[2024-01-24 11:20:04,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:04,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:04,061] [INFO] DQC Reference Directory: /var/lib/cwl/stga42bb215-da4b-4d09-b305-e5bd369186ee/dqc_reference
[2024-01-24 11:20:05,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:05,243] [INFO] Task started: Prodigal
[2024-01-24 11:20:05,243] [INFO] Running command: gunzip -c /var/lib/cwl/stg93de3dda-67ae-44af-baee-6af23627f4e6/GCF_003217295.1_ASM321729v1_genomic.fna.gz | prodigal -d GCF_003217295.1_ASM321729v1_genomic.fna/cds.fna -a GCF_003217295.1_ASM321729v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:12,326] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:12,326] [INFO] Task started: HMMsearch
[2024-01-24 11:20:12,326] [INFO] Running command: hmmsearch --tblout GCF_003217295.1_ASM321729v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga42bb215-da4b-4d09-b305-e5bd369186ee/dqc_reference/reference_markers.hmm GCF_003217295.1_ASM321729v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:12,532] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:12,533] [INFO] Found 6/6 markers.
[2024-01-24 11:20:12,563] [INFO] Query marker FASTA was written to GCF_003217295.1_ASM321729v1_genomic.fna/markers.fasta
[2024-01-24 11:20:12,563] [INFO] Task started: Blastn
[2024-01-24 11:20:12,563] [INFO] Running command: blastn -query GCF_003217295.1_ASM321729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga42bb215-da4b-4d09-b305-e5bd369186ee/dqc_reference/reference_markers.fasta -out GCF_003217295.1_ASM321729v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:13,148] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:13,151] [INFO] Selected 11 target genomes.
[2024-01-24 11:20:13,152] [INFO] Target genome list was writen to GCF_003217295.1_ASM321729v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:13,156] [INFO] Task started: fastANI
[2024-01-24 11:20:13,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg93de3dda-67ae-44af-baee-6af23627f4e6/GCF_003217295.1_ASM321729v1_genomic.fna.gz --refList GCF_003217295.1_ASM321729v1_genomic.fna/target_genomes.txt --output GCF_003217295.1_ASM321729v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:20,642] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:20,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga42bb215-da4b-4d09-b305-e5bd369186ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:20,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga42bb215-da4b-4d09-b305-e5bd369186ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:20,652] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:20:20,652] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:20,652] [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
Ureibacillus chungkukjangi	strain=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	100.0	1243	1248	95	conclusive
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	99.9939	1242	1248	95	conclusive
Ureibacillus sinduriensis	strain=JCM 15800	GCA_002200845.1	561440	561440	type	True	81.8424	672	1248	95	below_threshold
Ureibacillus sinduriensis	strain=JCM 15800	GCA_000772955.1	561440	561440	type	True	81.8424	672	1248	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	79.1901	339	1248	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	78.8708	363	1248	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	78.8667	360	1248	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	78.1476	198	1248	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	77.6103	158	1248	95	below_threshold
Paenisporosarcina cavernae	strain=K2R23-3	GCA_003595195.1	2320858	2320858	type	True	77.427	81	1248	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	75.953	53	1248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:20,656] [INFO] DFAST Taxonomy check result was written to GCF_003217295.1_ASM321729v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:20,657] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:20,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:20,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga42bb215-da4b-4d09-b305-e5bd369186ee/dqc_reference/checkm_data
[2024-01-24 11:20:20,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:20,694] [INFO] Task started: CheckM
[2024-01-24 11:20:20,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003217295.1_ASM321729v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003217295.1_ASM321729v1_genomic.fna/checkm_input GCF_003217295.1_ASM321729v1_genomic.fna/checkm_result
[2024-01-24 11:20:46,717] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:46,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:46,735] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:46,735] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:46,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003217295.1_ASM321729v1_genomic.fna/markers.fasta)
[2024-01-24 11:20:46,736] [INFO] Task started: Blastn
[2024-01-24 11:20:46,736] [INFO] Running command: blastn -query GCF_003217295.1_ASM321729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga42bb215-da4b-4d09-b305-e5bd369186ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_003217295.1_ASM321729v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:47,480] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:47,483] [INFO] Selected 11 target genomes.
[2024-01-24 11:20:47,484] [INFO] Target genome list was writen to GCF_003217295.1_ASM321729v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:47,494] [INFO] Task started: fastANI
[2024-01-24 11:20:47,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg93de3dda-67ae-44af-baee-6af23627f4e6/GCF_003217295.1_ASM321729v1_genomic.fna.gz --refList GCF_003217295.1_ASM321729v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003217295.1_ASM321729v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:20:55,775] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:55,784] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:20:55,784] [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_003217295.1	s__Ureibacillus chungkukjangi	100.0	1243	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_005491425.1	s__Ureibacillus sp005491425	84.225	888	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772955.1	s__Ureibacillus sinduriensis	81.8324	673	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003711845.1	s__Ureibacillus halotolerans	80.0772	474	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836845.1	s__Ureibacillus sp014836845	80.0004	510	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966145.1	s__Ureibacillus telephonicus	79.5708	457	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515775.1	s__Ureibacillus yapensis	79.489	428	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628435.1	s__Ureibacillus endophyticus	79.3282	394	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908465.1	s__Ureibacillus composti	78.8829	360	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014836905.1	s__Solibacillus sp014836905	78.1413	196	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813185.1	s__Viridibacillus sp002813185	77.5683	155	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	98.00	98.00	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:20:55,786] [INFO] GTDB search result was written to GCF_003217295.1_ASM321729v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:20:55,786] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:20:55,789] [INFO] DFAST_QC result json was written to GCF_003217295.1_ASM321729v1_genomic.fna/dqc_result.json
[2024-01-24 11:20:55,789] [INFO] DFAST_QC completed!
[2024-01-24 11:20:55,789] [INFO] Total running time: 0h0m52s