[2024-01-24 13:02:04,124] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:04,126] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:04,126] [INFO] DQC Reference Directory: /var/lib/cwl/stge976b848-9350-4c0e-9799-118697c3e86a/dqc_reference
[2024-01-24 13:02:05,372] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:05,373] [INFO] Task started: Prodigal
[2024-01-24 13:02:05,373] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfec9767-d66c-417f-8cb3-3120e5cc6db4/GCF_001584335.1_ASM158433v1_genomic.fna.gz | prodigal -d GCF_001584335.1_ASM158433v1_genomic.fna/cds.fna -a GCF_001584335.1_ASM158433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:15,866] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:15,867] [INFO] Task started: HMMsearch
[2024-01-24 13:02:15,867] [INFO] Running command: hmmsearch --tblout GCF_001584335.1_ASM158433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge976b848-9350-4c0e-9799-118697c3e86a/dqc_reference/reference_markers.hmm GCF_001584335.1_ASM158433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:16,116] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:16,118] [INFO] Found 6/6 markers.
[2024-01-24 13:02:16,155] [INFO] Query marker FASTA was written to GCF_001584335.1_ASM158433v1_genomic.fna/markers.fasta
[2024-01-24 13:02:16,155] [INFO] Task started: Blastn
[2024-01-24 13:02:16,155] [INFO] Running command: blastn -query GCF_001584335.1_ASM158433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge976b848-9350-4c0e-9799-118697c3e86a/dqc_reference/reference_markers.fasta -out GCF_001584335.1_ASM158433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:16,762] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:16,767] [INFO] Selected 15 target genomes.
[2024-01-24 13:02:16,767] [INFO] Target genome list was writen to GCF_001584335.1_ASM158433v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:16,773] [INFO] Task started: fastANI
[2024-01-24 13:02:16,773] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfec9767-d66c-417f-8cb3-3120e5cc6db4/GCF_001584335.1_ASM158433v1_genomic.fna.gz --refList GCF_001584335.1_ASM158433v1_genomic.fna/target_genomes.txt --output GCF_001584335.1_ASM158433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:28,639] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:28,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge976b848-9350-4c0e-9799-118697c3e86a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:28,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge976b848-9350-4c0e-9799-118697c3e86a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:28,651] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:02:28,651] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:28,651] [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 atrophaeus	strain=NRRL NRS 213	GCA_001584335.1	1452	1452	type	True	100.0	1376	1376	95	conclusive
Bacillus atrophaeus	strain=NBRC 15539	GCA_001591925.1	1452	1452	type	True	99.9903	1361	1376	95	conclusive
Bacillus halotolerans	strain=FJAT-2398	GCA_001637525.1	260554	260554	type	True	82.2924	935	1376	95	below_threshold
Bacillus halotolerans	strain=ATCC 25096	GCA_001517105.1	260554	260554	type	True	82.2316	945	1376	95	below_threshold
Bacillus mojavensis	strain=RO-H-1 = KCTC 3706	GCA_000507105.1	72360	72360	type	True	82.1083	912	1376	95	below_threshold
Bacillus inaquosorum	strain=KCTC 13429	GCA_003148415.1	483913	483913	type	True	82.0278	919	1376	95	below_threshold
Bacillus inaquosorum	strain=KCTC 13429	GCA_000332645.1	483913	483913	type	True	81.904	934	1376	95	below_threshold
Bacillus spizizenii	strain=NBRC 101239	GCA_007989785.1	96241	96241	type	True	81.8374	911	1376	95	below_threshold
Bacillus tequilensis	strain=KCTC 13622	GCA_000507145.1	227866	227866	type	True	81.6456	849	1376	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	81.6334	739	1376	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	81.4632	898	1376	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_002009095.1	135461	1423	type	True	81.4318	911	1376	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	81.269	780	1376	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:28,653] [INFO] DFAST Taxonomy check result was written to GCF_001584335.1_ASM158433v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:28,654] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:28,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:28,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge976b848-9350-4c0e-9799-118697c3e86a/dqc_reference/checkm_data
[2024-01-24 13:02:28,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:28,695] [INFO] Task started: CheckM
[2024-01-24 13:02:28,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001584335.1_ASM158433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001584335.1_ASM158433v1_genomic.fna/checkm_input GCF_001584335.1_ASM158433v1_genomic.fna/checkm_result
[2024-01-24 13:03:02,798] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:02,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:02,821] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:02,822] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:02,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001584335.1_ASM158433v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:02,822] [INFO] Task started: Blastn
[2024-01-24 13:03:02,822] [INFO] Running command: blastn -query GCF_001584335.1_ASM158433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge976b848-9350-4c0e-9799-118697c3e86a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001584335.1_ASM158433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:03,579] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:03,582] [INFO] Selected 11 target genomes.
[2024-01-24 13:03:03,583] [INFO] Target genome list was writen to GCF_001584335.1_ASM158433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:03,593] [INFO] Task started: fastANI
[2024-01-24 13:03:03,593] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfec9767-d66c-417f-8cb3-3120e5cc6db4/GCF_001584335.1_ASM158433v1_genomic.fna.gz --refList GCF_001584335.1_ASM158433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001584335.1_ASM158433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:12,881] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:12,891] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:12,891] [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_001584335.1	s__Bacillus atrophaeus	100.0	1376	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.59	97.38	0.93	0.89	38	conclusive
GCF_001517105.1	s__Bacillus halotolerans	82.2316	945	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4726	98.36	97.72	0.93	0.91	37	-
GCF_000245335.1	s__Bacillus mojavensis	82.0403	913	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4726	99.54	98.69	0.98	0.95	4	-
GCA_000332645.1	s__Bacillus inaquosorum	81.8909	936	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.57	97.81	0.94	0.91	20	-
GCF_000227465.1	s__Bacillus spizizenii	81.8372	923	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.29	95.06	0.95	0.89	32	-
GCF_004124315.1	s__Bacillus cabrialesii	81.7529	868	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	96.72	96.66	0.93	0.91	11	-
GCF_000507145.1	s__Bacillus tequilensis	81.6536	847	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.71	97.42	0.93	0.92	4	-
GCF_002153395.1	s__Bacillus subtilis_G	81.6384	880	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	97.72	0.95	0.93	3	-
GCF_000009045.1	s__Bacillus subtilis	81.4638	918	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	95.03	0.95	0.86	485	-
GCF_018613535.1	s__Bacillus sp018613535	81.2629	749	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.89	99.79	0.95	0.95	3	-
GCF_001584325.1	s__Bacillus nakamurai	81.1672	727	1376	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.07	99.07	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:12,894] [INFO] GTDB search result was written to GCF_001584335.1_ASM158433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:12,894] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:12,898] [INFO] DFAST_QC result json was written to GCF_001584335.1_ASM158433v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:12,898] [INFO] DFAST_QC completed!
[2024-01-24 13:03:12,898] [INFO] Total running time: 0h1m9s