[2024-01-24 12:13:59,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:59,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:59,061] [INFO] DQC Reference Directory: /var/lib/cwl/stgac912a81-f920-45dd-9c41-a5da646534d1/dqc_reference
[2024-01-24 12:14:00,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:00,482] [INFO] Task started: Prodigal
[2024-01-24 12:14:00,482] [INFO] Running command: gunzip -c /var/lib/cwl/stge8c9f791-a541-4937-99ec-9f2bd4990f44/GCF_002019795.1_ASM201979v1_genomic.fna.gz | prodigal -d GCF_002019795.1_ASM201979v1_genomic.fna/cds.fna -a GCF_002019795.1_ASM201979v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:10,399] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:10,399] [INFO] Task started: HMMsearch
[2024-01-24 12:14:10,399] [INFO] Running command: hmmsearch --tblout GCF_002019795.1_ASM201979v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac912a81-f920-45dd-9c41-a5da646534d1/dqc_reference/reference_markers.hmm GCF_002019795.1_ASM201979v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:10,798] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:10,799] [INFO] Found 6/6 markers.
[2024-01-24 12:14:10,844] [INFO] Query marker FASTA was written to GCF_002019795.1_ASM201979v1_genomic.fna/markers.fasta
[2024-01-24 12:14:10,845] [INFO] Task started: Blastn
[2024-01-24 12:14:10,845] [INFO] Running command: blastn -query GCF_002019795.1_ASM201979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac912a81-f920-45dd-9c41-a5da646534d1/dqc_reference/reference_markers.fasta -out GCF_002019795.1_ASM201979v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:11,556] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:11,559] [INFO] Selected 24 target genomes.
[2024-01-24 12:14:11,560] [INFO] Target genome list was writen to GCF_002019795.1_ASM201979v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:11,568] [INFO] Task started: fastANI
[2024-01-24 12:14:11,568] [INFO] Running command: fastANI --query /var/lib/cwl/stge8c9f791-a541-4937-99ec-9f2bd4990f44/GCF_002019795.1_ASM201979v1_genomic.fna.gz --refList GCF_002019795.1_ASM201979v1_genomic.fna/target_genomes.txt --output GCF_002019795.1_ASM201979v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:30,861] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:30,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac912a81-f920-45dd-9c41-a5da646534d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:30,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac912a81-f920-45dd-9c41-a5da646534d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:30,880] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:30,880] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:30,880] [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 alkalicellulosilyticus	strain=FJAT-44921	GCA_002019795.1	1912214	1912214	type	True	100.0	1577	1582	95	conclusive
Alkalihalobacillus clausii	strain=DSM 8716	GCA_002250115.1	79880	79880	suspected-type	True	80.4417	60	1582	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	78.8228	68	1582	95	below_threshold
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	78.3801	198	1582	95	below_threshold
Anaerobacillus isosaccharinicus	strain=NB2006	GCA_001866075.3	1532552	1532552	type	True	78.2388	130	1582	95	below_threshold
Alkalihalobacillus bogoriensis	strain=ATCC BAA-922	GCA_000621445.1	246272	246272	type	True	78.0195	331	1582	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	77.4998	133	1582	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	77.4782	134	1582	95	below_threshold
Alkalihalobacillus trypoxylicola	strain=KCTC 13244	GCA_001590785.1	519424	519424	type	True	77.1643	81	1582	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	77.1631	89	1582	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	76.9612	106	1582	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	76.8222	115	1582	95	below_threshold
Pseudalkalibacillus decolorationis	strain=DSM 14890	GCA_024609785.1	163879	163879	type	True	76.8103	52	1582	95	below_threshold
Texcoconibacillus texcoconensis	strain=DSM 24696	GCA_014202575.1	1095777	1095777	type	True	76.779	62	1582	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	76.7094	94	1582	95	below_threshold
Alkalihalobacillus trypoxylicola	strain=NBRC 102646	GCA_001592025.1	519424	519424	type	True	76.6505	79	1582	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	76.6089	112	1582	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.564	54	1582	95	below_threshold
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	76.5526	102	1582	95	below_threshold
Pseudalkalibacillus berkeleyi	strain=KCTC 12718	GCA_021608225.1	1069813	1069813	type	True	76.4889	50	1582	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:30,889] [INFO] DFAST Taxonomy check result was written to GCF_002019795.1_ASM201979v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:30,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:30,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:30,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac912a81-f920-45dd-9c41-a5da646534d1/dqc_reference/checkm_data
[2024-01-24 12:14:30,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:30,955] [INFO] Task started: CheckM
[2024-01-24 12:14:30,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002019795.1_ASM201979v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002019795.1_ASM201979v1_genomic.fna/checkm_input GCF_002019795.1_ASM201979v1_genomic.fna/checkm_result
[2024-01-24 12:15:06,198] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:06,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:06,218] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:06,218] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:06,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002019795.1_ASM201979v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:06,219] [INFO] Task started: Blastn
[2024-01-24 12:15:06,219] [INFO] Running command: blastn -query GCF_002019795.1_ASM201979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac912a81-f920-45dd-9c41-a5da646534d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002019795.1_ASM201979v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:07,029] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:07,034] [INFO] Selected 21 target genomes.
[2024-01-24 12:15:07,034] [INFO] Target genome list was writen to GCF_002019795.1_ASM201979v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:07,049] [INFO] Task started: fastANI
[2024-01-24 12:15:07,050] [INFO] Running command: fastANI --query /var/lib/cwl/stge8c9f791-a541-4937-99ec-9f2bd4990f44/GCF_002019795.1_ASM201979v1_genomic.fna.gz --refList GCF_002019795.1_ASM201979v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002019795.1_ASM201979v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:22,350] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:22,368] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:22,368] [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_002019795.1	s__Bacillus_AO alkalicellulosilyticus	100.0	1577	1582	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_002250115.1	s__Bacillus_H clausii	80.0757	58	1582	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.4953	98.66	98.17	0.95	0.92	12	-
GCF_002797395.1	s__45385 sp002797395	79.0752	135	1582	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_009497655.1	s__Priestia megaterium_A	78.8716	75	1582	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_002797325.1	s__Bacillus_S sp002797325	78.4502	120	1582	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_002019605.1	s__Bacillus_BH alkalinitrilicus	78.4018	199	1582	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_001866075.3	s__Anaerobacillus isosaccharinicus	78.3509	132	1582	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_000621445.1	s__Bacillus_AO bogoriensis	78.018	330	1582	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_002335805.1	s__FJAT-45350 sp002335805	77.9488	177	1582	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_000513135.1	s__Bacillus_L akibai	77.4998	133	1582	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_001590785.1	s__Alkalihalobacillus trypoxylicola	77.2365	80	1582	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_900197585.1	s__Bacillus_H sp900197585	77.1609	58	1582	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310635.1	s__Bacillus_L sp001310635	76.9522	116	1582	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_000292245.2	s__Alkalihalobacillus alcalophilus	76.8982	106	1582	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	99.90	99.82	0.98	0.98	3	-
GCF_017939705.1	s__Bacillus_L sp017939705	76.8647	113	1582	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_000474275.2	s__Bacillus_S marmarensis	76.6264	113	1582	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:22,370] [INFO] GTDB search result was written to GCF_002019795.1_ASM201979v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:22,371] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:22,374] [INFO] DFAST_QC result json was written to GCF_002019795.1_ASM201979v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:22,375] [INFO] DFAST_QC completed!
[2024-01-24 12:15:22,375] [INFO] Total running time: 0h1m23s