[2024-01-24 12:21:48,660] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:48,662] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:48,662] [INFO] DQC Reference Directory: /var/lib/cwl/stg53da5179-f608-4ac8-9137-663447ee0a2a/dqc_reference
[2024-01-24 12:21:49,872] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:49,873] [INFO] Task started: Prodigal
[2024-01-24 12:21:49,873] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d44a7d5-9d36-4d20-842e-d9ad7f2655f2/GCF_000621445.1_ASM62144v1_genomic.fna.gz | prodigal -d GCF_000621445.1_ASM62144v1_genomic.fna/cds.fna -a GCF_000621445.1_ASM62144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:00,321] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:00,322] [INFO] Task started: HMMsearch
[2024-01-24 12:22:00,322] [INFO] Running command: hmmsearch --tblout GCF_000621445.1_ASM62144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53da5179-f608-4ac8-9137-663447ee0a2a/dqc_reference/reference_markers.hmm GCF_000621445.1_ASM62144v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:00,756] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:00,757] [INFO] Found 6/6 markers.
[2024-01-24 12:22:00,802] [INFO] Query marker FASTA was written to GCF_000621445.1_ASM62144v1_genomic.fna/markers.fasta
[2024-01-24 12:22:00,803] [INFO] Task started: Blastn
[2024-01-24 12:22:00,803] [INFO] Running command: blastn -query GCF_000621445.1_ASM62144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53da5179-f608-4ac8-9137-663447ee0a2a/dqc_reference/reference_markers.fasta -out GCF_000621445.1_ASM62144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:01,487] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:01,491] [INFO] Selected 24 target genomes.
[2024-01-24 12:22:01,491] [INFO] Target genome list was writen to GCF_000621445.1_ASM62144v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:01,786] [INFO] Task started: fastANI
[2024-01-24 12:22:01,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d44a7d5-9d36-4d20-842e-d9ad7f2655f2/GCF_000621445.1_ASM62144v1_genomic.fna.gz --refList GCF_000621445.1_ASM62144v1_genomic.fna/target_genomes.txt --output GCF_000621445.1_ASM62144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:21,636] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:21,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53da5179-f608-4ac8-9137-663447ee0a2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:21,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53da5179-f608-4ac8-9137-663447ee0a2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:21,653] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:21,653] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:21,653] [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
Alkalihalobacillus bogoriensis	strain=ATCC BAA-922	GCA_000621445.1	246272	246272	type	True	100.0	1638	1641	95	conclusive
Bacillus alkalicellulosilyticus	strain=FJAT-44921	GCA_002019795.1	1912214	1912214	type	True	78.1472	312	1641	95	below_threshold
Alkalihalobacillus trypoxylicola	strain=KCTC 13244	GCA_001590785.1	519424	519424	type	True	77.4103	112	1641	95	below_threshold
Alkalihalobacillus trypoxylicola	strain=NBRC 102646	GCA_001592025.1	519424	519424	type	True	77.2833	108	1641	95	below_threshold
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	77.1114	216	1641	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	77.0587	159	1641	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_001315045.1	127891	127891	type	True	77.0587	159	1641	95	below_threshold
Alkalihalobacterium elongatum	strain=MEB199	GCA_019024285.1	2675466	2675466	type	True	77.0219	198	1641	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	76.8207	140	1641	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	76.8198	67	1641	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	76.8158	171	1641	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	76.7839	170	1641	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_002009555.1	38875	38875	type	True	76.577	63	1641	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.4556	84	1641	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.3901	67	1641	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.3446	93	1641	95	below_threshold
Anoxybacillus gonensis	strain=G2	GCA_001187595.1	198467	198467	suspected-type	True	76.1282	63	1641	95	below_threshold
Bacillus solimangrovi	strain=GH2-4	GCA_001742425.1	1305675	1305675	type	True	76.1267	74	1641	95	below_threshold
Anoxybacillus gonensis	strain=G2	GCA_000770375.1	198467	198467	suspected-type	True	76.0892	60	1641	95	below_threshold
Bacillus andreraoultii	strain=SIT1	GCA_001244735.1	1499685	1499685	type	True	76.0015	74	1641	95	below_threshold
Metabacillus fastidiosus	strain=NBRC 101226	GCA_001591625.1	1458	1458	type	True	75.8321	76	1641	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:21,655] [INFO] DFAST Taxonomy check result was written to GCF_000621445.1_ASM62144v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:21,655] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:21,656] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:21,656] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53da5179-f608-4ac8-9137-663447ee0a2a/dqc_reference/checkm_data
[2024-01-24 12:22:21,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:21,712] [INFO] Task started: CheckM
[2024-01-24 12:22:21,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621445.1_ASM62144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621445.1_ASM62144v1_genomic.fna/checkm_input GCF_000621445.1_ASM62144v1_genomic.fna/checkm_result
[2024-01-24 12:22:58,625] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:58,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:58,643] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:58,643] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:58,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621445.1_ASM62144v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:58,644] [INFO] Task started: Blastn
[2024-01-24 12:22:58,644] [INFO] Running command: blastn -query GCF_000621445.1_ASM62144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53da5179-f608-4ac8-9137-663447ee0a2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621445.1_ASM62144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:59,771] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:59,779] [INFO] Selected 22 target genomes.
[2024-01-24 12:22:59,779] [INFO] Target genome list was writen to GCF_000621445.1_ASM62144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:59,799] [INFO] Task started: fastANI
[2024-01-24 12:22:59,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d44a7d5-9d36-4d20-842e-d9ad7f2655f2/GCF_000621445.1_ASM62144v1_genomic.fna.gz --refList GCF_000621445.1_ASM62144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621445.1_ASM62144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:18,610] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:18,633] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:18,633] [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_000621445.1	s__Bacillus_AO bogoriensis	100.0	1638	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002019795.1	s__Bacillus_AO alkalicellulosilyticus	78.132	311	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590785.1	s__Alkalihalobacillus trypoxylicola	77.4103	112	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	98.48	96.97	0.95	0.90	3	-
GCF_017745675.1	s__Bacillus_BH sp017745675	77.2866	207	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002335805.1	s__FJAT-45350 sp002335805	77.1613	189	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__FJAT-45350	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019605.1	s__Bacillus_BH alkalinitrilicus	77.1114	216	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	97.46	97.46	0.83	0.83	2	-
GCF_000513095.1	s__Bacillus_L wakoensis	77.0587	159	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	0.99	0.99	2	-
GCF_019024285.1	s__Bacillus_BH sp019024285	77.0219	198	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797325.1	s__Bacillus_S sp002797325	76.9181	125	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866075.3	s__Anaerobacillus isosaccharinicus	76.8571	148	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513115.1	s__Bacillus_L hemicellulosilyticus	76.8545	138	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003726095.1	s__Niallia circulans_A	76.8007	75	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.27	98.85	0.92	0.89	8	-
GCF_000513135.1	s__Bacillus_L akibai	76.7839	170	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009818105.1	s__Anaerobacillus_A sp009818105	76.4679	65	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563635.1	s__Anaerobacillus_A sp002563635	76.3478	62	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	96.09	95.80	0.90	0.90	3	-
GCF_001187595.1	s__Anoxybacillus gonensis	76.1258	66	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	98.51	96.49	0.91	0.88	6	-
GCF_001742425.1	s__Bacillus_AV solimangrovi	76.0775	72	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Bacillaceae_N;g__Bacillus_AV	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742685.1	s__Anoxybacillus flavithermus_E	76.0437	52	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	99.92	99.92	0.93	0.93	2	-
GCF_001244735.1	s__Bacillus_J andreraoultii	75.9205	74	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_J	95.0	100.00	100.00	0.99	0.99	4	-
GCF_001591625.1	s__Metabacillus fastidiosus	75.8321	76	1641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:18,634] [INFO] GTDB search result was written to GCF_000621445.1_ASM62144v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:18,635] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:18,639] [INFO] DFAST_QC result json was written to GCF_000621445.1_ASM62144v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:18,639] [INFO] DFAST_QC completed!
[2024-01-24 12:23:18,639] [INFO] Total running time: 0h1m30s