[2024-01-24 15:18:36,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:36,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:36,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg124a3ae3-ef02-47d0-bd55-e8037e6fc2cd/dqc_reference
[2024-01-24 15:18:38,356] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:38,357] [INFO] Task started: Prodigal
[2024-01-24 15:18:38,358] [INFO] Running command: gunzip -c /var/lib/cwl/stg700f3d4d-d898-4d9b-9824-38faf319e186/GCF_006094335.1_ASM609433v1_genomic.fna.gz | prodigal -d GCF_006094335.1_ASM609433v1_genomic.fna/cds.fna -a GCF_006094335.1_ASM609433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:49,961] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:49,962] [INFO] Task started: HMMsearch
[2024-01-24 15:18:49,962] [INFO] Running command: hmmsearch --tblout GCF_006094335.1_ASM609433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg124a3ae3-ef02-47d0-bd55-e8037e6fc2cd/dqc_reference/reference_markers.hmm GCF_006094335.1_ASM609433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:50,328] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:50,329] [INFO] Found 6/6 markers.
[2024-01-24 15:18:50,372] [INFO] Query marker FASTA was written to GCF_006094335.1_ASM609433v1_genomic.fna/markers.fasta
[2024-01-24 15:18:50,373] [INFO] Task started: Blastn
[2024-01-24 15:18:50,373] [INFO] Running command: blastn -query GCF_006094335.1_ASM609433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg124a3ae3-ef02-47d0-bd55-e8037e6fc2cd/dqc_reference/reference_markers.fasta -out GCF_006094335.1_ASM609433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:51,009] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:51,012] [INFO] Selected 10 target genomes.
[2024-01-24 15:18:51,012] [INFO] Target genome list was writen to GCF_006094335.1_ASM609433v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:51,017] [INFO] Task started: fastANI
[2024-01-24 15:18:51,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg700f3d4d-d898-4d9b-9824-38faf319e186/GCF_006094335.1_ASM609433v1_genomic.fna.gz --refList GCF_006094335.1_ASM609433v1_genomic.fna/target_genomes.txt --output GCF_006094335.1_ASM609433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:01,418] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:01,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg124a3ae3-ef02-47d0-bd55-e8037e6fc2cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:01,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg124a3ae3-ef02-47d0-bd55-e8037e6fc2cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:01,436] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 15:19:01,437] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:01,437] [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 licheniformis	strain=ATCC 14580	GCA_006094335.1	1402	1402	type	True	100.0	1407	1413	95	conclusive
Bacillus licheniformis	strain=DSM 13	GCA_000008425.1	1402	1402	type	True	99.9994	1402	1413	95	conclusive
Bacillus licheniformis	strain=ATCC 14580; DSM 13	GCA_000011645.1	1402	1402	type	True	99.9992	1402	1413	95	conclusive
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	99.6369	1348	1413	95	conclusive
Bacillus swezeyi	strain=NRRL B-41294	GCA_001969815.1	1925020	1925020	type	True	83.9813	1090	1413	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	80.3166	62	1413	95	below_threshold
Peribacillus frigoritolerans	strain=DSM 8801	GCA_024169475.1	450367	450367	type	True	80.0178	71	1413	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	78.8628	107	1413	95	below_threshold
Aeribacillus composti	strain=KCTC 33824	GCA_007827555.1	1868734	1868734	type	True	76.8315	64	1413	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.6186	59	1413	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:01,457] [INFO] DFAST Taxonomy check result was written to GCF_006094335.1_ASM609433v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:01,457] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:01,458] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:01,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg124a3ae3-ef02-47d0-bd55-e8037e6fc2cd/dqc_reference/checkm_data
[2024-01-24 15:19:01,459] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:01,519] [INFO] Task started: CheckM
[2024-01-24 15:19:01,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006094335.1_ASM609433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006094335.1_ASM609433v1_genomic.fna/checkm_input GCF_006094335.1_ASM609433v1_genomic.fna/checkm_result
[2024-01-24 15:19:40,910] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:40,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:40,932] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:40,932] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:40,932] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006094335.1_ASM609433v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:40,933] [INFO] Task started: Blastn
[2024-01-24 15:19:40,933] [INFO] Running command: blastn -query GCF_006094335.1_ASM609433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg124a3ae3-ef02-47d0-bd55-e8037e6fc2cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_006094335.1_ASM609433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:41,733] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:41,736] [INFO] Selected 9 target genomes.
[2024-01-24 15:19:41,736] [INFO] Target genome list was writen to GCF_006094335.1_ASM609433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:41,743] [INFO] Task started: fastANI
[2024-01-24 15:19:41,743] [INFO] Running command: fastANI --query /var/lib/cwl/stg700f3d4d-d898-4d9b-9824-38faf319e186/GCF_006094335.1_ASM609433v1_genomic.fna.gz --refList GCF_006094335.1_ASM609433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006094335.1_ASM609433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:51,272] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:51,285] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 15:19:51,285] [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_000011645.1	s__Bacillus licheniformis	99.9992	1402	1413	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	99.64	99.26	0.97	0.81	213	inconclusive
GCF_001969855.1	s__Bacillus haynesii	95.4573	1276	1413	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	97.08	96.53	0.93	0.92	6	inconclusive
GCF_001042485.2	s__Bacillus paralicheniformis	94.5852	1302	1413	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0745	98.70	96.39	0.96	0.84	103	-
GCF_001969815.1	s__Bacillus swezeyi	83.9848	1088	1413	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.68	96.91	0.92	0.90	5	-
GCF_900166645.1	s__Bacillus sonorensis_A	83.5122	1098	1413	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.48	99.48	0.95	0.95	2	-
GCF_001592005.1	s__Bacillus sonorensis	82.9439	998	1413	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.75	99.65	0.97	0.94	11	-
GCF_001042475.2	s__Bacillus glycinifermentans	82.6094	966	1413	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.06	95.94	0.90	0.86	8	-
GCF_013155385.1	s__Bacillus sp013155385	79.9372	525	1413	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827555.1	s__Aeribacillus composti	76.7139	63	1413	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Aeribacillaceae;g__Aeribacillus	95.0	98.74	98.37	0.88	0.77	10	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:51,287] [INFO] GTDB search result was written to GCF_006094335.1_ASM609433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:51,288] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:51,292] [INFO] DFAST_QC result json was written to GCF_006094335.1_ASM609433v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:51,292] [INFO] DFAST_QC completed!
[2024-01-24 15:19:51,292] [INFO] Total running time: 0h1m15s