[2024-01-24 13:49:00,075] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:00,079] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:00,079] [INFO] DQC Reference Directory: /var/lib/cwl/stga4c2b524-b809-4d8f-887f-ccc3e2548f1f/dqc_reference
[2024-01-24 13:49:01,401] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,402] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,402] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4051f08-5312-4720-a1d0-838c709410f8/GCF_001591545.1_ASM159154v1_genomic.fna.gz | prodigal -d GCF_001591545.1_ASM159154v1_genomic.fna/cds.fna -a GCF_001591545.1_ASM159154v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:10,396] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:10,396] [INFO] Task started: HMMsearch
[2024-01-24 13:49:10,396] [INFO] Running command: hmmsearch --tblout GCF_001591545.1_ASM159154v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4c2b524-b809-4d8f-887f-ccc3e2548f1f/dqc_reference/reference_markers.hmm GCF_001591545.1_ASM159154v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:10,712] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:10,713] [INFO] Found 6/6 markers.
[2024-01-24 13:49:10,754] [INFO] Query marker FASTA was written to GCF_001591545.1_ASM159154v1_genomic.fna/markers.fasta
[2024-01-24 13:49:10,755] [INFO] Task started: Blastn
[2024-01-24 13:49:10,755] [INFO] Running command: blastn -query GCF_001591545.1_ASM159154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4c2b524-b809-4d8f-887f-ccc3e2548f1f/dqc_reference/reference_markers.fasta -out GCF_001591545.1_ASM159154v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:11,344] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:11,348] [INFO] Selected 20 target genomes.
[2024-01-24 13:49:11,348] [INFO] Target genome list was writen to GCF_001591545.1_ASM159154v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:11,395] [INFO] Task started: fastANI
[2024-01-24 13:49:11,395] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4051f08-5312-4720-a1d0-838c709410f8/GCF_001591545.1_ASM159154v1_genomic.fna.gz --refList GCF_001591545.1_ASM159154v1_genomic.fna/target_genomes.txt --output GCF_001591545.1_ASM159154v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:24,346] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:24,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4c2b524-b809-4d8f-887f-ccc3e2548f1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:24,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4c2b524-b809-4d8f-887f-ccc3e2548f1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:24,370] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:24,371] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:24,371] [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
Lederbergia lenta	strain=NBRC 16444	GCA_001591545.1	1467	1467	type	True	100.0	1432	1434	95	conclusive
Lederbergia lenta	strain=NCTC4824	GCA_900478165.1	1467	1467	type	True	99.999	1433	1434	95	conclusive
Lederbergia galactosidilytica	strain=DSM 15595	GCA_017873565.1	217031	217031	type	True	77.0298	179	1434	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	76.7029	89	1434	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_016785185.1	46224	46224	type	True	76.6312	92	1434	95	below_threshold
Metabacillus fastidiosus	strain=NBRC 101226	GCA_001591625.1	1458	1458	type	True	76.5441	75	1434	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_001420715.1	157838	157838	type	True	76.51	94	1434	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_003055085.1	46224	46224	type	True	76.4988	86	1434	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_002009555.1	38875	38875	type	True	76.4425	99	1434	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	76.4008	110	1434	95	below_threshold
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	76.3988	52	1434	95	below_threshold
Weizmannia ginsengihumi	strain=Gsoil 114	GCA_011008565.1	363870	363870	type	True	76.3836	81	1434	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	76.3689	108	1434	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	76.3265	71	1434	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.0461	65	1434	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:24,373] [INFO] DFAST Taxonomy check result was written to GCF_001591545.1_ASM159154v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:24,373] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:24,373] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:24,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4c2b524-b809-4d8f-887f-ccc3e2548f1f/dqc_reference/checkm_data
[2024-01-24 13:49:24,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:24,417] [INFO] Task started: CheckM
[2024-01-24 13:49:24,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591545.1_ASM159154v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591545.1_ASM159154v1_genomic.fna/checkm_input GCF_001591545.1_ASM159154v1_genomic.fna/checkm_result
[2024-01-24 13:49:56,407] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:56,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:56,431] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:56,431] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:56,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591545.1_ASM159154v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:56,432] [INFO] Task started: Blastn
[2024-01-24 13:49:56,432] [INFO] Running command: blastn -query GCF_001591545.1_ASM159154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4c2b524-b809-4d8f-887f-ccc3e2548f1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591545.1_ASM159154v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:57,260] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:57,264] [INFO] Selected 24 target genomes.
[2024-01-24 13:49:57,264] [INFO] Target genome list was writen to GCF_001591545.1_ASM159154v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:57,353] [INFO] Task started: fastANI
[2024-01-24 13:49:57,353] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4051f08-5312-4720-a1d0-838c709410f8/GCF_001591545.1_ASM159154v1_genomic.fna.gz --refList GCF_001591545.1_ASM159154v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591545.1_ASM159154v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:14,709] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:14,731] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:14,732] [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_001591545.1	s__Bacillus_AH lentus	100.0	1432	1434	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AH	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_018343515.1	s__Bacillus_AH sp018343515	77.9934	295	1434	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343525.1	s__FJAT-49754 sp018343525	77.9912	321	1434	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49754	95.0	98.88	98.76	0.94	0.94	3	-
GCF_018343715.1	s__FJAT-49711 sp018343715	77.4193	213	1434	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49711	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679095.1	s__DE0126 sp007679095	77.0009	174	1434	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__DE0126	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873565.1	s__Lederbergia galactosidilytica	76.9657	181	1434	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Lederbergia	95.0	99.35	99.18	0.94	0.93	4	-
GCF_001420595.1	s__Cytobacillus solani	76.6293	88	1434	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_004006295.1	s__Peribacillus asahii_A	76.5779	79	1434	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_016756695.1	s__Heyndrickxia sporothermodurans	76.577	89	1434	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	99.73	97.95	0.95	0.84	38	-
GCF_001591625.1	s__Metabacillus fastidiosus	76.5441	75	1434	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420715.1	s__Margalitia shackletonii	76.51	94	1434	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_002844575.1	s__Margalitia camelliae	76.4012	93	1434	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.53	99.53	0.93	0.93	2	-
GCF_003073175.1	s__Bacillus_BN acanthi	76.3988	52	1434	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011008565.1	s__Weizmannia ginsengihum	76.3836	81	1434	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Weizmannia	95.0	99.62	99.53	0.95	0.92	4	-
GCF_017809215.1	s__Heyndrickxia oleronia	76.3689	108	1434	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	98.68	97.33	0.92	0.89	7	-
GCF_003667865.1	s__Bacillus_BQ marisflavi_A	76.2821	78	1434	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_001889165.1	s__Metabacillus weihaiensis	76.242	63	1434	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	97.24	97.24	0.88	0.88	2	-
GCF_004341175.1	s__Neobacillus sp004341175	76.1873	79	1434	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_902374955.1	s__Bacillus_AD massilioanorexius	76.1542	61	1434	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	-
GCA_017656295.1	s__JACDOC01 sp017656295	76.01	51	1434	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__JACDOC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001595725.1	s__Bacillus_A thuringiensis_K	75.9957	59	1434	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:14,734] [INFO] GTDB search result was written to GCF_001591545.1_ASM159154v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:14,735] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:14,744] [INFO] DFAST_QC result json was written to GCF_001591545.1_ASM159154v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:14,745] [INFO] DFAST_QC completed!
[2024-01-24 13:50:14,745] [INFO] Total running time: 0h1m15s