[2024-01-24 14:05:14,432] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:14,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:14,434] [INFO] DQC Reference Directory: /var/lib/cwl/stgc26810b1-be07-41bb-8e2e-60687096a420/dqc_reference
[2024-01-24 14:05:15,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:15,690] [INFO] Task started: Prodigal
[2024-01-24 14:05:15,690] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fa70f41-5e7e-4633-9537-754b31e3b775/GCF_014643595.1_ASM1464359v1_genomic.fna.gz | prodigal -d GCF_014643595.1_ASM1464359v1_genomic.fna/cds.fna -a GCF_014643595.1_ASM1464359v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:22,172] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:22,173] [INFO] Task started: HMMsearch
[2024-01-24 14:05:22,173] [INFO] Running command: hmmsearch --tblout GCF_014643595.1_ASM1464359v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc26810b1-be07-41bb-8e2e-60687096a420/dqc_reference/reference_markers.hmm GCF_014643595.1_ASM1464359v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:22,450] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:22,452] [INFO] Found 6/6 markers.
[2024-01-24 14:05:22,489] [INFO] Query marker FASTA was written to GCF_014643595.1_ASM1464359v1_genomic.fna/markers.fasta
[2024-01-24 14:05:22,490] [INFO] Task started: Blastn
[2024-01-24 14:05:22,490] [INFO] Running command: blastn -query GCF_014643595.1_ASM1464359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc26810b1-be07-41bb-8e2e-60687096a420/dqc_reference/reference_markers.fasta -out GCF_014643595.1_ASM1464359v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:23,066] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:23,070] [INFO] Selected 31 target genomes.
[2024-01-24 14:05:23,070] [INFO] Target genome list was writen to GCF_014643595.1_ASM1464359v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:23,150] [INFO] Task started: fastANI
[2024-01-24 14:05:23,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fa70f41-5e7e-4633-9537-754b31e3b775/GCF_014643595.1_ASM1464359v1_genomic.fna.gz --refList GCF_014643595.1_ASM1464359v1_genomic.fna/target_genomes.txt --output GCF_014643595.1_ASM1464359v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:40,736] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:40,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc26810b1-be07-41bb-8e2e-60687096a420/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:40,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc26810b1-be07-41bb-8e2e-60687096a420/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:40,757] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:05:40,757] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:05:40,757] [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
Lysinibacillus agricola	strain=FJAT-51161	GCA_016638705.1	2590012	2590012	type	True	78.3373	158	1055	95	below_threshold
Lysinibacillus mangiferihumi	strain=CCTCC AB 2010389	GCA_005217845.1	1130819	1130819	type	True	78.3093	181	1055	95	below_threshold
Lysinibacillus mangiferihumi	strain=M-GX18	GCA_003049665.1	1130819	1130819	type	True	78.2697	189	1055	95	below_threshold
Lysinibacillus parviboronicapiens	strain=BAM-582	GCA_003049575.1	436516	436516	type	True	78.1965	164	1055	95	below_threshold
Lysinibacillus sphaericus	strain=NRRL B-23268	GCA_005217555.1	1421	1421	suspected-type	True	77.9896	197	1055	95	below_threshold
Ureibacillus chungkukjangi	strain=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	77.988	113	1055	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	77.9681	126	1055	95	below_threshold
Lysinibacillus macroides	strain=DSM 54	GCA_001281525.1	33935	33935	type	True	77.9254	184	1055	95	below_threshold
Lysinibacillus sphaericus	strain=NCTC10338	GCA_900445465.1	1421	1421	suspected-type	True	77.9004	199	1055	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	77.8982	126	1055	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	77.8894	122	1055	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	77.8409	119	1055	95	below_threshold
Kurthia zopfii	strain=ATCC 33403	GCA_003143955.1	1650	1650	type	True	77.7278	87	1055	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	77.6955	175	1055	95	below_threshold
Lysinibacillus boronitolerans	strain=NBRC 103108	GCA_002200915.1	309788	309788	type	True	77.6795	163	1055	95	below_threshold
Lysinibacillus boronitolerans	strain=NBRC 103108	GCA_000772935.1	309788	309788	type	True	77.6795	163	1055	95	below_threshold
Lysinibacillus sphaericus	strain=NBRC 15095	GCA_006539805.1	1421	1421	suspected-type	True	77.6391	197	1055	95	below_threshold
Lysinibacillus fusiformis	strain=ATCC 7055	GCA_003049525.1	28031	28031	type	True	77.6061	174	1055	95	below_threshold
Lysinibacillus fusiformis	strain=NRRL NRS-350	GCA_003367495.1	28031	28031	type	True	77.5973	176	1055	95	below_threshold
Lysinibacillus fusiformis	strain=NBRC 15717	GCA_006540205.1	28031	28031	type	True	77.4354	170	1055	95	below_threshold
Ureibacillus acetophenoni	strain=JC23	GCA_900220965.1	614649	614649	type	True	77.4319	123	1055	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	77.4242	135	1055	95	below_threshold
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	77.4202	126	1055	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	77.3804	112	1055	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	77.3628	122	1055	95	below_threshold
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	77.3628	122	1055	95	below_threshold
Viridibacillus arvi	strain=DSM 16317	GCA_001274945.1	263475	263475	type	True	77.3536	119	1055	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:40,759] [INFO] DFAST Taxonomy check result was written to GCF_014643595.1_ASM1464359v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:40,760] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:40,760] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:40,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc26810b1-be07-41bb-8e2e-60687096a420/dqc_reference/checkm_data
[2024-01-24 14:05:40,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:40,793] [INFO] Task started: CheckM
[2024-01-24 14:05:40,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643595.1_ASM1464359v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643595.1_ASM1464359v1_genomic.fna/checkm_input GCF_014643595.1_ASM1464359v1_genomic.fna/checkm_result
[2024-01-24 14:06:06,605] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:06,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:06,640] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:06,640] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:06,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643595.1_ASM1464359v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:06,641] [INFO] Task started: Blastn
[2024-01-24 14:06:06,641] [INFO] Running command: blastn -query GCF_014643595.1_ASM1464359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc26810b1-be07-41bb-8e2e-60687096a420/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643595.1_ASM1464359v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:07,474] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:07,478] [INFO] Selected 24 target genomes.
[2024-01-24 14:06:07,478] [INFO] Target genome list was writen to GCF_014643595.1_ASM1464359v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:07,530] [INFO] Task started: fastANI
[2024-01-24 14:06:07,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fa70f41-5e7e-4633-9537-754b31e3b775/GCF_014643595.1_ASM1464359v1_genomic.fna.gz --refList GCF_014643595.1_ASM1464359v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643595.1_ASM1464359v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:24,283] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:24,308] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:24,309] [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_014643595.1	s__Metalysinibacillus alkalisoli	100.0	1053	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metalysinibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003057615.1	s__Metalysinibacillus jejuensis	79.685	325	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metalysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000935965.1	s__Metalysinibacillus saudimassiliensis	79.2821	330	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metalysinibacillus	95.0	96.72	96.72	0.89	0.89	2	-
GCF_003049665.1	s__Lysinibacillus mangiferihumi	78.2496	190	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.9114	99.98	99.98	0.98	0.98	2	-
GCF_002845985.1	s__Lysinibacillus fusiformis_D	78.2245	167	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.12	98.25	0.94	0.92	9	-
GCF_003049575.1	s__Lysinibacillus parviboronicapiens	78.1965	164	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.01	98.61	0.95	0.92	4	-
GCF_003049645.1	s__Metasolibacillus fluoroglycofenilyticus	78.0358	139	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	98.96	98.96	0.94	0.94	2	-
GCF_002982115.1	s__Lysinibacillus sphaericus	77.9801	196	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.9114	99.42	98.91	0.95	0.90	10	-
GCF_001281525.1	s__Lysinibacillus macroides	77.9254	184	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.95	99.95	0.98	0.98	2	-
GCF_016908465.1	s__Ureibacillus composti	77.8982	126	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001629735.1	s__Lysinibacillus sphaericus_A	77.897	168	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.64	99.33	0.95	0.90	29	-
GCF_014836935.1	s__Solibacillus sp014836935	77.8894	122	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005491425.1	s__Ureibacillus sp005491425	77.8296	110	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772935.1	s__Lysinibacillus boronitolerans	77.6795	163	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.1183	99.49	98.68	0.97	0.91	4	-
GCF_001308875.1	s__Lysinibacillus sp001308875	77.6677	175	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836845.1	s__Ureibacillus sp014836845	77.6651	137	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016925635.1	s__Lysinibacillus fusiformis_F	77.6509	180	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049525.1	s__Lysinibacillus fusiformis	77.6061	174	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	98.17	95.55	0.92	0.87	32	-
GCA_002360295.1	s__Metasolibacillus sp002360295	77.4362	126	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278945.1	s__Lysinibacillus contaminans	77.424	135	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813185.1	s__Viridibacillus sp002813185	77.406	124	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	98.00	98.00	0.85	0.85	2	-
GCF_014836905.1	s__Solibacillus sp014836905	77.3675	129	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772965.1	s__Ureibacillus massiliensis	77.3628	122	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003991225.1	s__Kurthia intestinigallinarum	77.036	109	1055	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	98.65	98.48	0.94	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:24,311] [INFO] GTDB search result was written to GCF_014643595.1_ASM1464359v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:24,311] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:24,316] [INFO] DFAST_QC result json was written to GCF_014643595.1_ASM1464359v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:24,317] [INFO] DFAST_QC completed!
[2024-01-24 14:06:24,317] [INFO] Total running time: 0h1m10s