[2024-01-24 13:41:10,381] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,382] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,383] [INFO] DQC Reference Directory: /var/lib/cwl/stg3dfde45a-3bb4-4b57-966b-3cb63ee85b22/dqc_reference
[2024-01-24 13:41:11,801] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:11,802] [INFO] Task started: Prodigal
[2024-01-24 13:41:11,802] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd9ca627-43aa-40ec-b533-ea69658cee35/GCF_006540205.1_ASM654020v1_genomic.fna.gz | prodigal -d GCF_006540205.1_ASM654020v1_genomic.fna/cds.fna -a GCF_006540205.1_ASM654020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:21,448] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:21,448] [INFO] Task started: HMMsearch
[2024-01-24 13:41:21,448] [INFO] Running command: hmmsearch --tblout GCF_006540205.1_ASM654020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3dfde45a-3bb4-4b57-966b-3cb63ee85b22/dqc_reference/reference_markers.hmm GCF_006540205.1_ASM654020v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:21,713] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:21,715] [INFO] Found 6/6 markers.
[2024-01-24 13:41:21,760] [INFO] Query marker FASTA was written to GCF_006540205.1_ASM654020v1_genomic.fna/markers.fasta
[2024-01-24 13:41:21,761] [INFO] Task started: Blastn
[2024-01-24 13:41:21,761] [INFO] Running command: blastn -query GCF_006540205.1_ASM654020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3dfde45a-3bb4-4b57-966b-3cb63ee85b22/dqc_reference/reference_markers.fasta -out GCF_006540205.1_ASM654020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:22,376] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:22,379] [INFO] Selected 10 target genomes.
[2024-01-24 13:41:22,380] [INFO] Target genome list was writen to GCF_006540205.1_ASM654020v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:22,383] [INFO] Task started: fastANI
[2024-01-24 13:41:22,383] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd9ca627-43aa-40ec-b533-ea69658cee35/GCF_006540205.1_ASM654020v1_genomic.fna.gz --refList GCF_006540205.1_ASM654020v1_genomic.fna/target_genomes.txt --output GCF_006540205.1_ASM654020v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:32,576] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:32,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3dfde45a-3bb4-4b57-966b-3cb63ee85b22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:32,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3dfde45a-3bb4-4b57-966b-3cb63ee85b22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:32,588] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:41:32,588] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:32,588] [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
Lysinibacillus fusiformis	strain=NBRC 15717	GCA_006540205.1	28031	28031	type	True	100.0	1548	1551	95	conclusive
Lysinibacillus fusiformis	strain=ATCC 7055	GCA_003049525.1	28031	28031	type	True	99.9998	1549	1551	95	conclusive
Lysinibacillus fusiformis	strain=NRRL NRS-350	GCA_003367495.1	28031	28031	type	True	99.9797	1522	1551	95	conclusive
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	85.6773	1215	1551	95	below_threshold
Lysinibacillus capsici	strain=PB300	GCA_003367505.1	2115968	2115968	type	True	84.8289	1150	1551	95	below_threshold
Lysinibacillus boronitolerans	strain=NBRC 103108	GCA_000772935.1	309788	309788	type	True	84.817	1116	1551	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	79.7077	499	1551	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	78.1574	195	1551	95	below_threshold
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	78.055	196	1551	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.6459	74	1551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:32,590] [INFO] DFAST Taxonomy check result was written to GCF_006540205.1_ASM654020v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:32,590] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:32,591] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:32,591] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3dfde45a-3bb4-4b57-966b-3cb63ee85b22/dqc_reference/checkm_data
[2024-01-24 13:41:32,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:32,639] [INFO] Task started: CheckM
[2024-01-24 13:41:32,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006540205.1_ASM654020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006540205.1_ASM654020v1_genomic.fna/checkm_input GCF_006540205.1_ASM654020v1_genomic.fna/checkm_result
[2024-01-24 13:42:06,382] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:06,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:06,404] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:06,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:06,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006540205.1_ASM654020v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:06,405] [INFO] Task started: Blastn
[2024-01-24 13:42:06,405] [INFO] Running command: blastn -query GCF_006540205.1_ASM654020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3dfde45a-3bb4-4b57-966b-3cb63ee85b22/dqc_reference/reference_markers_gtdb.fasta -out GCF_006540205.1_ASM654020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:07,187] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:07,190] [INFO] Selected 11 target genomes.
[2024-01-24 13:42:07,191] [INFO] Target genome list was writen to GCF_006540205.1_ASM654020v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:07,237] [INFO] Task started: fastANI
[2024-01-24 13:42:07,237] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd9ca627-43aa-40ec-b533-ea69658cee35/GCF_006540205.1_ASM654020v1_genomic.fna.gz --refList GCF_006540205.1_ASM654020v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006540205.1_ASM654020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:17,732] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:17,740] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:17,741] [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_003049525.1	s__Lysinibacillus fusiformis	99.9998	1549	1551	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	98.17	95.55	0.92	0.87	32	conclusive
GCF_001629735.1	s__Lysinibacillus sphaericus_A	93.0267	1329	1551	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.64	99.33	0.95	0.90	29	-
GCF_001308875.1	s__Lysinibacillus sp001308875	89.6424	1282	1551	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009724685.1	s__Lysinibacillus sp009724685	85.6773	1215	1551	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002845985.1	s__Lysinibacillus fusiformis_D	85.4897	1189	1551	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.12	98.25	0.94	0.92	9	-
GCF_016925635.1	s__Lysinibacillus fusiformis_F	85.1257	1178	1551	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367505.1	s__Lysinibacillus capsici	84.8289	1150	1551	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.1183	97.93	96.58	0.91	0.87	16	-
GCF_006864135.1	s__Lysinibacillus sp006864135	81.7976	848	1551	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	95.97	95.97	0.86	0.86	2	-
GCA_002360295.1	s__Metasolibacillus sp002360295	77.6891	217	1551	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:17,745] [INFO] GTDB search result was written to GCF_006540205.1_ASM654020v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:17,746] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:17,749] [INFO] DFAST_QC result json was written to GCF_006540205.1_ASM654020v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:17,749] [INFO] DFAST_QC completed!
[2024-01-24 13:42:17,749] [INFO] Total running time: 0h1m7s