[2024-01-24 13:01:25,485] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:25,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:25,519] [INFO] DQC Reference Directory: /var/lib/cwl/stgac32b490-8cfe-4b54-97a6-d716bfc531f3/dqc_reference
[2024-01-24 13:01:26,933] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:26,934] [INFO] Task started: Prodigal
[2024-01-24 13:01:26,934] [INFO] Running command: gunzip -c /var/lib/cwl/stg75e394f2-40c9-4347-8767-a7c8da63b68d/GCF_001315045.1_ASM131504v1_genomic.fna.gz | prodigal -d GCF_001315045.1_ASM131504v1_genomic.fna/cds.fna -a GCF_001315045.1_ASM131504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:36,388] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:36,388] [INFO] Task started: HMMsearch
[2024-01-24 13:01:36,389] [INFO] Running command: hmmsearch --tblout GCF_001315045.1_ASM131504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac32b490-8cfe-4b54-97a6-d716bfc531f3/dqc_reference/reference_markers.hmm GCF_001315045.1_ASM131504v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:36,713] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:36,716] [INFO] Found 6/6 markers.
[2024-01-24 13:01:36,759] [INFO] Query marker FASTA was written to GCF_001315045.1_ASM131504v1_genomic.fna/markers.fasta
[2024-01-24 13:01:36,760] [INFO] Task started: Blastn
[2024-01-24 13:01:36,760] [INFO] Running command: blastn -query GCF_001315045.1_ASM131504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac32b490-8cfe-4b54-97a6-d716bfc531f3/dqc_reference/reference_markers.fasta -out GCF_001315045.1_ASM131504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:37,403] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:37,406] [INFO] Selected 26 target genomes.
[2024-01-24 13:01:37,406] [INFO] Target genome list was writen to GCF_001315045.1_ASM131504v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:37,417] [INFO] Task started: fastANI
[2024-01-24 13:01:37,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg75e394f2-40c9-4347-8767-a7c8da63b68d/GCF_001315045.1_ASM131504v1_genomic.fna.gz --refList GCF_001315045.1_ASM131504v1_genomic.fna/target_genomes.txt --output GCF_001315045.1_ASM131504v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:57,663] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:57,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac32b490-8cfe-4b54-97a6-d716bfc531f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:57,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac32b490-8cfe-4b54-97a6-d716bfc531f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:57,680] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:57,680] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:57,681] [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 wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	100.0	1413	1422	95	conclusive
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_001315045.1	127891	127891	type	True	100.0	1413	1422	95	conclusive
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	81.3951	634	1422	95	below_threshold
Alkalihalobacillus hemicellulosilyticus	strain=JCM 9152	GCA_000513115.1	127886	127886	type	True	80.9395	200	1422	95	below_threshold
Alkalihalobacillus hemicellulosilyticus	strain=JCM 9152	GCA_001315065.1	127886	127886	type	True	80.9395	200	1422	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	80.1152	411	1422	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	78.701	365	1422	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	78.6807	365	1422	95	below_threshold
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	78.2339	246	1422	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	78.0341	237	1422	95	below_threshold
Halalkalibacterium ligniniphilum	strain=L1	GCA_000334155.1	1134413	1134413	type	True	77.4202	136	1422	95	below_threshold
Anaerobacillus isosaccharinicus	strain=NB2006	GCA_001866075.3	1532552	1532552	type	True	77.2847	114	1422	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	76.7971	60	1422	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	76.6109	86	1422	95	below_threshold
Bacillus thuringiensis	strain=ATCC 10792	GCA_000161615.1	1428	1428	suspected-type	True	76.5894	68	1422	95	below_threshold
Bacillus thuringiensis	strain=ATCC 10792	GCA_002119445.1	1428	1428	suspected-type	True	76.4208	59	1422	95	below_threshold
Salipaludibacillus neizhouensis	strain=KCTC 13187	GCA_003615245.1	885475	885475	type	True	76.3677	69	1422	95	below_threshold
Gottfriedia acidiceleris	strain=DSM 18954	GCA_002128425.1	371036	371036	type	True	76.3389	69	1422	95	below_threshold
Bacillus nitratireducens	strain=4049	GCA_001884135.1	2026193	2026193	type	True	76.2723	61	1422	95	below_threshold
Gottfriedia acidiceleris	strain=NRRL B-41736	GCA_002156925.1	371036	371036	type	True	76.0561	67	1422	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:57,682] [INFO] DFAST Taxonomy check result was written to GCF_001315045.1_ASM131504v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:57,683] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:57,683] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:57,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac32b490-8cfe-4b54-97a6-d716bfc531f3/dqc_reference/checkm_data
[2024-01-24 13:01:57,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:57,730] [INFO] Task started: CheckM
[2024-01-24 13:01:57,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001315045.1_ASM131504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001315045.1_ASM131504v1_genomic.fna/checkm_input GCF_001315045.1_ASM131504v1_genomic.fna/checkm_result
[2024-01-24 13:02:30,344] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:30,346] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:30,369] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:30,369] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:30,370] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001315045.1_ASM131504v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:30,370] [INFO] Task started: Blastn
[2024-01-24 13:02:30,370] [INFO] Running command: blastn -query GCF_001315045.1_ASM131504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac32b490-8cfe-4b54-97a6-d716bfc531f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001315045.1_ASM131504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:31,104] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:31,109] [INFO] Selected 24 target genomes.
[2024-01-24 13:02:31,109] [INFO] Target genome list was writen to GCF_001315045.1_ASM131504v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:31,126] [INFO] Task started: fastANI
[2024-01-24 13:02:31,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg75e394f2-40c9-4347-8767-a7c8da63b68d/GCF_001315045.1_ASM131504v1_genomic.fna.gz --refList GCF_001315045.1_ASM131504v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001315045.1_ASM131504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:49,824] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:49,853] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:49,853] [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_000513095.1	s__Bacillus_L wakoensis	100.0	1413	1422	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	conclusive
GCF_000787375.1	s__Bacillus_L okhensis	81.4657	627	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513115.1	s__Bacillus_L hemicellulosilyticus	80.9088	201	1422	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_000513135.1	s__Bacillus_L akibai	80.0723	414	1422	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_002109385.1	s__Bacillus_L krulwichiae	78.7002	366	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007830185.1	s__Bacillus_L nanhaiisediminis	78.2333	246	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017939705.1	s__Bacillus_L sp017939705	78.0694	235	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310635.1	s__Bacillus_L sp001310635	77.7246	160	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797395.1	s__45385 sp002797395	77.6675	181	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000334155.1	s__Bacillus_AN ligniniphilus	77.4302	136	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_AN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866075.3	s__Anaerobacillus isosaccharinicus	77.2286	114	1422	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_002335805.1	s__FJAT-45350 sp002335805	77.2176	153	1422	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_018742245.1	s__Bacillus_A cereus_U	77.1182	59	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.53	95.81	0.88	0.84	34	-
GCF_002019795.1	s__Bacillus_AO alkalicellulosilyticus	77.0234	127	1422	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_002200015.1	s__Bacillus_A cereus_AZ	76.7281	62	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	96.9563	N/A	N/A	N/A	N/A	1	-
GCF_016820555.1	s__FJAT-46582 sp016820555	76.608	65	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019645.1	s__Litchfieldia alkalitelluris	76.588	86	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006384875.1	s__Bacillus_A bombysepticus	76.5513	63	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	97.0513	98.50	97.53	0.88	0.81	586	-
GCF_001595725.1	s__Bacillus_A thuringiensis_K	76.5463	64	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	96.827	99.05	98.75	0.91	0.78	20	-
GCF_002567495.1	s__Bacillus_A cereus_AQ	76.4624	69	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	98.10	96.80	0.92	0.88	3	-
GCF_001884135.1	s__Bacillus_A nitratireducens	76.2821	61	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	98.14	95.62	0.90	0.85	78	-
GCF_002128425.1	s__Gottfriedia acidiceler	76.2598	68	1422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	98.12	96.26	0.94	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:49,855] [INFO] GTDB search result was written to GCF_001315045.1_ASM131504v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:49,855] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:49,861] [INFO] DFAST_QC result json was written to GCF_001315045.1_ASM131504v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:49,861] [INFO] DFAST_QC completed!
[2024-01-24 13:02:49,861] [INFO] Total running time: 0h1m24s