[2024-01-24 13:17:42,245] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:42,246] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:42,247] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f9f10d6-881b-4661-9e40-2ee52d57ac8b/dqc_reference
[2024-01-24 13:17:43,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:43,467] [INFO] Task started: Prodigal
[2024-01-24 13:17:43,468] [INFO] Running command: gunzip -c /var/lib/cwl/stg477c0fc5-b2ea-4be1-94de-b6ff1dbe6250/GCF_019024285.1_ASM1902428v1_genomic.fna.gz | prodigal -d GCF_019024285.1_ASM1902428v1_genomic.fna/cds.fna -a GCF_019024285.1_ASM1902428v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:52,485] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:52,485] [INFO] Task started: HMMsearch
[2024-01-24 13:17:52,485] [INFO] Running command: hmmsearch --tblout GCF_019024285.1_ASM1902428v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f9f10d6-881b-4661-9e40-2ee52d57ac8b/dqc_reference/reference_markers.hmm GCF_019024285.1_ASM1902428v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:52,853] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:52,854] [INFO] Found 6/6 markers.
[2024-01-24 13:17:52,895] [INFO] Query marker FASTA was written to GCF_019024285.1_ASM1902428v1_genomic.fna/markers.fasta
[2024-01-24 13:17:52,895] [INFO] Task started: Blastn
[2024-01-24 13:17:52,896] [INFO] Running command: blastn -query GCF_019024285.1_ASM1902428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f9f10d6-881b-4661-9e40-2ee52d57ac8b/dqc_reference/reference_markers.fasta -out GCF_019024285.1_ASM1902428v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:53,497] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:53,501] [INFO] Selected 21 target genomes.
[2024-01-24 13:17:53,501] [INFO] Target genome list was writen to GCF_019024285.1_ASM1902428v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:53,528] [INFO] Task started: fastANI
[2024-01-24 13:17:53,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg477c0fc5-b2ea-4be1-94de-b6ff1dbe6250/GCF_019024285.1_ASM1902428v1_genomic.fna.gz --refList GCF_019024285.1_ASM1902428v1_genomic.fna/target_genomes.txt --output GCF_019024285.1_ASM1902428v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:09,247] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:09,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f9f10d6-881b-4661-9e40-2ee52d57ac8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:09,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f9f10d6-881b-4661-9e40-2ee52d57ac8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:09,261] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:09,261] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:09,261] [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
Alkalihalobacterium elongatum	strain=MEB199	GCA_019024285.1	2675466	2675466	type	True	100.0	1572	1574	95	conclusive
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	80.7479	766	1574	95	below_threshold
Alkalihalobacillus bogoriensis	strain=ATCC BAA-922	GCA_000621445.1	246272	246272	type	True	77.1195	177	1574	95	below_threshold
Desertibacillus haloalkaliphilus	strain=KJ1-10-99	GCA_019039105.1	1328930	1328930	type	True	77.0153	148	1574	95	below_threshold
Bacillus alkalicellulosilyticus	strain=FJAT-44921	GCA_002019795.1	1912214	1912214	type	True	76.8722	153	1574	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	76.7348	131	1574	95	below_threshold
Anaerobacillus arseniciselenatis	strain=DSM 15340	GCA_001865995.1	85682	85682	type	True	76.6806	107	1574	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	76.6615	108	1574	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	76.6499	140	1574	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	76.6101	138	1574	95	below_threshold
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	76.6088	99	1574	95	below_threshold
Bacillus clarus	strain=BHP	GCA_000746925.1	2338372	2338372	type	True	76.4604	84	1574	95	below_threshold
Bacillus clarus	strain=PS00077A	GCA_003428195.1	2338372	2338372	type	True	76.4389	79	1574	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	76.4226	85	1574	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	76.2659	54	1574	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	76.2463	60	1574	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:09,263] [INFO] DFAST Taxonomy check result was written to GCF_019024285.1_ASM1902428v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:09,263] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:09,263] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:09,264] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f9f10d6-881b-4661-9e40-2ee52d57ac8b/dqc_reference/checkm_data
[2024-01-24 13:18:09,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:09,317] [INFO] Task started: CheckM
[2024-01-24 13:18:09,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019024285.1_ASM1902428v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019024285.1_ASM1902428v1_genomic.fna/checkm_input GCF_019024285.1_ASM1902428v1_genomic.fna/checkm_result
[2024-01-24 13:18:42,677] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:42,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:42,704] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:42,704] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:42,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019024285.1_ASM1902428v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:42,705] [INFO] Task started: Blastn
[2024-01-24 13:18:42,705] [INFO] Running command: blastn -query GCF_019024285.1_ASM1902428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f9f10d6-881b-4661-9e40-2ee52d57ac8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_019024285.1_ASM1902428v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:43,559] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:43,563] [INFO] Selected 21 target genomes.
[2024-01-24 13:18:43,563] [INFO] Target genome list was writen to GCF_019024285.1_ASM1902428v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:43,621] [INFO] Task started: fastANI
[2024-01-24 13:18:43,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg477c0fc5-b2ea-4be1-94de-b6ff1dbe6250/GCF_019024285.1_ASM1902428v1_genomic.fna.gz --refList GCF_019024285.1_ASM1902428v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019024285.1_ASM1902428v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:59,659] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:59,678] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:59,679] [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_019024285.1	s__Bacillus_BH sp019024285	100.0	1572	1574	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	conclusive
GCF_002019605.1	s__Bacillus_BH alkalinitrilicus	80.7446	767	1574	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_017745675.1	s__Bacillus_BH sp017745675	80.6601	719	1574	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	77.3139	202	1574	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_000621445.1	s__Bacillus_AO bogoriensis	77.1347	180	1574	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_019039105.1	s__Desertibacillus haloalkaliphilus	76.9944	147	1574	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__KJ1-10-99;g__Desertibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019795.1	s__Bacillus_AO alkalicellulosilyticus	76.8986	153	1574	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_017939705.1	s__Bacillus_L sp017939705	76.8318	103	1574	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_001866055.1	s__Anaerobacillus alkalidiazotrophicus	76.7669	119	1574	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_001865995.1	s__Anaerobacillus arseniciselenatis	76.7316	106	1574	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_002109385.1	s__Bacillus_L krulwichiae	76.6818	138	1574	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_000292245.2	s__Alkalihalobacillus alcalophilus	76.6611	107	1574	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_000746925.1	s__Bacillus_A clarus	76.4585	82	1574	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900104555.1	s__Litchfieldia salsa	76.45	83	1574	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002582035.1	s__Bacillus_A pseudomycoides_B	76.0393	81	1574	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_003628435.1	s__Ureibacillus endophyticus	75.9174	59	1574	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:59,680] [INFO] GTDB search result was written to GCF_019024285.1_ASM1902428v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:59,681] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:59,685] [INFO] DFAST_QC result json was written to GCF_019024285.1_ASM1902428v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:59,685] [INFO] DFAST_QC completed!
[2024-01-24 13:18:59,685] [INFO] Total running time: 0h1m17s