[2024-01-24 13:28:13,286] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:13,288] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:13,288] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8fb8f4a-ec8e-4563-ae6d-e84f95ae18fd/dqc_reference
[2024-01-24 13:28:14,579] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:14,581] [INFO] Task started: Prodigal
[2024-01-24 13:28:14,581] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2be847b-7e6a-4042-aeb8-ec3373f206c4/GCF_008923245.1_ASM892324v1_genomic.fna.gz | prodigal -d GCF_008923245.1_ASM892324v1_genomic.fna/cds.fna -a GCF_008923245.1_ASM892324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:25,655] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:25,656] [INFO] Task started: HMMsearch
[2024-01-24 13:28:25,656] [INFO] Running command: hmmsearch --tblout GCF_008923245.1_ASM892324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8fb8f4a-ec8e-4563-ae6d-e84f95ae18fd/dqc_reference/reference_markers.hmm GCF_008923245.1_ASM892324v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:26,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:26,095] [INFO] Found 6/6 markers.
[2024-01-24 13:28:26,136] [INFO] Query marker FASTA was written to GCF_008923245.1_ASM892324v1_genomic.fna/markers.fasta
[2024-01-24 13:28:26,136] [INFO] Task started: Blastn
[2024-01-24 13:28:26,137] [INFO] Running command: blastn -query GCF_008923245.1_ASM892324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8fb8f4a-ec8e-4563-ae6d-e84f95ae18fd/dqc_reference/reference_markers.fasta -out GCF_008923245.1_ASM892324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:26,768] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:26,772] [INFO] Selected 26 target genomes.
[2024-01-24 13:28:26,772] [INFO] Target genome list was writen to GCF_008923245.1_ASM892324v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:26,796] [INFO] Task started: fastANI
[2024-01-24 13:28:26,797] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2be847b-7e6a-4042-aeb8-ec3373f206c4/GCF_008923245.1_ASM892324v1_genomic.fna.gz --refList GCF_008923245.1_ASM892324v1_genomic.fna/target_genomes.txt --output GCF_008923245.1_ASM892324v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:49,454] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:49,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8fb8f4a-ec8e-4563-ae6d-e84f95ae18fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:49,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8fb8f4a-ec8e-4563-ae6d-e84f95ae18fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:49,476] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:49,476] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:49,477] [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 depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	100.0	1772	1774	95	conclusive
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	79.6647	588	1774	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	78.5976	427	1774	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	78.2297	402	1774	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	78.1651	205	1774	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	78.0933	325	1774	95	below_threshold
Bacillus testis	strain=SIT10	GCA_001243895.1	1622072	1622072	type	True	77.9555	67	1774	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	77.6672	216	1774	95	below_threshold
Bacillus massilionigeriensis	strain=Marseille-P2384	GCA_900117315.1	1805475	1805475	type	True	77.566	170	1774	95	below_threshold
Peribacillus frigoritolerans	strain=DSM 8801	GCA_024169475.1	450367	450367	type	True	77.5436	121	1774	95	below_threshold
Peribacillus frigoritolerans	strain=FJAT-2396	GCA_001636405.1	450367	450367	type	True	77.4844	129	1774	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	77.4665	189	1774	95	below_threshold
Mesobacillus jeotgali	strain=DSM 18226	GCA_002874535.1	129985	129985	type	True	77.3484	129	1774	95	below_threshold
Bacillus pakistanensis	strain=DSM 24834	GCA_016908495.1	992288	992288	type	True	77.3138	120	1774	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	77.1821	106	1774	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	77.1328	96	1774	95	below_threshold
Mangrovibacillus cuniculi	strain=R1DC41	GCA_015482585.1	2593652	2593652	type	True	77.0725	66	1774	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	77.0383	71	1774	95	below_threshold
Cytobacillus luteolus	strain=YIM 93174	GCA_014982515.1	682179	682179	type	True	76.957	103	1774	95	below_threshold
Cytobacillus luteolus	strain=DSM 22388	GCA_017873715.1	682179	682179	type	True	76.8972	104	1774	95	below_threshold
Bacillus tepidiphilus	strain=SYSU G01002	GCA_009466385.1	2652445	2652445	type	True	76.8963	112	1774	95	below_threshold
Anoxybacillus calidus	strain=DSM 25220	GCA_013760845.1	575178	575178	type	True	76.8122	75	1774	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_019915265.1	2672567	2672567	type	True	76.7806	122	1774	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_011008855.1	2672567	2672567	type	True	76.6622	121	1774	95	below_threshold
Bacillus andreraoultii	strain=SIT1	GCA_001244735.1	1499685	1499685	type	True	76.4609	73	1774	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:49,482] [INFO] DFAST Taxonomy check result was written to GCF_008923245.1_ASM892324v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:49,483] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:49,483] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:49,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8fb8f4a-ec8e-4563-ae6d-e84f95ae18fd/dqc_reference/checkm_data
[2024-01-24 13:28:49,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:49,546] [INFO] Task started: CheckM
[2024-01-24 13:28:49,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008923245.1_ASM892324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008923245.1_ASM892324v1_genomic.fna/checkm_input GCF_008923245.1_ASM892324v1_genomic.fna/checkm_result
[2024-01-24 13:29:27,739] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:27,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:27,758] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:27,758] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:27,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008923245.1_ASM892324v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:27,759] [INFO] Task started: Blastn
[2024-01-24 13:29:27,759] [INFO] Running command: blastn -query GCF_008923245.1_ASM892324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8fb8f4a-ec8e-4563-ae6d-e84f95ae18fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_008923245.1_ASM892324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:28,538] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:28,542] [INFO] Selected 18 target genomes.
[2024-01-24 13:29:28,542] [INFO] Target genome list was writen to GCF_008923245.1_ASM892324v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:28,567] [INFO] Task started: fastANI
[2024-01-24 13:29:28,567] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2be847b-7e6a-4042-aeb8-ec3373f206c4/GCF_008923245.1_ASM892324v1_genomic.fna.gz --refList GCF_008923245.1_ASM892324v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008923245.1_ASM892324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:47,441] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:47,455] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:47,455] [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_008923245.1	s__Cytobacillus depressus	100.0	1772	1774	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_001509555.1	s__Cytobacillus sp001509555	81.1763	808	1774	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_018343665.1	s__Cytobacillus sp018343665	79.9017	643	1774	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_019039215.1	s__Cytobacillus sp019039215	79.7619	544	1774	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_007995155.1	s__Cytobacillus dafuensis	79.6655	586	1774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900103525.1	s__Neobacillus sp900103525	78.2245	188	1774	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_900199725.1	s__Cytobacillus massiliigabonensis	78.1581	435	1774	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_017874625.1	s__Cytobacillus eiseniae	78.0935	323	1774	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	78.0088	262	1774	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_001243895.1	s__Bacillus_AD testis	77.9555	67	1774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007830235.1	s__Cytobacillus oceanisediminis	77.8937	280	1774	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_018613035.1	s__Cytobacillus sp018613035	77.7683	261	1774	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_016908835.1	s__Bacillus_AD endoradicis	77.7352	109	1774	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_900166665.1	s__Cytobacillus gottheilii_A	77.5637	209	1774	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_011393025.1	s__URHB0009 sp011393025	77.2086	148	1774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__URHB0009	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013760845.1	s__Anoxybacillus_B calidus	76.8122	75	1774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902374955.1	s__Bacillus_AD massilioanorexius	76.6552	105	1774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:47,457] [INFO] GTDB search result was written to GCF_008923245.1_ASM892324v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:47,457] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:47,466] [INFO] DFAST_QC result json was written to GCF_008923245.1_ASM892324v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:47,466] [INFO] DFAST_QC completed!
[2024-01-24 13:29:47,467] [INFO] Total running time: 0h1m34s