[2024-01-25 19:46:50,766] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:50,767] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:50,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg2999a0b7-d4d5-425a-a8b8-768ca90eeb70/dqc_reference
[2024-01-25 19:46:51,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:51,885] [INFO] Task started: Prodigal
[2024-01-25 19:46:51,886] [INFO] Running command: gunzip -c /var/lib/cwl/stg15c32d63-2de3-407e-827d-05720f924d70/GCF_000196735.1_ASM19673v1_genomic.fna.gz | prodigal -d GCF_000196735.1_ASM19673v1_genomic.fna/cds.fna -a GCF_000196735.1_ASM19673v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:01,458] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:01,459] [INFO] Task started: HMMsearch
[2024-01-25 19:47:01,459] [INFO] Running command: hmmsearch --tblout GCF_000196735.1_ASM19673v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2999a0b7-d4d5-425a-a8b8-768ca90eeb70/dqc_reference/reference_markers.hmm GCF_000196735.1_ASM19673v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:01,758] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:01,759] [INFO] Found 6/6 markers.
[2024-01-25 19:47:01,793] [INFO] Query marker FASTA was written to GCF_000196735.1_ASM19673v1_genomic.fna/markers.fasta
[2024-01-25 19:47:01,793] [INFO] Task started: Blastn
[2024-01-25 19:47:01,793] [INFO] Running command: blastn -query GCF_000196735.1_ASM19673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2999a0b7-d4d5-425a-a8b8-768ca90eeb70/dqc_reference/reference_markers.fasta -out GCF_000196735.1_ASM19673v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:02,352] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:02,354] [INFO] Selected 14 target genomes.
[2024-01-25 19:47:02,355] [INFO] Target genome list was writen to GCF_000196735.1_ASM19673v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:02,363] [INFO] Task started: fastANI
[2024-01-25 19:47:02,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg15c32d63-2de3-407e-827d-05720f924d70/GCF_000196735.1_ASM19673v1_genomic.fna.gz --refList GCF_000196735.1_ASM19673v1_genomic.fna/target_genomes.txt --output GCF_000196735.1_ASM19673v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:13,766] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:13,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2999a0b7-d4d5-425a-a8b8-768ca90eeb70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:13,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2999a0b7-d4d5-425a-a8b8-768ca90eeb70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:13,775] [WARNING] Following organisms are indistinguishable with ANI. [Bacillus amyloliquefaciens(1390), Bacillus velezensis(492670)]
[2024-01-25 19:47:13,776] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:13,776] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:13,776] [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 amyloliquefaciens	strain=DSM 7	GCA_000196735.1	1390	1390	suspected-type	True	100.0	1318	1326	95	conclusive
Bacillus velezensis	strain=NRRL B-41580	GCA_001461825.1	492670	492670	type	True	93.8979	1139	1326	95	below_threshold
Bacillus velezensis	strain=KCTC 13012	GCA_001267695.1	492670	492670	type	True	93.8694	1157	1326	95	below_threshold
Bacillus siamensis	strain=KCTC 13613	GCA_000262045.1	659243	659243	type	True	93.68	1133	1326	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	81.3982	603	1326	95	below_threshold
Bacillus halotolerans	strain=FJAT-2398	GCA_001637525.1	260554	260554	type	True	81.2988	701	1326	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	80.9898	695	1326	95	below_threshold
Bacillus tequilensis	strain=KCTC 13622	GCA_000507145.1	227866	227866	type	True	80.9121	674	1326	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_002009095.1	135461	1423	type	True	80.8964	701	1326	95	below_threshold
Bacillus mojavensis	strain=RO-H-1 = KCTC 3706	GCA_000507105.1	72360	72360	type	True	80.7182	682	1326	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	80.4152	603	1326	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	79.1358	97	1326	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	77.1122	62	1326	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:13,777] [INFO] DFAST Taxonomy check result was written to GCF_000196735.1_ASM19673v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:13,778] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:13,778] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:13,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2999a0b7-d4d5-425a-a8b8-768ca90eeb70/dqc_reference/checkm_data
[2024-01-25 19:47:13,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:13,817] [INFO] Task started: CheckM
[2024-01-25 19:47:13,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000196735.1_ASM19673v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000196735.1_ASM19673v1_genomic.fna/checkm_input GCF_000196735.1_ASM19673v1_genomic.fna/checkm_result
[2024-01-25 19:47:46,649] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:46,650] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:46,665] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:46,666] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:46,666] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000196735.1_ASM19673v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:46,666] [INFO] Task started: Blastn
[2024-01-25 19:47:46,666] [INFO] Running command: blastn -query GCF_000196735.1_ASM19673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2999a0b7-d4d5-425a-a8b8-768ca90eeb70/dqc_reference/reference_markers_gtdb.fasta -out GCF_000196735.1_ASM19673v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:47,445] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:47,447] [INFO] Selected 9 target genomes.
[2024-01-25 19:47:47,447] [INFO] Target genome list was writen to GCF_000196735.1_ASM19673v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:47,457] [INFO] Task started: fastANI
[2024-01-25 19:47:47,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg15c32d63-2de3-407e-827d-05720f924d70/GCF_000196735.1_ASM19673v1_genomic.fna.gz --refList GCF_000196735.1_ASM19673v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000196735.1_ASM19673v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:55,508] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:55,514] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:55,515] [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_000196735.1	s__Bacillus amyloliquefaciens	100.0	1318	1326	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.08	97.42	0.94	0.89	27	conclusive
GCF_001461825.1	s__Bacillus velezensis	93.8979	1139	1326	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.12	97.33	0.94	0.90	498	-
GCF_000262045.1	s__Bacillus siamensis	93.68	1133	1326	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.57	97.73	0.95	0.92	11	-
GCF_001584325.1	s__Bacillus nakamurai	86.9643	1054	1326	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	86.9463	1025	1326	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.89	99.79	0.95	0.95	3	-
GCF_004124315.1	s__Bacillus cabrialesii	80.8171	687	1326	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	96.72	96.66	0.93	0.91	11	-
GCF_004116955.1	s__Bacillus vallismortis	80.6895	683	1326	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.90	97.68	0.96	0.94	6	-
GCF_000715205.1	s__Bacillus zhangzhouensis	77.5041	209	1326	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.04	95.33	0.94	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:55,516] [INFO] GTDB search result was written to GCF_000196735.1_ASM19673v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:55,516] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:55,519] [INFO] DFAST_QC result json was written to GCF_000196735.1_ASM19673v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:55,519] [INFO] DFAST_QC completed!
[2024-01-25 19:47:55,519] [INFO] Total running time: 0h1m5s