[2024-01-25 17:41:05,525] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:05,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:05,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b667872-512e-415f-85fd-0cf23f41ca4e/dqc_reference
[2024-01-25 17:41:06,691] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:06,691] [INFO] Task started: Prodigal
[2024-01-25 17:41:06,692] [INFO] Running command: gunzip -c /var/lib/cwl/stg85959dea-4ab3-479e-aef5-e5bda053814a/GCF_002262935.1_ASM226293v1_genomic.fna.gz | prodigal -d GCF_002262935.1_ASM226293v1_genomic.fna/cds.fna -a GCF_002262935.1_ASM226293v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:11,685] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:11,685] [INFO] Task started: HMMsearch
[2024-01-25 17:41:11,685] [INFO] Running command: hmmsearch --tblout GCF_002262935.1_ASM226293v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b667872-512e-415f-85fd-0cf23f41ca4e/dqc_reference/reference_markers.hmm GCF_002262935.1_ASM226293v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:11,953] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:11,954] [INFO] Found 6/6 markers.
[2024-01-25 17:41:11,980] [INFO] Query marker FASTA was written to GCF_002262935.1_ASM226293v1_genomic.fna/markers.fasta
[2024-01-25 17:41:11,980] [INFO] Task started: Blastn
[2024-01-25 17:41:11,981] [INFO] Running command: blastn -query GCF_002262935.1_ASM226293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b667872-512e-415f-85fd-0cf23f41ca4e/dqc_reference/reference_markers.fasta -out GCF_002262935.1_ASM226293v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:12,578] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:12,581] [INFO] Selected 28 target genomes.
[2024-01-25 17:41:12,581] [INFO] Target genome list was writen to GCF_002262935.1_ASM226293v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:12,591] [INFO] Task started: fastANI
[2024-01-25 17:41:12,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg85959dea-4ab3-479e-aef5-e5bda053814a/GCF_002262935.1_ASM226293v1_genomic.fna.gz --refList GCF_002262935.1_ASM226293v1_genomic.fna/target_genomes.txt --output GCF_002262935.1_ASM226293v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:30,395] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:30,395] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b667872-512e-415f-85fd-0cf23f41ca4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:30,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b667872-512e-415f-85fd-0cf23f41ca4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:30,407] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:41:30,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:30,407] [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
Lottiidibacillus patelloidae	strain=SA5d-4	GCA_002262935.1	2670334	2670334	type	True	100.0	995	997	95	conclusive
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	77.3012	65	997	95	below_threshold
Priestia taiwanensis	strain=CGMCC 1.12698	GCA_014638355.1	1347902	1347902	type	True	77.2912	63	997	95	below_threshold
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	77.1231	78	997	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	77.0932	79	997	95	below_threshold
Calidifontibacillus oryziterrae	strain=ZYK	GCA_000331575.1	1191699	1191699	type	True	77.0507	59	997	95	below_threshold
Priestia taiwanensis	strain=DSM 27845	GCA_016908755.1	1347902	1347902	type	True	77.0426	60	997	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_011008805.1	157838	157838	type	True	76.9774	55	997	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.9316	96	997	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_001420715.1	157838	157838	type	True	76.9156	58	997	95	below_threshold
Gottfriedia acidiceleris	strain=DSM 18954	GCA_002128425.1	371036	371036	type	True	76.889	77	997	95	below_threshold
Gottfriedia luciferensis	strain=DSM 18845	GCA_002156865.1	178774	178774	type	True	76.8503	85	997	95	below_threshold
Bacillus toyonensis	strain=BCT-7112	GCA_000496285.1	155322	155322	type	True	76.8043	100	997	95	below_threshold
Bacillus nitratireducens	strain=4049	GCA_001884135.1	2026193	2026193	type	True	76.7856	82	997	95	below_threshold
Pseudalkalibacillus decolorationis	strain=DSM 14890	GCA_024609785.1	163879	163879	type	True	76.7318	50	997	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.6788	55	997	95	below_threshold
Bacillus proteolyticus	strain=TD42	GCA_001884065.1	2026192	2026192	type	True	76.5611	76	997	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.5517	85	997	95	below_threshold
Schinkia azotoformans	strain=LMG 9581	GCA_000307855.1	1454	1454	type	True	76.354	51	997	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:30,409] [INFO] DFAST Taxonomy check result was written to GCF_002262935.1_ASM226293v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:30,409] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:30,409] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:30,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b667872-512e-415f-85fd-0cf23f41ca4e/dqc_reference/checkm_data
[2024-01-25 17:41:30,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:30,441] [INFO] Task started: CheckM
[2024-01-25 17:41:30,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002262935.1_ASM226293v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002262935.1_ASM226293v1_genomic.fna/checkm_input GCF_002262935.1_ASM226293v1_genomic.fna/checkm_result
[2024-01-25 17:41:51,113] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:51,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:51,136] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:51,136] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:51,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002262935.1_ASM226293v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:51,137] [INFO] Task started: Blastn
[2024-01-25 17:41:51,137] [INFO] Running command: blastn -query GCF_002262935.1_ASM226293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b667872-512e-415f-85fd-0cf23f41ca4e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002262935.1_ASM226293v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:52,120] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:52,124] [INFO] Selected 28 target genomes.
[2024-01-25 17:41:52,124] [INFO] Target genome list was writen to GCF_002262935.1_ASM226293v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:52,147] [INFO] Task started: fastANI
[2024-01-25 17:41:52,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg85959dea-4ab3-479e-aef5-e5bda053814a/GCF_002262935.1_ASM226293v1_genomic.fna.gz --refList GCF_002262935.1_ASM226293v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002262935.1_ASM226293v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:12,316] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:12,328] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:12,328] [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_002262935.1	s__Lottiidibacillus patelloidae	100.0	995	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_E;f__SA5d-4;g__Lottiidibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003053645.1	s__Gottfriedia sp003053645	77.3417	74	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902829255.1	s__Metabacillus niabensis	77.3389	63	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.58	98.41	0.91	0.90	3	-
GCF_018343615.1	s__Margalitia sp018343615	77.2955	58	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001712755.1	s__Gottfriedia luciferensis_B	77.2953	71	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	99.30	99.28	0.95	0.93	3	-
GCF_014638355.1	s__Priestia_D taiwanensis	77.1966	62	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Priestia_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002128405.1	s__Gottfriedia solisilvae	77.0898	79	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	98.14	96.28	0.93	0.87	3	-
GCF_000331575.1	s__Calidifontibacillus oryziterrae	77.0507	59	997	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	-
GCF_002156865.1	s__Gottfriedia luciferensis	76.9495	85	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420715.1	s__Margalitia shackletonii	76.9156	58	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.16	98.74	0.93	0.89	4	-
GCF_000956595.1	s__Priestia aryabhattai	76.915	65	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	96.022	97.07	96.58	0.92	0.91	12	-
GCF_016890225.1	s__Bacillus_BS sp016890225	76.8862	96	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591565.1	s__Priestia flexa	76.8658	65	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	99.12	98.83	0.89	0.87	15	-
GCF_000496285.1	s__Bacillus_A toyonensis	76.7996	99	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.12	96.74	0.93	0.83	279	-
GCF_003726095.1	s__Niallia circulans_A	76.798	57	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.27	98.85	0.92	0.89	8	-
GCF_002574955.1	s__Bacillus_A cereus_AT	76.7837	88	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.1182	99.26	96.80	0.94	0.81	6	-
GCF_000686805.1	s__Neobacillus sp000686805	76.5538	61	997	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_001884235.1	s__Bacillus_A paramycoides	76.43	82	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.72	97.18	0.88	0.85	10	-
GCF_002577655.1	s__Metabacillus sp002577655	76.3826	84	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:12,330] [INFO] GTDB search result was written to GCF_002262935.1_ASM226293v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:12,331] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:12,335] [INFO] DFAST_QC result json was written to GCF_002262935.1_ASM226293v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:12,335] [INFO] DFAST_QC completed!
[2024-01-25 17:42:12,335] [INFO] Total running time: 0h1m7s