[2024-01-24 14:47:20,225] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:20,227] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:20,227] [INFO] DQC Reference Directory: /var/lib/cwl/stgad34f1bc-ff8d-4761-a36d-6b9a84fa0abd/dqc_reference
[2024-01-24 14:47:21,501] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:21,502] [INFO] Task started: Prodigal
[2024-01-24 14:47:21,502] [INFO] Running command: gunzip -c /var/lib/cwl/stga1f7d2b0-fd82-44ec-b2dd-9ef6acc41305/GCF_002009135.1_ASM200913v1_genomic.fna.gz | prodigal -d GCF_002009135.1_ASM200913v1_genomic.fna/cds.fna -a GCF_002009135.1_ASM200913v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:32,716] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:32,716] [INFO] Task started: HMMsearch
[2024-01-24 14:47:32,716] [INFO] Running command: hmmsearch --tblout GCF_002009135.1_ASM200913v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad34f1bc-ff8d-4761-a36d-6b9a84fa0abd/dqc_reference/reference_markers.hmm GCF_002009135.1_ASM200913v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:33,105] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:33,108] [INFO] Found 6/6 markers.
[2024-01-24 14:47:33,153] [INFO] Query marker FASTA was written to GCF_002009135.1_ASM200913v1_genomic.fna/markers.fasta
[2024-01-24 14:47:33,154] [INFO] Task started: Blastn
[2024-01-24 14:47:33,154] [INFO] Running command: blastn -query GCF_002009135.1_ASM200913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad34f1bc-ff8d-4761-a36d-6b9a84fa0abd/dqc_reference/reference_markers.fasta -out GCF_002009135.1_ASM200913v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:33,743] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:33,746] [INFO] Selected 10 target genomes.
[2024-01-24 14:47:33,747] [INFO] Target genome list was writen to GCF_002009135.1_ASM200913v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:33,752] [INFO] Task started: fastANI
[2024-01-24 14:47:33,752] [INFO] Running command: fastANI --query /var/lib/cwl/stga1f7d2b0-fd82-44ec-b2dd-9ef6acc41305/GCF_002009135.1_ASM200913v1_genomic.fna.gz --refList GCF_002009135.1_ASM200913v1_genomic.fna/target_genomes.txt --output GCF_002009135.1_ASM200913v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:43,915] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:43,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad34f1bc-ff8d-4761-a36d-6b9a84fa0abd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:43,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad34f1bc-ff8d-4761-a36d-6b9a84fa0abd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:43,925] [INFO] Found 9 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 14:47:43,926] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:43,926] [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 subtilis subsp. subtilis	strain=168	GCA_002009135.1	135461	1423	type	True	100.0	1405	1405	95	conclusive
Bacillus subtilis subsp. subtilis	strain=168	GCA_002009095.1	135461	1423	type	True	99.998	1405	1405	95	conclusive
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	99.9928	1400	1405	95	conclusive
Bacillus subtilis subsp. subtilis	strain=6051-HGW	GCA_000344745.1	135461	1423	type	True	99.9928	1404	1405	95	conclusive
Bacillus subtilis subsp. subtilis	strain=NCIB 3610	GCA_000186085.1	135461	1423	type	True	99.9792	1403	1405	95	conclusive
Bacillus subtilis subsp. subtilis	strain=DSM 10	GCA_014389245.2	135461	1423	type	True	99.9772	1383	1405	95	conclusive
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	91.3464	1016	1405	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	90.5087	1073	1405	95	below_threshold
Neobacillus notoginsengisoli	strain=JCM 30743	GCA_003515685.1	1578198	1578198	type	True	77.0998	55	1405	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:43,927] [INFO] DFAST Taxonomy check result was written to GCF_002009135.1_ASM200913v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:43,929] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:43,929] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:43,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad34f1bc-ff8d-4761-a36d-6b9a84fa0abd/dqc_reference/checkm_data
[2024-01-24 14:47:43,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:43,979] [INFO] Task started: CheckM
[2024-01-24 14:47:43,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002009135.1_ASM200913v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002009135.1_ASM200913v1_genomic.fna/checkm_input GCF_002009135.1_ASM200913v1_genomic.fna/checkm_result
[2024-01-24 14:48:23,374] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:23,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:23,399] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:23,400] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:23,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002009135.1_ASM200913v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:23,401] [INFO] Task started: Blastn
[2024-01-24 14:48:23,401] [INFO] Running command: blastn -query GCF_002009135.1_ASM200913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad34f1bc-ff8d-4761-a36d-6b9a84fa0abd/dqc_reference/reference_markers_gtdb.fasta -out GCF_002009135.1_ASM200913v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:24,151] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:24,156] [INFO] Selected 8 target genomes.
[2024-01-24 14:48:24,156] [INFO] Target genome list was writen to GCF_002009135.1_ASM200913v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:24,163] [INFO] Task started: fastANI
[2024-01-24 14:48:24,163] [INFO] Running command: fastANI --query /var/lib/cwl/stga1f7d2b0-fd82-44ec-b2dd-9ef6acc41305/GCF_002009135.1_ASM200913v1_genomic.fna.gz --refList GCF_002009135.1_ASM200913v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002009135.1_ASM200913v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:32,539] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:32,546] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:32,547] [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_000009045.1	s__Bacillus subtilis	99.9935	1404	1405	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	95.03	0.95	0.86	485	conclusive
GCF_000227465.1	s__Bacillus spizizenii	92.8898	1243	1405	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.29	95.06	0.95	0.89	32	-
GCA_000332645.1	s__Bacillus inaquosorum	92.6144	1250	1405	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.57	97.81	0.94	0.91	20	-
GCF_004124315.1	s__Bacillus cabrialesii	92.24	1241	1405	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	96.72	96.66	0.93	0.91	11	-
GCF_002153395.1	s__Bacillus subtilis_G	91.3329	1190	1405	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	97.72	0.95	0.93	3	-
GCF_000507145.1	s__Bacillus tequilensis	91.2705	1158	1405	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.71	97.42	0.93	0.92	4	-
GCF_004116955.1	s__Bacillus vallismortis	90.6127	1210	1405	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.90	97.68	0.96	0.94	6	-
GCF_010093085.1	s__Bacillus sp010093085	89.6171	1049	1405	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:32,548] [INFO] GTDB search result was written to GCF_002009135.1_ASM200913v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:32,549] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:32,552] [INFO] DFAST_QC result json was written to GCF_002009135.1_ASM200913v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:32,552] [INFO] DFAST_QC completed!
[2024-01-24 14:48:32,552] [INFO] Total running time: 0h1m12s