[2024-01-25 18:08:35,793] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:35,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:35,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgfefed5ea-4f1e-478e-b5e9-64efefe85e15/dqc_reference
[2024-01-25 18:08:36,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:36,963] [INFO] Task started: Prodigal
[2024-01-25 18:08:36,963] [INFO] Running command: gunzip -c /var/lib/cwl/stg3218d4e2-551c-4ad7-9df9-31b7a34e5ec7/GCF_001591565.1_ASM159156v1_genomic.fna.gz | prodigal -d GCF_001591565.1_ASM159156v1_genomic.fna/cds.fna -a GCF_001591565.1_ASM159156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:42,992] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:42,993] [INFO] Task started: HMMsearch
[2024-01-25 18:08:42,993] [INFO] Running command: hmmsearch --tblout GCF_001591565.1_ASM159156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfefed5ea-4f1e-478e-b5e9-64efefe85e15/dqc_reference/reference_markers.hmm GCF_001591565.1_ASM159156v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:43,224] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:43,226] [INFO] Found 6/6 markers.
[2024-01-25 18:08:43,257] [INFO] Query marker FASTA was written to GCF_001591565.1_ASM159156v1_genomic.fna/markers.fasta
[2024-01-25 18:08:43,258] [INFO] Task started: Blastn
[2024-01-25 18:08:43,258] [INFO] Running command: blastn -query GCF_001591565.1_ASM159156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfefed5ea-4f1e-478e-b5e9-64efefe85e15/dqc_reference/reference_markers.fasta -out GCF_001591565.1_ASM159156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:43,841] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:43,845] [INFO] Selected 30 target genomes.
[2024-01-25 18:08:43,846] [INFO] Target genome list was writen to GCF_001591565.1_ASM159156v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:43,870] [INFO] Task started: fastANI
[2024-01-25 18:08:43,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg3218d4e2-551c-4ad7-9df9-31b7a34e5ec7/GCF_001591565.1_ASM159156v1_genomic.fna.gz --refList GCF_001591565.1_ASM159156v1_genomic.fna/target_genomes.txt --output GCF_001591565.1_ASM159156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:03,851] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:03,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfefed5ea-4f1e-478e-b5e9-64efefe85e15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:03,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfefed5ea-4f1e-478e-b5e9-64efefe85e15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:03,867] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:09:03,868] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:09:03,868] [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
Priestia megaterium	strain=ATCC 14581	GCA_006094495.1	1404	1404	type	True	79.5923	412	1174	95	below_threshold
Priestia megaterium	strain=NCTC10342	GCA_900445485.1	1404	1404	type	True	79.5697	409	1174	95	below_threshold
Priestia megaterium	strain=ATCC 14581	GCA_000832985.1	1404	1404	type	True	79.5049	420	1174	95	below_threshold
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	79.4198	409	1174	95	below_threshold
Priestia megaterium	strain=ATCC 14581	GCA_900113355.1	1404	1404	suspected-type	True	79.3417	410	1174	95	below_threshold
Priestia aryabhattai	strain=B8W22	GCA_000956595.1	412384	412384	type	True	79.2012	404	1174	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	78.2104	96	1174	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	78.186	273	1174	95	below_threshold
Priestia koreensis	strain=DSM 16467	GCA_001274935.1	284581	284581	type	True	77.6367	202	1174	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	77.4939	104	1174	95	below_threshold
Bacillus tropicus	strain=N24	GCA_001884035.1	2026188	2026188	type	True	77.1652	104	1174	95	below_threshold
Bacillus tepidiphilus	strain=SYSU G01002	GCA_009466385.1	2652445	2652445	type	True	77.0085	86	1174	95	below_threshold
Cytobacillus luteolus	strain=YIM 93174	GCA_014982515.1	682179	682179	type	True	77.0033	111	1174	95	below_threshold
Cytobacillus luteolus	strain=DSM 22388	GCA_017873715.1	682179	682179	type	True	76.9865	107	1174	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_000007825.1	1396	1396	suspected-type	True	76.9773	104	1174	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	76.9718	115	1174	95	below_threshold
Bacillus massilionigeriensis	strain=Marseille-P2384	GCA_900117315.1	1805475	1805475	type	True	76.9708	62	1174	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.9679	100	1174	95	below_threshold
Priestia taiwanensis	strain=CGMCC 1.12698	GCA_014638355.1	1347902	1347902	type	True	76.922	90	1174	95	below_threshold
Priestia taiwanensis	strain=DSM 27845	GCA_016908755.1	1347902	1347902	type	True	76.9088	88	1174	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.8944	118	1174	95	below_threshold
Peribacillus frigoritolerans	strain=DSM 8801	GCA_024169475.1	450367	450367	type	True	76.8498	58	1174	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_004801455.1	2567941	2567941	type	True	76.8448	115	1174	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_011008855.1	2672567	2672567	type	True	76.7459	77	1174	95	below_threshold
Peribacillus frigoritolerans	strain=FJAT-2396	GCA_001636405.1	450367	450367	type	True	76.6928	59	1174	95	below_threshold
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	76.6466	62	1174	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:03,869] [INFO] DFAST Taxonomy check result was written to GCF_001591565.1_ASM159156v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:03,870] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:03,870] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:03,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfefed5ea-4f1e-478e-b5e9-64efefe85e15/dqc_reference/checkm_data
[2024-01-25 18:09:03,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:03,912] [INFO] Task started: CheckM
[2024-01-25 18:09:03,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591565.1_ASM159156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591565.1_ASM159156v1_genomic.fna/checkm_input GCF_001591565.1_ASM159156v1_genomic.fna/checkm_result
[2024-01-25 18:09:27,118] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:27,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:27,138] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:27,138] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:27,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591565.1_ASM159156v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:27,138] [INFO] Task started: Blastn
[2024-01-25 18:09:27,138] [INFO] Running command: blastn -query GCF_001591565.1_ASM159156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfefed5ea-4f1e-478e-b5e9-64efefe85e15/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591565.1_ASM159156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:27,946] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:27,950] [INFO] Selected 15 target genomes.
[2024-01-25 18:09:27,950] [INFO] Target genome list was writen to GCF_001591565.1_ASM159156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:27,966] [INFO] Task started: fastANI
[2024-01-25 18:09:27,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg3218d4e2-551c-4ad7-9df9-31b7a34e5ec7/GCF_001591565.1_ASM159156v1_genomic.fna.gz --refList GCF_001591565.1_ASM159156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591565.1_ASM159156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:40,218] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:40,228] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:40,228] [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_001591565.1	s__Priestia flexa	100.0	1163	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	99.12	98.83	0.89	0.87	15	conclusive
GCF_002265635.1	s__Priestia aryabhattai_A	92.1254	1029	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	98.53	98.16	0.94	0.93	4	-
GCF_008180335.1	s__Priestia megaterium_B	79.7765	481	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832985.1	s__Priestia megaterium	79.5054	420	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.5311	96.82	95.69	0.88	0.73	151	-
GCF_009497655.1	s__Priestia megaterium_A	79.2578	401	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	96.022	98.08	96.36	0.92	0.89	34	-
GCF_000956595.1	s__Priestia aryabhattai	79.1894	405	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	96.022	97.07	96.58	0.92	0.91	12	-
GCF_003184905.1	s__Priestia sp003184905	78.6736	283	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280205.1	s__Robertmurraya yapensis	78.3972	95	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016909075.1	s__Priestia iocasae	78.186	273	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274935.1	s__Bacillus_AG koreensis	77.6477	203	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Bacillus_AG	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002571225.1	s__Bacillus_A sp002571225	77.1792	115	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001884035.1	s__Bacillus_A tropicus	77.1522	103	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.3658	96.52	95.65	0.91	0.83	109	-
GCF_014217835.1	s__Metabacillus litoralis_A	77.0874	104	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_009466385.1	s__Bacillus_BN tepidiphilus	77.0085	86	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638355.1	s__Priestia_D taiwanensis	76.916	88	1174	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Priestia_D	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:40,230] [INFO] GTDB search result was written to GCF_001591565.1_ASM159156v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:40,230] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:40,234] [INFO] DFAST_QC result json was written to GCF_001591565.1_ASM159156v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:40,234] [INFO] DFAST_QC completed!
[2024-01-25 18:09:40,234] [INFO] Total running time: 0h1m4s