[2024-01-24 14:55:24,966] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:24,968] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:24,968] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7755321-e6c4-419c-8565-61e58c10f6d2/dqc_reference
[2024-01-24 14:55:26,230] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:26,231] [INFO] Task started: Prodigal
[2024-01-24 14:55:26,231] [INFO] Running command: gunzip -c /var/lib/cwl/stg850f9cf2-ef19-4ef3-893f-be3042e9392e/GCF_001591925.1_ASM159192v1_genomic.fna.gz | prodigal -d GCF_001591925.1_ASM159192v1_genomic.fna/cds.fna -a GCF_001591925.1_ASM159192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:36,978] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:36,978] [INFO] Task started: HMMsearch
[2024-01-24 14:55:36,979] [INFO] Running command: hmmsearch --tblout GCF_001591925.1_ASM159192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7755321-e6c4-419c-8565-61e58c10f6d2/dqc_reference/reference_markers.hmm GCF_001591925.1_ASM159192v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:37,293] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:37,294] [INFO] Found 6/6 markers.
[2024-01-24 14:55:37,331] [INFO] Query marker FASTA was written to GCF_001591925.1_ASM159192v1_genomic.fna/markers.fasta
[2024-01-24 14:55:37,332] [INFO] Task started: Blastn
[2024-01-24 14:55:37,332] [INFO] Running command: blastn -query GCF_001591925.1_ASM159192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7755321-e6c4-419c-8565-61e58c10f6d2/dqc_reference/reference_markers.fasta -out GCF_001591925.1_ASM159192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:37,998] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:38,002] [INFO] Selected 15 target genomes.
[2024-01-24 14:55:38,003] [INFO] Target genome list was writen to GCF_001591925.1_ASM159192v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:38,019] [INFO] Task started: fastANI
[2024-01-24 14:55:38,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg850f9cf2-ef19-4ef3-893f-be3042e9392e/GCF_001591925.1_ASM159192v1_genomic.fna.gz --refList GCF_001591925.1_ASM159192v1_genomic.fna/target_genomes.txt --output GCF_001591925.1_ASM159192v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:50,626] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:50,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7755321-e6c4-419c-8565-61e58c10f6d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:50,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7755321-e6c4-419c-8565-61e58c10f6d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:50,638] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:55:50,639] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:50,639] [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=NBRC 15539	GCA_001591925.1	1452	1452	type	True	100.0	1370	1371	95	conclusive
Bacillus atrophaeus	strain=NRRL NRS 213	GCA_001584335.1	1452	1452	type	True	99.9985	1368	1371	95	conclusive
Bacillus halotolerans	strain=FJAT-2398	GCA_001637525.1	260554	260554	type	True	82.3023	940	1371	95	below_threshold
Bacillus mojavensis	strain=RO-H-1 = KCTC 3706	GCA_000507105.1	72360	72360	type	True	82.2387	886	1371	95	below_threshold
Bacillus halotolerans	strain=ATCC 25096	GCA_001517105.1	260554	260554	type	True	82.227	933	1371	95	below_threshold
Bacillus inaquosorum	strain=KCTC 13429	GCA_003148415.1	483913	483913	type	True	81.9428	908	1371	95	below_threshold
Bacillus inaquosorum	strain=KCTC 13429	GCA_000332645.1	483913	483913	type	True	81.9052	927	1371	95	below_threshold
Bacillus spizizenii	strain=NBRC 101239	GCA_007989785.1	96241	96241	type	True	81.7785	912	1371	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	81.7133	740	1371	95	below_threshold
Bacillus tequilensis	strain=KCTC 13622	GCA_000507145.1	227866	227866	type	True	81.6837	837	1371	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	81.5271	881	1371	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_002009095.1	135461	1423	type	True	81.4836	873	1371	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	81.3355	764	1371	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:50,641] [INFO] DFAST Taxonomy check result was written to GCF_001591925.1_ASM159192v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:50,641] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:50,641] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:50,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7755321-e6c4-419c-8565-61e58c10f6d2/dqc_reference/checkm_data
[2024-01-24 14:55:50,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:50,684] [INFO] Task started: CheckM
[2024-01-24 14:55:50,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591925.1_ASM159192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591925.1_ASM159192v1_genomic.fna/checkm_input GCF_001591925.1_ASM159192v1_genomic.fna/checkm_result
[2024-01-24 14:56:29,568] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:29,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:29,596] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:29,596] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:29,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591925.1_ASM159192v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:29,597] [INFO] Task started: Blastn
[2024-01-24 14:56:29,597] [INFO] Running command: blastn -query GCF_001591925.1_ASM159192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7755321-e6c4-419c-8565-61e58c10f6d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591925.1_ASM159192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:30,402] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:30,406] [INFO] Selected 11 target genomes.
[2024-01-24 14:56:30,406] [INFO] Target genome list was writen to GCF_001591925.1_ASM159192v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:30,413] [INFO] Task started: fastANI
[2024-01-24 14:56:30,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg850f9cf2-ef19-4ef3-893f-be3042e9392e/GCF_001591925.1_ASM159192v1_genomic.fna.gz --refList GCF_001591925.1_ASM159192v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591925.1_ASM159192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:40,114] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:40,124] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:40,125] [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	99.9985	1368	1371	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	82.2294	933	1371	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	82.2178	891	1371	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	81.9056	928	1371	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	81.7957	907	1371	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	81.785	846	1371	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	81.6807	837	1371	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	81.6783	871	1371	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	81.5257	880	1371	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	81.2326	746	1371	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	81.1998	725	1371	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 14:56:40,127] [INFO] GTDB search result was written to GCF_001591925.1_ASM159192v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:40,127] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:40,131] [INFO] DFAST_QC result json was written to GCF_001591925.1_ASM159192v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:40,131] [INFO] DFAST_QC completed!
[2024-01-24 14:56:40,131] [INFO] Total running time: 0h1m15s