[2024-01-24 14:06:44,730] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:44,738] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:44,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg775bb0ea-afe4-491f-a153-7a012ebf33b9/dqc_reference
[2024-01-24 14:06:46,002] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:46,003] [INFO] Task started: Prodigal
[2024-01-24 14:06:46,004] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0d41a25-cfb8-4768-be0a-254adc037b1e/GCF_004375095.1_ASM437509v1_genomic.fna.gz | prodigal -d GCF_004375095.1_ASM437509v1_genomic.fna/cds.fna -a GCF_004375095.1_ASM437509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:55,182] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:55,182] [INFO] Task started: HMMsearch
[2024-01-24 14:06:55,182] [INFO] Running command: hmmsearch --tblout GCF_004375095.1_ASM437509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg775bb0ea-afe4-491f-a153-7a012ebf33b9/dqc_reference/reference_markers.hmm GCF_004375095.1_ASM437509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:55,474] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:55,475] [INFO] Found 6/6 markers.
[2024-01-24 14:06:55,514] [INFO] Query marker FASTA was written to GCF_004375095.1_ASM437509v1_genomic.fna/markers.fasta
[2024-01-24 14:06:55,514] [INFO] Task started: Blastn
[2024-01-24 14:06:55,514] [INFO] Running command: blastn -query GCF_004375095.1_ASM437509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg775bb0ea-afe4-491f-a153-7a012ebf33b9/dqc_reference/reference_markers.fasta -out GCF_004375095.1_ASM437509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:56,092] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:56,096] [INFO] Selected 34 target genomes.
[2024-01-24 14:06:56,097] [INFO] Target genome list was writen to GCF_004375095.1_ASM437509v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:56,120] [INFO] Task started: fastANI
[2024-01-24 14:06:56,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0d41a25-cfb8-4768-be0a-254adc037b1e/GCF_004375095.1_ASM437509v1_genomic.fna.gz --refList GCF_004375095.1_ASM437509v1_genomic.fna/target_genomes.txt --output GCF_004375095.1_ASM437509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:18,565] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:18,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg775bb0ea-afe4-491f-a153-7a012ebf33b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:18,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg775bb0ea-afe4-491f-a153-7a012ebf33b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:18,582] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:07:18,582] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:07:18,582] [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	79.1698	61	1327	95	below_threshold
Alkalihalobacillus patagoniensis	strain=DSM 16117	GCA_002019705.1	228576	228576	type	True	78.8817	250	1327	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	78.6128	98	1327	95	below_threshold
Anaerobacillus isosaccharinicus	strain=NB2006	GCA_001866075.3	1532552	1532552	type	True	78.5327	61	1327	95	below_threshold
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	78.4969	72	1327	95	below_threshold
Anaerobacillus alkalilacustris	strain=DSM 18345	GCA_001866005.1	393763	393763	type	True	78.4243	50	1327	95	below_threshold
Halalkalibacterium halodurans	strain=DSM 497	GCA_004376175.1	86665	86665	type	True	77.9329	53	1327	95	below_threshold
Anaerobacillus alkaliphilus	strain=B16-10	GCA_004116265.1	1548597	1548597	type	True	77.6228	50	1327	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	77.4799	85	1327	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	77.1414	87	1327	95	below_threshold
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	77.1157	76	1327	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	76.8979	74	1327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:18,584] [INFO] DFAST Taxonomy check result was written to GCF_004375095.1_ASM437509v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:18,585] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:18,585] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:18,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg775bb0ea-afe4-491f-a153-7a012ebf33b9/dqc_reference/checkm_data
[2024-01-24 14:07:18,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:18,630] [INFO] Task started: CheckM
[2024-01-24 14:07:18,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004375095.1_ASM437509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004375095.1_ASM437509v1_genomic.fna/checkm_input GCF_004375095.1_ASM437509v1_genomic.fna/checkm_result
[2024-01-24 14:07:49,987] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:49,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:50,010] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:50,011] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:50,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004375095.1_ASM437509v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:50,012] [INFO] Task started: Blastn
[2024-01-24 14:07:50,012] [INFO] Running command: blastn -query GCF_004375095.1_ASM437509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg775bb0ea-afe4-491f-a153-7a012ebf33b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_004375095.1_ASM437509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:50,772] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:50,776] [INFO] Selected 20 target genomes.
[2024-01-24 14:07:50,776] [INFO] Target genome list was writen to GCF_004375095.1_ASM437509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:50,791] [INFO] Task started: fastANI
[2024-01-24 14:07:50,792] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0d41a25-cfb8-4768-be0a-254adc037b1e/GCF_004375095.1_ASM437509v1_genomic.fna.gz --refList GCF_004375095.1_ASM437509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004375095.1_ASM437509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:06,434] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:06,454] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:06,455] [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_002019765.1	s__Bacillus_H oshimensis	98.6712	1250	1327	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	98.95	98.65	0.95	0.93	6	conclusive
GCF_007725405.1	s__Bacillus_H miscanthi	91.0576	1198	1327	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	99.10	99.10	0.94	0.93	3	-
GCF_900197585.1	s__Bacillus_H sp900197585	80.2592	565	1327	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_002019795.1	s__Bacillus_AO alkalicellulosilyticus	79.2828	59	1327	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_002797325.1	s__Bacillus_S sp002797325	79.1001	79	1327	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	79.0237	62	1327	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_002019705.1	s__Bacillus_H patagoniensis	78.9541	252	1327	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_016907895.1	s__Bacillus_H xiaoxiensis	78.4127	289	1327	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	97.73	97.69	0.93	0.93	4	-
GCF_002109385.1	s__Bacillus_L krulwichiae	78.3506	96	1327	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	-
GCA_001310375.1	s__Bacillus_H sp001310375	78.3061	223	1327	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	-
GCA_001038565.1	s__Alkalihalobacillus pseudalcaliphilus	77.9022	66	1327	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004116265.1	s__Anaerobacillus alkaliphilus	77.6453	51	1327	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_000513095.1	s__Bacillus_L wakoensis	77.5255	68	1327	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_000292245.2	s__Alkalihalobacillus alcalophilus	77.4966	85	1327	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_000474275.2	s__Bacillus_S marmarensis	76.8666	74	1327	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 14:08:06,457] [INFO] GTDB search result was written to GCF_004375095.1_ASM437509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:06,457] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:06,461] [INFO] DFAST_QC result json was written to GCF_004375095.1_ASM437509v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:06,462] [INFO] DFAST_QC completed!
[2024-01-24 14:08:06,462] [INFO] Total running time: 0h1m22s