[2024-01-25 19:46:20,447] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:20,450] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:20,450] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c01de67-34c8-4022-813f-7742b00d384e/dqc_reference
[2024-01-25 19:46:21,647] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:21,648] [INFO] Task started: Prodigal
[2024-01-25 19:46:21,648] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a6b15dd-e18b-492c-9230-7b265db222a5/GCF_030812975.1_ASM3081297v1_genomic.fna.gz | prodigal -d GCF_030812975.1_ASM3081297v1_genomic.fna/cds.fna -a GCF_030812975.1_ASM3081297v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:29,797] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:29,798] [INFO] Task started: HMMsearch
[2024-01-25 19:46:29,798] [INFO] Running command: hmmsearch --tblout GCF_030812975.1_ASM3081297v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c01de67-34c8-4022-813f-7742b00d384e/dqc_reference/reference_markers.hmm GCF_030812975.1_ASM3081297v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:30,067] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:30,068] [INFO] Found 6/6 markers.
[2024-01-25 19:46:30,107] [INFO] Query marker FASTA was written to GCF_030812975.1_ASM3081297v1_genomic.fna/markers.fasta
[2024-01-25 19:46:30,107] [INFO] Task started: Blastn
[2024-01-25 19:46:30,107] [INFO] Running command: blastn -query GCF_030812975.1_ASM3081297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c01de67-34c8-4022-813f-7742b00d384e/dqc_reference/reference_markers.fasta -out GCF_030812975.1_ASM3081297v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:30,687] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:30,690] [INFO] Selected 25 target genomes.
[2024-01-25 19:46:30,690] [INFO] Target genome list was writen to GCF_030812975.1_ASM3081297v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:30,704] [INFO] Task started: fastANI
[2024-01-25 19:46:30,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a6b15dd-e18b-492c-9230-7b265db222a5/GCF_030812975.1_ASM3081297v1_genomic.fna.gz --refList GCF_030812975.1_ASM3081297v1_genomic.fna/target_genomes.txt --output GCF_030812975.1_ASM3081297v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:50,137] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:50,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c01de67-34c8-4022-813f-7742b00d384e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:50,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c01de67-34c8-4022-813f-7742b00d384e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:50,152] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:46:50,153] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:46:50,153] [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
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	92.4699	1295	1544	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	78.6024	410	1544	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.712	164	1544	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	77.6877	155	1544	95	below_threshold
Bacillus benzoevorans	strain=DSM 5391	GCA_014207535.1	1456	1456	type	True	77.6111	78	1544	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	77.3481	125	1544	95	below_threshold
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	77.3471	88	1544	95	below_threshold
Bacillus tepidiphilus	strain=SYSU G01002	GCA_009466385.1	2652445	2652445	type	True	77.2314	77	1544	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	77.0642	87	1544	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.0485	92	1544	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	77.037	101	1544	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	76.9131	80	1544	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	76.8092	98	1544	95	below_threshold
Bacillus gaemokensis	strain=KCTC 13318	GCA_001590835.1	574375	574375	type	True	76.7769	99	1544	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	76.6975	120	1544	95	below_threshold
Bacillus solimangrovi	strain=GH2-4	GCA_001742425.1	1305675	1305675	type	True	76.4036	68	1544	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	76.3365	52	1544	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:50,157] [INFO] DFAST Taxonomy check result was written to GCF_030812975.1_ASM3081297v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:50,159] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:50,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:50,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c01de67-34c8-4022-813f-7742b00d384e/dqc_reference/checkm_data
[2024-01-25 19:46:50,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:50,216] [INFO] Task started: CheckM
[2024-01-25 19:46:50,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030812975.1_ASM3081297v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030812975.1_ASM3081297v1_genomic.fna/checkm_input GCF_030812975.1_ASM3081297v1_genomic.fna/checkm_result
[2024-01-25 19:47:18,512] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:18,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:18,544] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:18,544] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:18,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030812975.1_ASM3081297v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:18,545] [INFO] Task started: Blastn
[2024-01-25 19:47:18,545] [INFO] Running command: blastn -query GCF_030812975.1_ASM3081297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c01de67-34c8-4022-813f-7742b00d384e/dqc_reference/reference_markers_gtdb.fasta -out GCF_030812975.1_ASM3081297v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:19,367] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:19,370] [INFO] Selected 21 target genomes.
[2024-01-25 19:47:19,370] [INFO] Target genome list was writen to GCF_030812975.1_ASM3081297v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:19,409] [INFO] Task started: fastANI
[2024-01-25 19:47:19,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a6b15dd-e18b-492c-9230-7b265db222a5/GCF_030812975.1_ASM3081297v1_genomic.fna.gz --refList GCF_030812975.1_ASM3081297v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030812975.1_ASM3081297v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:36,629] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:36,642] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:36,643] [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_002276165.1	s__Cytobacillus kochii	99.1966	1459	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014836495.1	s__Cytobacillus sp014836495	92.4699	1295	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835735.1	s__Cytobacillus horneckiae	78.6126	409	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.87	98.22	0.90	0.90	3	-
GCF_005116465.1	s__Robertmurraya kyonggiensis	78.2113	134	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009849585.1	s__Cytobacillus sp009849585	78.178	139	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956215.1	s__Cytobacillus sp001956215	77.8942	130	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636345.1	s__Cytobacillus gottheilii	77.8717	165	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	96.50	95.11	0.87	0.87	3	-
GCF_900166665.1	s__Cytobacillus gottheilii_A	77.8395	157	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420595.1	s__Cytobacillus solani	77.712	164	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_018343665.1	s__Cytobacillus sp018343665	77.6178	155	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001439605.1	s__Cytobacillus praedii	77.548	174	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.20	99.20	0.93	0.93	2	-
GCF_002860285.1	s__Peribacillus_A sp002860285	77.452	74	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001076885.1	s__Niallia sp001076885	77.258	123	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.59	99.45	0.92	0.91	4	-
GCF_009466385.1	s__Bacillus_BN tepidiphilus	77.2314	77	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019645.1	s__Litchfieldia alkalitelluris	77.1721	79	1544	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_014656545.1	s__Neobacillus sp014656545	76.9946	91	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837155.1	s__Litchfieldia sp014837155	76.9537	105	1544	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_000380245.2	s__Bacillus_AD massiliogorillae	76.9008	115	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002577655.1	s__Metabacillus sp002577655	76.8037	114	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590835.1	s__Bacillus_A gaemokensis	76.801	98	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002561295.1	s__Bacillus_A cereus_S	76.4557	101	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.16	96.34	0.94	0.87	9	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:36,644] [INFO] GTDB search result was written to GCF_030812975.1_ASM3081297v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:36,645] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:36,648] [INFO] DFAST_QC result json was written to GCF_030812975.1_ASM3081297v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:36,648] [INFO] DFAST_QC completed!
[2024-01-25 19:47:36,648] [INFO] Total running time: 0h1m16s