[2024-01-24 11:12:54,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:54,959] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:54,959] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0184d03-c4f7-4096-9bc3-329d533b7e0c/dqc_reference
[2024-01-24 11:12:56,275] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:56,276] [INFO] Task started: Prodigal
[2024-01-24 11:12:56,277] [INFO] Running command: gunzip -c /var/lib/cwl/stgdef2d936-a006-4ced-b036-3b93db8f674c/GCF_024609785.1_ASM2460978v1_genomic.fna.gz | prodigal -d GCF_024609785.1_ASM2460978v1_genomic.fna/cds.fna -a GCF_024609785.1_ASM2460978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:07,826] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:07,827] [INFO] Task started: HMMsearch
[2024-01-24 11:13:07,827] [INFO] Running command: hmmsearch --tblout GCF_024609785.1_ASM2460978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0184d03-c4f7-4096-9bc3-329d533b7e0c/dqc_reference/reference_markers.hmm GCF_024609785.1_ASM2460978v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:08,209] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:08,210] [INFO] Found 6/6 markers.
[2024-01-24 11:13:08,258] [INFO] Query marker FASTA was written to GCF_024609785.1_ASM2460978v1_genomic.fna/markers.fasta
[2024-01-24 11:13:08,259] [INFO] Task started: Blastn
[2024-01-24 11:13:08,259] [INFO] Running command: blastn -query GCF_024609785.1_ASM2460978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0184d03-c4f7-4096-9bc3-329d533b7e0c/dqc_reference/reference_markers.fasta -out GCF_024609785.1_ASM2460978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:08,872] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:08,875] [INFO] Selected 25 target genomes.
[2024-01-24 11:13:08,875] [INFO] Target genome list was writen to GCF_024609785.1_ASM2460978v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:08,884] [INFO] Task started: fastANI
[2024-01-24 11:13:08,884] [INFO] Running command: fastANI --query /var/lib/cwl/stgdef2d936-a006-4ced-b036-3b93db8f674c/GCF_024609785.1_ASM2460978v1_genomic.fna.gz --refList GCF_024609785.1_ASM2460978v1_genomic.fna/target_genomes.txt --output GCF_024609785.1_ASM2460978v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:29,255] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:29,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0184d03-c4f7-4096-9bc3-329d533b7e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:29,256] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0184d03-c4f7-4096-9bc3-329d533b7e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:29,265] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:29,265] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:29,265] [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
Pseudalkalibacillus decolorationis	strain=DSM 14890	GCA_024609785.1	163879	163879	type	True	100.0	1715	1717	95	conclusive
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	77.3736	50	1717	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_001420715.1	157838	157838	type	True	76.9906	52	1717	95	below_threshold
Bacillus taeanensis	strain=BH030017	GCA_003318295.1	273032	273032	type	True	76.7755	87	1717	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	76.6162	56	1717	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	76.6079	56	1717	95	below_threshold
Fictibacillus macauensis	strain=ZFHKF-1	GCA_000269865.1	245160	245160	type	True	76.4258	60	1717	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.2666	54	1717	95	below_threshold
Gottfriedia acidiceleris	strain=DSM 18954	GCA_002128425.1	371036	371036	type	True	76.0662	51	1717	95	below_threshold
Gottfriedia acidiceleris	strain=NRRL B-41736	GCA_002156925.1	371036	371036	type	True	76.0625	54	1717	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:29,267] [INFO] DFAST Taxonomy check result was written to GCF_024609785.1_ASM2460978v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:29,267] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:29,267] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:29,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0184d03-c4f7-4096-9bc3-329d533b7e0c/dqc_reference/checkm_data
[2024-01-24 11:13:29,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:29,323] [INFO] Task started: CheckM
[2024-01-24 11:13:29,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024609785.1_ASM2460978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024609785.1_ASM2460978v1_genomic.fna/checkm_input GCF_024609785.1_ASM2460978v1_genomic.fna/checkm_result
[2024-01-24 11:14:07,928] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:07,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:07,948] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:07,949] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:07,949] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024609785.1_ASM2460978v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:07,950] [INFO] Task started: Blastn
[2024-01-24 11:14:07,950] [INFO] Running command: blastn -query GCF_024609785.1_ASM2460978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0184d03-c4f7-4096-9bc3-329d533b7e0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_024609785.1_ASM2460978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:08,697] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:08,701] [INFO] Selected 31 target genomes.
[2024-01-24 11:14:08,701] [INFO] Target genome list was writen to GCF_024609785.1_ASM2460978v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:08,721] [INFO] Task started: fastANI
[2024-01-24 11:14:08,721] [INFO] Running command: fastANI --query /var/lib/cwl/stgdef2d936-a006-4ced-b036-3b93db8f674c/GCF_024609785.1_ASM2460978v1_genomic.fna.gz --refList GCF_024609785.1_ASM2460978v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024609785.1_ASM2460978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:30,022] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:30,042] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:14:30,043] [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_002584535.1	s__Bacillus_A cereus_AW	77.802	51	1717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.12	98.24	0.93	0.90	5	-
GCF_000787375.1	s__Bacillus_L okhensis	77.3736	50	1717	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_001274725.1	s__Cytobacillus globisporus	77.2793	56	1717	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_001420715.1	s__Margalitia shackletonii	77.0365	51	1717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.16	98.74	0.93	0.89	4	-
GCF_003318295.1	s__Maribacillus taeanensis	76.8362	89	1717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__UBA6769;g__Maribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001439605.1	s__Cytobacillus praedii	76.7554	59	1717	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_003184905.1	s__Priestia sp003184905	76.614	52	1717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017809215.1	s__Heyndrickxia oleronia	76.5683	54	1717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	98.68	97.33	0.92	0.89	7	-
GCF_001619875.1	s__Fictibacillus phosphorivorans_B	76.5086	59	1717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621445.1	s__Bacillus_AO bogoriensis	76.4936	63	1717	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_000269865.1	s__Fictibacillus_C macauensis	76.3919	61	1717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518865.1	s__Metabacillus sp000518865	76.375	75	1717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144865.1	s__Anaerobacillus_A hwajinpoensis_A	76.2364	50	1717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019665.1	s__Sutcliffiella_A halmapala	76.162	54	1717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340305.1	s__Gottfriedia sp004340305	76.155	57	1717	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002128425.1	s__Gottfriedia acidiceler	76.0887	52	1717	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 11:14:30,044] [INFO] GTDB search result was written to GCF_024609785.1_ASM2460978v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:30,045] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:30,048] [INFO] DFAST_QC result json was written to GCF_024609785.1_ASM2460978v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:30,048] [INFO] DFAST_QC completed!
[2024-01-24 11:14:30,048] [INFO] Total running time: 0h1m35s