[2024-01-24 15:02:07,445] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:07,447] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:07,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg60992dea-86fb-4320-bf0e-ed7c22279adc/dqc_reference
[2024-01-24 15:02:09,601] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:09,602] [INFO] Task started: Prodigal
[2024-01-24 15:02:09,603] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a1cdd99-8e1e-46d0-ae95-3d348e380a34/GCF_000430785.1_ASM43078v1_genomic.fna.gz | prodigal -d GCF_000430785.1_ASM43078v1_genomic.fna/cds.fna -a GCF_000430785.1_ASM43078v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:21,454] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:21,455] [INFO] Task started: HMMsearch
[2024-01-24 15:02:21,455] [INFO] Running command: hmmsearch --tblout GCF_000430785.1_ASM43078v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60992dea-86fb-4320-bf0e-ed7c22279adc/dqc_reference/reference_markers.hmm GCF_000430785.1_ASM43078v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:21,707] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:21,708] [INFO] Found 6/6 markers.
[2024-01-24 15:02:21,751] [INFO] Query marker FASTA was written to GCF_000430785.1_ASM43078v1_genomic.fna/markers.fasta
[2024-01-24 15:02:21,751] [INFO] Task started: Blastn
[2024-01-24 15:02:21,752] [INFO] Running command: blastn -query GCF_000430785.1_ASM43078v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60992dea-86fb-4320-bf0e-ed7c22279adc/dqc_reference/reference_markers.fasta -out GCF_000430785.1_ASM43078v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:22,385] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:22,389] [INFO] Selected 27 target genomes.
[2024-01-24 15:02:22,390] [INFO] Target genome list was writen to GCF_000430785.1_ASM43078v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:22,410] [INFO] Task started: fastANI
[2024-01-24 15:02:22,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a1cdd99-8e1e-46d0-ae95-3d348e380a34/GCF_000430785.1_ASM43078v1_genomic.fna.gz --refList GCF_000430785.1_ASM43078v1_genomic.fna/target_genomes.txt --output GCF_000430785.1_ASM43078v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:45,618] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:45,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60992dea-86fb-4320-bf0e-ed7c22279adc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:45,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60992dea-86fb-4320-bf0e-ed7c22279adc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:45,633] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:45,633] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:45,633] [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
Ectobacillus panaciterrae	strain=DSM 19096	GCA_000430785.1	363872	363872	type	True	100.0	1695	1707	95	conclusive
Ectobacillus antri	strain=SYSU K30001	GCA_003852715.1	2486280	2486280	type	True	78.6142	325	1707	95	below_threshold
Bacillus gaemokensis	strain=KCTC 13318	GCA_001590835.1	574375	574375	type	True	78.1026	263	1707	95	below_threshold
Bacillus clarus	strain=BHP	GCA_000746925.1	2338372	2338372	type	True	78.0909	264	1707	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	78.0881	257	1707	95	below_threshold
Bacillus cereus	strain=NCTC2599	GCA_900445355.1	1396	1396	suspected-type	True	78.074	227	1707	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_006094295.1	1396	1396	suspected-type	True	78.0565	229	1707	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_000007825.1	1396	1396	suspected-type	True	78.0524	229	1707	95	below_threshold
Bacillus cytotoxicus	strain=NVH 391-98	GCA_000017425.1	580165	580165	type	True	77.9939	209	1707	95	below_threshold
Bacillus cereus	strain=FSL M8-0473	GCA_002014665.1	1396	1396	suspected-type	True	77.9844	229	1707	95	below_threshold
Bacillus clarus	strain=PS00077A	GCA_003428195.1	2338372	2338372	type	True	77.9314	257	1707	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.2867	103	1707	95	below_threshold
Priestia megaterium	strain=ATCC 14581	GCA_900113355.1	1404	1404	suspected-type	True	76.9824	138	1707	95	below_threshold
Priestia megaterium	strain=NCTC10342	GCA_900445485.1	1404	1404	type	True	76.9594	135	1707	95	below_threshold
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	76.8054	128	1707	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	76.7139	85	1707	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.6079	62	1707	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:45,641] [INFO] DFAST Taxonomy check result was written to GCF_000430785.1_ASM43078v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:45,642] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:45,643] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:45,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60992dea-86fb-4320-bf0e-ed7c22279adc/dqc_reference/checkm_data
[2024-01-24 15:02:45,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:45,700] [INFO] Task started: CheckM
[2024-01-24 15:02:45,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430785.1_ASM43078v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430785.1_ASM43078v1_genomic.fna/checkm_input GCF_000430785.1_ASM43078v1_genomic.fna/checkm_result
[2024-01-24 15:03:26,694] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:26,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:26,717] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:26,717] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:26,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430785.1_ASM43078v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:26,718] [INFO] Task started: Blastn
[2024-01-24 15:03:26,718] [INFO] Running command: blastn -query GCF_000430785.1_ASM43078v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60992dea-86fb-4320-bf0e-ed7c22279adc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430785.1_ASM43078v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:27,550] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:27,553] [INFO] Selected 23 target genomes.
[2024-01-24 15:03:27,554] [INFO] Target genome list was writen to GCF_000430785.1_ASM43078v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:27,583] [INFO] Task started: fastANI
[2024-01-24 15:03:27,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a1cdd99-8e1e-46d0-ae95-3d348e380a34/GCF_000430785.1_ASM43078v1_genomic.fna.gz --refList GCF_000430785.1_ASM43078v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430785.1_ASM43078v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:53,043] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:53,065] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:53,066] [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_000430785.1	s__Ectobacillus panaciterrae	100.0	1697	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Ectobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004138295.1	s__Ectobacillus funiculus	79.0952	376	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Ectobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002560985.1	s__Bacillus_A sp002560985	79.0406	343	1707	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	-
GCA_002582035.1	s__Bacillus_A pseudomycoides_B	78.7445	339	1707	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_003852715.1	s__Ectobacillus antri	78.6229	326	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Ectobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002551005.1	s__Bacillus_A pseudomycoides_C	78.4627	305	1707	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_002559665.1	s__Bacillus_A cereus_AV	78.3947	266	1707	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_000383235.1	s__Bacillus_A sp000383235	78.322	260	1707	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_000161455.1	s__Bacillus_A pseudomycoides	78.2189	286	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.62	95.81	0.91	0.85	116	-
GCF_002584535.1	s__Bacillus_A cereus_AW	78.201	276	1707	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_002551815.1	s__Bacillus_A sp002551815	78.1329	255	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.80	99.69	0.94	0.92	5	-
GCF_001590835.1	s__Bacillus_A gaemokensis	78.1015	263	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000746925.1	s__Bacillus_A clarus	78.0781	264	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000007825.1	s__Bacillus_A cereus	78.0374	230	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	97.0513	98.55	97.64	0.91	0.84	235	-
GCF_000017425.1	s__Bacillus_A cytotoxicus	77.976	209	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.49	99.12	0.95	0.93	21	-
GCF_001595725.1	s__Bacillus_A thuringiensis_K	77.8661	244	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	96.827	99.05	98.75	0.91	0.78	20	-
GCF_017742235.1	s__JAGHKQ01 sp017742235	77.8441	264	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__JAGHKQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007673305.1	s__Bacillus_A mycoides_C	77.6326	221	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	95.83	95.78	0.82	0.81	3	-
GCF_900199725.1	s__Cytobacillus massiliigabonensis	77.3392	88	1707	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_003667865.1	s__Bacillus_BQ marisflavi_A	77.0591	52	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BQ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003184905.1	s__Priestia sp003184905	76.7407	90	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016841285.1	s__Calidifontibacillus sp016841285	76.4072	52	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:53,068] [INFO] GTDB search result was written to GCF_000430785.1_ASM43078v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:53,069] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:53,074] [INFO] DFAST_QC result json was written to GCF_000430785.1_ASM43078v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:53,074] [INFO] DFAST_QC completed!
[2024-01-24 15:03:53,074] [INFO] Total running time: 0h1m46s