[2024-01-25 18:45:50,787] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:50,788] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:50,788] [INFO] DQC Reference Directory: /var/lib/cwl/stg683fea30-fe53-4560-af5f-f8642b8a4202/dqc_reference
[2024-01-25 18:45:51,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:51,909] [INFO] Task started: Prodigal
[2024-01-25 18:45:51,909] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e1dcb4e-3dc1-4b9b-bbbf-b0e997de09da/GCF_002019645.1_ASM201964v1_genomic.fna.gz | prodigal -d GCF_002019645.1_ASM201964v1_genomic.fna/cds.fna -a GCF_002019645.1_ASM201964v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:01,171] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:01,171] [INFO] Task started: HMMsearch
[2024-01-25 18:46:01,171] [INFO] Running command: hmmsearch --tblout GCF_002019645.1_ASM201964v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg683fea30-fe53-4560-af5f-f8642b8a4202/dqc_reference/reference_markers.hmm GCF_002019645.1_ASM201964v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:01,449] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:01,450] [INFO] Found 6/6 markers.
[2024-01-25 18:46:01,491] [INFO] Query marker FASTA was written to GCF_002019645.1_ASM201964v1_genomic.fna/markers.fasta
[2024-01-25 18:46:01,491] [INFO] Task started: Blastn
[2024-01-25 18:46:01,491] [INFO] Running command: blastn -query GCF_002019645.1_ASM201964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg683fea30-fe53-4560-af5f-f8642b8a4202/dqc_reference/reference_markers.fasta -out GCF_002019645.1_ASM201964v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:02,073] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:02,075] [INFO] Selected 28 target genomes.
[2024-01-25 18:46:02,076] [INFO] Target genome list was writen to GCF_002019645.1_ASM201964v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:02,116] [INFO] Task started: fastANI
[2024-01-25 18:46:02,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e1dcb4e-3dc1-4b9b-bbbf-b0e997de09da/GCF_002019645.1_ASM201964v1_genomic.fna.gz --refList GCF_002019645.1_ASM201964v1_genomic.fna/target_genomes.txt --output GCF_002019645.1_ASM201964v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:25,933] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:25,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg683fea30-fe53-4560-af5f-f8642b8a4202/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:25,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg683fea30-fe53-4560-af5f-f8642b8a4202/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:25,945] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:46:25,945] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:46:25,946] [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
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	99.9955	1804	1808	95	conclusive
Sporosarcina ureilytica	strain=LMG 22257	GCA_001753205.1	298596	298596	type	True	79.7262	50	1808	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	79.5763	599	1808	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_001420715.1	157838	157838	type	True	79.0084	99	1808	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	78.7562	191	1808	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	78.3395	214	1808	95	below_threshold
Fredinandcohnia onubensis	strain=0911MAR22V3	GCA_002734215.1	1571209	1571209	type	True	77.7955	167	1808	95	below_threshold
Cytobacillus luteolus	strain=YIM 93174	GCA_014982515.1	682179	682179	type	True	77.6355	215	1808	95	below_threshold
Cytobacillus luteolus	strain=DSM 22388	GCA_017873715.1	682179	682179	type	True	77.6066	214	1808	95	below_threshold
Bacillus tepidiphilus	strain=SYSU G01002	GCA_009466385.1	2652445	2652445	type	True	77.4707	89	1808	95	below_threshold
Ectobacillus panaciterrae	strain=DSM 19096	GCA_000430785.1	363872	363872	type	True	77.3962	74	1808	95	below_threshold
Mesobacillus subterraneus	strain=DSM 13966	GCA_003937825.1	285983	285983	suspected-type	True	77.2848	77	1808	95	below_threshold
Anaerobacillus alkaliphilus	strain=B16-10	GCA_004116265.1	1548597	1548597	type	True	77.2388	101	1808	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	77.1843	209	1808	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	77.0478	217	1808	95	below_threshold
Bacillus benzoevorans	strain=DSM 5391	GCA_014207535.1	1456	1456	type	True	76.9775	70	1808	95	below_threshold
Gottfriedia luciferensis	strain=DSM 18845	GCA_002156865.1	178774	178774	type	True	76.8689	108	1808	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.8618	141	1808	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	76.8318	57	1808	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.6862	87	1808	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:25,947] [INFO] DFAST Taxonomy check result was written to GCF_002019645.1_ASM201964v1_genomic.fna/tc_result.tsv
[2024-01-25 18:46:25,947] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:25,947] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:25,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg683fea30-fe53-4560-af5f-f8642b8a4202/dqc_reference/checkm_data
[2024-01-25 18:46:25,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:26,001] [INFO] Task started: CheckM
[2024-01-25 18:46:26,001] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002019645.1_ASM201964v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002019645.1_ASM201964v1_genomic.fna/checkm_input GCF_002019645.1_ASM201964v1_genomic.fna/checkm_result
[2024-01-25 18:46:57,807] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:57,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:57,825] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:57,825] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:57,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002019645.1_ASM201964v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:57,826] [INFO] Task started: Blastn
[2024-01-25 18:46:57,826] [INFO] Running command: blastn -query GCF_002019645.1_ASM201964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg683fea30-fe53-4560-af5f-f8642b8a4202/dqc_reference/reference_markers_gtdb.fasta -out GCF_002019645.1_ASM201964v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:58,671] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:58,682] [INFO] Selected 24 target genomes.
[2024-01-25 18:46:58,683] [INFO] Target genome list was writen to GCF_002019645.1_ASM201964v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:58,717] [INFO] Task started: fastANI
[2024-01-25 18:46:58,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e1dcb4e-3dc1-4b9b-bbbf-b0e997de09da/GCF_002019645.1_ASM201964v1_genomic.fna.gz --refList GCF_002019645.1_ASM201964v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002019645.1_ASM201964v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:24,122] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:24,136] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:24,136] [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_002019645.1	s__Litchfieldia alkalitelluris	99.9955	1803	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005154805.1	s__Neobacillus sp005154805	79.7659	113	1808	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_900104555.1	s__Litchfieldia salsa	79.5422	604	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177675.1	s__Neobacillus sp900177675	79.3535	105	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.52	98.52	0.84	0.84	2	-
GCF_014837155.1	s__Litchfieldia sp014837155	79.3035	488	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156865.1	s__Fredinandcohnia sinesaloumensis	78.8663	188	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014960805.1	s__Bacillus_BV sp014960805	78.7084	228	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Bacillus_BV	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002734215.1	s__Fredinandcohnia onubensis	77.8145	166	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343525.1	s__FJAT-49754 sp018343525	77.7647	86	1808	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_002734285.1	s__Fredinandcohnia onubensis_A	77.6725	181	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003400205.1	s__Fredinandcohnia sp003400205	77.6656	167	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873715.1	s__Bacillus_BV luteolus	77.6223	215	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Bacillus_BV	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000285535.1	s__Fredinandcohnia timonensis	77.573	183	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018613065.1	s__Neobacillus sp018613065	77.3749	105	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.53	95.32	0.78	0.75	6	-
GCF_009466385.1	s__Bacillus_BN tepidiphilus	77.3457	89	1808	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_002585305.1	s__Neobacillus sp002585305	77.1914	96	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.64	95.53	0.90	0.84	3	-
GCF_000759675.1	s__Neobacillus niacini_A	76.986	141	1808	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_001712755.1	s__Gottfriedia luciferensis_B	76.9144	110	1808	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_002860255.1	s__Neobacillus cucumis_A	76.9117	124	1808	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_001591645.1	s__Robertmurraya korlensis	76.8938	150	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006546985.1	s__VATK01 sp006546985	76.7426	106	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__VATK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000307875.1	s__Neobacillus bataviensis	76.6349	97	1808	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_016879755.1	s__Bacillus_AZ sp016879755	76.6224	120	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:24,138] [INFO] GTDB search result was written to GCF_002019645.1_ASM201964v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:24,138] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:24,143] [INFO] DFAST_QC result json was written to GCF_002019645.1_ASM201964v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:24,144] [INFO] DFAST_QC completed!
[2024-01-25 18:47:24,144] [INFO] Total running time: 0h1m33s