[2024-01-24 13:28:14,373] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:14,376] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:14,376] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dba639b-7932-48a5-88d8-b74897936216/dqc_reference
[2024-01-24 13:28:15,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:15,669] [INFO] Task started: Prodigal
[2024-01-24 13:28:15,669] [INFO] Running command: gunzip -c /var/lib/cwl/stg869f420e-c0a4-4961-bb26-6f49f697d6a7/GCF_008923265.1_ASM892326v1_genomic.fna.gz | prodigal -d GCF_008923265.1_ASM892326v1_genomic.fna/cds.fna -a GCF_008923265.1_ASM892326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:25,542] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:25,542] [INFO] Task started: HMMsearch
[2024-01-24 13:28:25,543] [INFO] Running command: hmmsearch --tblout GCF_008923265.1_ASM892326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dba639b-7932-48a5-88d8-b74897936216/dqc_reference/reference_markers.hmm GCF_008923265.1_ASM892326v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:25,870] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:25,871] [INFO] Found 6/6 markers.
[2024-01-24 13:28:25,925] [INFO] Query marker FASTA was written to GCF_008923265.1_ASM892326v1_genomic.fna/markers.fasta
[2024-01-24 13:28:25,925] [INFO] Task started: Blastn
[2024-01-24 13:28:25,926] [INFO] Running command: blastn -query GCF_008923265.1_ASM892326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dba639b-7932-48a5-88d8-b74897936216/dqc_reference/reference_markers.fasta -out GCF_008923265.1_ASM892326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:26,552] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:26,555] [INFO] Selected 25 target genomes.
[2024-01-24 13:28:26,556] [INFO] Target genome list was writen to GCF_008923265.1_ASM892326v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:26,589] [INFO] Task started: fastANI
[2024-01-24 13:28:26,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg869f420e-c0a4-4961-bb26-6f49f697d6a7/GCF_008923265.1_ASM892326v1_genomic.fna.gz --refList GCF_008923265.1_ASM892326v1_genomic.fna/target_genomes.txt --output GCF_008923265.1_ASM892326v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:45,149] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:45,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dba639b-7932-48a5-88d8-b74897936216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:45,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dba639b-7932-48a5-88d8-b74897936216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:45,165] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:45,166] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:45,166] [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 firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	78.2508	232	1505	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	78.0509	229	1505	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	77.8914	226	1505	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.8201	230	1505	95	below_threshold
Bacillus benzoevorans	strain=DSM 5391	GCA_014207535.1	1456	1456	type	True	77.7075	105	1505	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	77.6766	203	1505	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	77.6684	216	1505	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	77.6467	249	1505	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	77.6215	154	1505	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	77.603	153	1505	95	below_threshold
Mesobacillus selenatarsenatis	strain=SF-1	GCA_000813125.1	388741	388741	type	True	77.4587	125	1505	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	77.4255	125	1505	95	below_threshold
Robertmurraya siralis	strain=171544	GCA_005502275.1	77777	77777	type	True	77.147	168	1505	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	77.1021	112	1505	95	below_threshold
Bacillus methanolicus	strain=PB1	GCA_000262755.1	1471	1471	suspected-type	True	77.0611	129	1505	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	76.9915	128	1505	95	below_threshold
Bacillus clarus	strain=BHP	GCA_000746925.1	2338372	2338372	type	True	76.9823	68	1505	95	below_threshold
Bacillus clarus	strain=PS00077A	GCA_003428195.1	2338372	2338372	type	True	76.9211	68	1505	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	76.8537	80	1505	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	76.6653	51	1505	95	below_threshold
Metabacillus fastidiosus	strain=NBRC 101226	GCA_001591625.1	1458	1458	type	True	76.3926	97	1505	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:45,167] [INFO] DFAST Taxonomy check result was written to GCF_008923265.1_ASM892326v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:45,168] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:45,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:45,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dba639b-7932-48a5-88d8-b74897936216/dqc_reference/checkm_data
[2024-01-24 13:28:45,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:45,212] [INFO] Task started: CheckM
[2024-01-24 13:28:45,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008923265.1_ASM892326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008923265.1_ASM892326v1_genomic.fna/checkm_input GCF_008923265.1_ASM892326v1_genomic.fna/checkm_result
[2024-01-24 13:29:19,663] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:19,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:19,687] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:19,688] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:19,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008923265.1_ASM892326v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:19,689] [INFO] Task started: Blastn
[2024-01-24 13:29:19,689] [INFO] Running command: blastn -query GCF_008923265.1_ASM892326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dba639b-7932-48a5-88d8-b74897936216/dqc_reference/reference_markers_gtdb.fasta -out GCF_008923265.1_ASM892326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:20,536] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:20,565] [INFO] Selected 21 target genomes.
[2024-01-24 13:29:20,566] [INFO] Target genome list was writen to GCF_008923265.1_ASM892326v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:20,612] [INFO] Task started: fastANI
[2024-01-24 13:29:20,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg869f420e-c0a4-4961-bb26-6f49f697d6a7/GCF_008923265.1_ASM892326v1_genomic.fna.gz --refList GCF_008923265.1_ASM892326v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008923265.1_ASM892326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:37,118] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:37,136] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:37,136] [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_001636345.1	s__Cytobacillus gottheilii	95.0358	1310	1505	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	conclusive
GCF_900166665.1	s__Cytobacillus gottheilii_A	88.6933	1185	1505	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_001038755.1	s__Cytobacillus firmus_B	78.5751	224	1505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	97.85	96.97	0.92	0.91	5	-
GCF_000294775.2	s__Cytobacillus oceanisediminis_B	78.4557	245	1505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.75	98.26	0.86	0.83	6	-
GCF_018613035.1	s__Cytobacillus sp018613035	78.3107	241	1505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.97	99.97	0.97	0.97	2	-
GCF_003182355.1	s__Cytobacillus oceanisediminis_A	78.307	248	1505	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	78.305	232	1505	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_001274725.1	s__Cytobacillus globisporus	78.2786	231	1505	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_017303275.1	s__Cytobacillus sp017303275	78.2345	244	1505	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_000518885.1	s__Cytobacillus sp000518885	78.1797	236	1505	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_002276165.1	s__Cytobacillus kochii	77.8777	165	1505	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	77.785	229	1505	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	77.7751	204	1505	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_008923245.1	s__Cytobacillus depressus	77.6646	203	1505	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	77.6467	249	1505	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_004006295.1	s__Peribacillus asahii_A	77.5845	113	1505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003570725.1	s__Peribacillus asahii	77.1021	112	1505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001048695.1	s__Neobacillus massiliamazoniensis	76.9915	128	1505	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:37,138] [INFO] GTDB search result was written to GCF_008923265.1_ASM892326v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:37,139] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:37,146] [INFO] DFAST_QC result json was written to GCF_008923265.1_ASM892326v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:37,146] [INFO] DFAST_QC completed!
[2024-01-24 13:29:37,146] [INFO] Total running time: 0h1m23s