,734] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:31,737] [INFO] Selected 6 target genomes.
[2024-01-24 12:47:31,737] [INFO] Target genome list was writen to GCF_000262045.1_KCTC_13613_01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:31,742] [INFO] Task started: fastANI
[2024-01-24 12:47:31,743] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd9f3157-7f82-4073-9940-6f3ce2529e8a/GCF_000262045.1_KCTC_13613_01_genomic.fna.gz --refList GCF_000262045.1_KCTC_13613_01_genomic.fna/target_genomes_gtdb.txt --output GCF_000262045.1_KCTC_13613_01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:37,342] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:37,348] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:37,349] [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_000262045.1	s__Bacillus siamensis	100.0	1244	1246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.57	97.73	0.95	0.92	11	conclusive
GCF_001461825.1	s__Bacillus velezensis	94.2372	1162	1246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.12	97.33	0.94	0.90	498	-
GCF_000196735.1	s__Bacillus amyloliquefaciens	93.6758	1137	1246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.08	97.42	0.94	0.89	27	-
GCF_001584325.1	s__Bacillus nakamurai	86.565	1003	1246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.07	99.07	0.94	0.94	2	-
GCF_018613535.1	s__Bacillus sp018613535	86.5023	1021	1246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.89	99.79	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:37,350] [INFO] GTDB search result was written to GCF_000262045.1_KCTC_13613_01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:37,351] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:37,355] [INFO] DFAST_QC result json was written to GCF_000262045.1_KCTC_13613_01_genomic.fna/dqc_result.json
[2024-01-24 12:47:37,355] [INFO] DFAST_QC completed!
[2024-01-24 12:47:37,355] [INFO] Total running time: 0h1m3s