[2024-01-24 14:07:31,199] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:31,201] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:31,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fbc77e9-1595-4648-8e33-210e0a316557/dqc_reference
[2024-01-24 14:07:32,494] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:32,495] [INFO] Task started: Prodigal
[2024-01-24 14:07:32,495] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a64c5e8-8fee-40c9-9b88-5c62800960cd/GCF_001884045.1_ASM188404v1_genomic.fna.gz | prodigal -d GCF_001884045.1_ASM188404v1_genomic.fna/cds.fna -a GCF_001884045.1_ASM188404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:43,010] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:43,010] [INFO] Task started: HMMsearch
[2024-01-24 14:07:43,010] [INFO] Running command: hmmsearch --tblout GCF_001884045.1_ASM188404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fbc77e9-1595-4648-8e33-210e0a316557/dqc_reference/reference_markers.hmm GCF_001884045.1_ASM188404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:43,340] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:43,341] [INFO] Found 6/6 markers.
[2024-01-24 14:07:43,396] [INFO] Query marker FASTA was written to GCF_001884045.1_ASM188404v1_genomic.fna/markers.fasta
[2024-01-24 14:07:43,397] [INFO] Task started: Blastn
[2024-01-24 14:07:43,397] [INFO] Running command: blastn -query GCF_001884045.1_ASM188404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fbc77e9-1595-4648-8e33-210e0a316557/dqc_reference/reference_markers.fasta -out GCF_001884045.1_ASM188404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:44,062] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:44,065] [INFO] Selected 19 target genomes.
[2024-01-24 14:07:44,066] [INFO] Target genome list was writen to GCF_001884045.1_ASM188404v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:44,073] [INFO] Task started: fastANI
[2024-01-24 14:07:44,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a64c5e8-8fee-40c9-9b88-5c62800960cd/GCF_001884045.1_ASM188404v1_genomic.fna.gz --refList GCF_001884045.1_ASM188404v1_genomic.fna/target_genomes.txt --output GCF_001884045.1_ASM188404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:08:05,714] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:05,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fbc77e9-1595-4648-8e33-210e0a316557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:08:05,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fbc77e9-1595-4648-8e33-210e0a316557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:08:05,729] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:08:05,730] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:08:05,730] [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 sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	94.4888	1357	1828	95	below_threshold
Bacillus pacificus	strain=EB422	GCA_001884025.1	2026187	2026187	type	True	93.2252	1498	1828	95	below_threshold
Bacillus tropicus	strain=N24	GCA_001884035.1	2026188	2026188	type	True	93.211	1472	1828	95	below_threshold
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	92.9208	1484	1828	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_000742895.1	1392	1392	type	True	92.8489	1507	1828	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	92.8278	1491	1828	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_000167275.1	1392	1392	type	True	92.7828	1473	1828	95	below_threshold
Bacillus anthracis	strain=A0488	GCA_000181835.1	1392	1392	type	True	92.7581	1455	1828	95	below_threshold
Bacillus luti	strain=TD41	GCA_001884105.1	2026191	2026191	type	True	91.444	1429	1828	95	below_threshold
Bacillus thuringiensis	strain=ATCC 10792	GCA_002119445.1	1428	1428	suspected-type	True	91.0485	1494	1828	95	below_threshold
Bacillus nitratireducens	strain=4049	GCA_001884135.1	2026193	2026193	type	True	90.843	1432	1828	95	below_threshold
Bacillus proteolyticus	strain=TD42	GCA_001884065.1	2026192	2026192	type	True	90.1954	1415	1828	95	below_threshold
Bacillus mycoides	strain=ATCC 6462	GCA_000832605.1	1405	1405	type	True	90.1308	1413	1828	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_000003925.1	1405	1405	type	True	90.0937	1400	1828	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	90.068	1432	1828	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	76.9943	151	1828	95	below_threshold
Anoxybacillus kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	76.7616	61	1828	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:08:05,732] [INFO] DFAST Taxonomy check result was written to GCF_001884045.1_ASM188404v1_genomic.fna/tc_result.tsv
[2024-01-24 14:08:05,732] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:08:05,732] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:08:05,732] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fbc77e9-1595-4648-8e33-210e0a316557/dqc_reference/checkm_data
[2024-01-24 14:08:05,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:08:05,789] [INFO] Task started: CheckM
[2024-01-24 14:08:05,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001884045.1_ASM188404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001884045.1_ASM188404v1_genomic.fna/checkm_input GCF_001884045.1_ASM188404v1_genomic.fna/checkm_result
[2024-01-24 14:08:43,873] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:43,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:43,906] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:43,906] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:43,907] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001884045.1_ASM188404v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:43,907] [INFO] Task started: Blastn
[2024-01-24 14:08:43,908] [INFO] Running command: blastn -query GCF_001884045.1_ASM188404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fbc77e9-1595-4648-8e33-210e0a316557/dqc_reference/reference_markers_gtdb.fasta -out GCF_001884045.1_ASM188404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:44,789] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:44,796] [INFO] Selected 14 target genomes.
[2024-01-24 14:08:44,796] [INFO] Target genome list was writen to GCF_001884045.1_ASM188404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:44,805] [INFO] Task started: fastANI
[2024-01-24 14:08:44,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a64c5e8-8fee-40c9-9b88-5c62800960cd/GCF_001884045.1_ASM188404v1_genomic.fna.gz --refList GCF_001884045.1_ASM188404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001884045.1_ASM188404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:02,881] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:02,896] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:02,896] [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_001884045.1	s__Bacillus_A mobilis	100.0	1822	1828	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	96.91	95.80	0.85	0.81	33	conclusive
GCF_900094905.1	s__Bacillus_A cereus_AG	94.804	1496	1828	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.51	99.13	0.92	0.90	3	-
GCF_008923725.1	s__Bacillus_A sp008923725	94.6455	1501	1828	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001583695.1	s__Bacillus_A wiedmannii	94.6214	1471	1828	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	96.52	95.09	0.90	0.85	225	-
GCF_018332475.1	s__Bacillus_A sp018332475	94.4888	1357	1828	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	95.31	95.31	0.87	0.87	2	-
GCF_001884185.1	s__Bacillus_A albus	93.8108	1479	1828	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.54	95.46	0.90	0.83	25	-
GCF_002571225.1	s__Bacillus_A sp002571225	93.6301	1449	1828	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_001455345.1	s__Bacillus_A thuringiensis_N	93.3846	1491	1828	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.23	95.30	0.91	0.84	24	-
GCF_002746455.1	s__Bacillus_A fungorum	93.2578	1409	1828	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.51	97.51	0.90	0.90	2	-
GCF_001884035.1	s__Bacillus_A tropicus	93.211	1472	1828	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.3658	96.52	95.65	0.91	0.83	109	-
GCF_006494425.1	s__Bacillus_A sp006494425	93.143	1491	1828	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_000742895.1	s__Bacillus_A anthracis	92.8489	1507	1828	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.2518	99.29	95.34	0.96	0.83	417	-
GCF_001884105.1	s__Bacillus_A luti	91.4441	1429	1828	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.24	95.75	0.91	0.89	10	-
GCF_001884065.1	s__Bacillus_A proteolyticus	90.1954	1415	1828	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.1182	98.61	98.37	0.91	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:02,898] [INFO] GTDB search result was written to GCF_001884045.1_ASM188404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:02,899] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:02,903] [INFO] DFAST_QC result json was written to GCF_001884045.1_ASM188404v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:02,903] [INFO] DFAST_QC completed!
[2024-01-24 14:09:02,903] [INFO] Total running time: 0h1m32s