[2024-01-24 13:41:40,627] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,629] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ae738d3-4ccf-48e5-9fc6-44b6ec22c94d/dqc_reference
[2024-01-24 13:41:42,013] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,014] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,014] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe11d015-b62a-448b-9c86-f6e8ac541f8f/GCF_003570725.1_ASM357072v1_genomic.fna.gz | prodigal -d GCF_003570725.1_ASM357072v1_genomic.fna/cds.fna -a GCF_003570725.1_ASM357072v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:50,824] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:50,824] [INFO] Task started: HMMsearch
[2024-01-24 13:41:50,825] [INFO] Running command: hmmsearch --tblout GCF_003570725.1_ASM357072v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ae738d3-4ccf-48e5-9fc6-44b6ec22c94d/dqc_reference/reference_markers.hmm GCF_003570725.1_ASM357072v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:51,133] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:51,135] [INFO] Found 6/6 markers.
[2024-01-24 13:41:51,176] [INFO] Query marker FASTA was written to GCF_003570725.1_ASM357072v1_genomic.fna/markers.fasta
[2024-01-24 13:41:51,176] [INFO] Task started: Blastn
[2024-01-24 13:41:51,177] [INFO] Running command: blastn -query GCF_003570725.1_ASM357072v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ae738d3-4ccf-48e5-9fc6-44b6ec22c94d/dqc_reference/reference_markers.fasta -out GCF_003570725.1_ASM357072v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:51,815] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:51,819] [INFO] Selected 25 target genomes.
[2024-01-24 13:41:51,820] [INFO] Target genome list was writen to GCF_003570725.1_ASM357072v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:51,834] [INFO] Task started: fastANI
[2024-01-24 13:41:51,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe11d015-b62a-448b-9c86-f6e8ac541f8f/GCF_003570725.1_ASM357072v1_genomic.fna.gz --refList GCF_003570725.1_ASM357072v1_genomic.fna/target_genomes.txt --output GCF_003570725.1_ASM357072v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:08,995] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:08,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ae738d3-4ccf-48e5-9fc6-44b6ec22c94d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:08,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ae738d3-4ccf-48e5-9fc6-44b6ec22c94d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:09,018] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:09,019] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:09,019] [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
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	100.0	1401	1403	95	conclusive
Peribacillus butanolivorans	strain=DSM 18926	GCA_001273755.1	421767	421767	type	True	78.5692	313	1403	95	below_threshold
Peribacillus simplex	strain=DSM 1321	GCA_002243645.1	1478	1478	suspected-type	True	78.206	287	1403	95	below_threshold
Peribacillus simplex	strain=NBRC 15720	GCA_001591785.1	1478	1478	suspected-type	True	78.1839	281	1403	95	below_threshold
Peribacillus loiseleuriae	strain=FJAT-27997	GCA_001183985.1	1679170	1679170	type	True	78.0739	232	1403	95	below_threshold
Peribacillus muralis	strain=DSM 16288	GCA_001439925.1	264697	264697	type	True	78.0332	217	1403	95	below_threshold
Peribacillus psychrosaccharolyticus	strain=ATCC 23296	GCA_000305495.2	1407	1407	type	True	77.7494	157	1403	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	77.2584	127	1403	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	77.2584	127	1403	95	below_threshold
Peribacillus faecalis	strain=AGMB 02131	GCA_014712675.1	2772559	2772559	type	True	77.1234	102	1403	95	below_threshold
Bacillus wudalianchiensis	strain=FJAT-27215	GCA_001685015.1	1743143	1743143	type	True	77.0851	84	1403	95	below_threshold
Bacillus marasmi	strain=Marseille-P3556	GCA_902168435.1	1926279	1926279	type	True	77.0477	109	1403	95	below_threshold
Psychrobacillus insolitus	strain=DSM 5	GCA_003254155.1	1461	1461	type	True	77.0226	92	1403	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.7836	102	1403	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	76.764	89	1403	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.758	118	1403	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.6805	113	1403	95	below_threshold
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	76.5688	109	1403	95	below_threshold
Schinkia azotoformans	strain=LMG 9581	GCA_000307855.1	1454	1454	type	True	76.5244	79	1403	95	below_threshold
Anoxybacillus gonensis	strain=G2	GCA_000770375.1	198467	198467	suspected-type	True	76.1322	62	1403	95	below_threshold
Anoxybacillus gonensis	strain=G2	GCA_001187595.1	198467	198467	suspected-type	True	76.1279	62	1403	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:09,021] [INFO] DFAST Taxonomy check result was written to GCF_003570725.1_ASM357072v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:09,022] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:09,022] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:09,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ae738d3-4ccf-48e5-9fc6-44b6ec22c94d/dqc_reference/checkm_data
[2024-01-24 13:42:09,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:09,068] [INFO] Task started: CheckM
[2024-01-24 13:42:09,069] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003570725.1_ASM357072v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003570725.1_ASM357072v1_genomic.fna/checkm_input GCF_003570725.1_ASM357072v1_genomic.fna/checkm_result
[2024-01-24 13:42:39,574] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:39,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:39,597] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:39,598] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:39,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003570725.1_ASM357072v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:39,599] [INFO] Task started: Blastn
[2024-01-24 13:42:39,599] [INFO] Running command: blastn -query GCF_003570725.1_ASM357072v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ae738d3-4ccf-48e5-9fc6-44b6ec22c94d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003570725.1_ASM357072v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:40,378] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:40,383] [INFO] Selected 19 target genomes.
[2024-01-24 13:42:40,383] [INFO] Target genome list was writen to GCF_003570725.1_ASM357072v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:40,429] [INFO] Task started: fastANI
[2024-01-24 13:42:40,429] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe11d015-b62a-448b-9c86-f6e8ac541f8f/GCF_003570725.1_ASM357072v1_genomic.fna.gz --refList GCF_003570725.1_ASM357072v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003570725.1_ASM357072v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:55,027] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:55,046] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:55,047] [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_003570725.1	s__Peribacillus asahii	100.0	1401	1403	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	conclusive
GCF_004006295.1	s__Peribacillus asahii_A	94.6892	1179	1403	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_001273755.1	s__Peribacillus butanolivorans	78.5571	314	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	97.70	97.35	0.87	0.86	10	-
GCF_001510645.1	s__Peribacillus sp001510645	78.1661	230	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001183985.1	s__Peribacillus loiseleuriae	78.0991	231	1403	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_009183415.1	s__Niallia sp009183415	77.9235	104	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138605.1	s__Peribacillus huizhouensis	77.8792	237	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	98.72	98.72	0.94	0.94	2	-
GCF_000305495.1	s__Peribacillus psychrosaccharolyticus	77.7899	155	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	99.97	99.97	1.00	1.00	2	-
GCF_016908835.1	s__Bacillus_AD endoradicis	77.5445	147	1403	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_005280205.1	s__Robertmurraya yapensis	77.2584	127	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014712675.1	s__Bacillus_AD faecalis	77.1234	102	1403	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_000746925.1	s__Bacillus_A clarus	77.0351	110	1403	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_003400205.1	s__Fredinandcohnia sp003400205	76.8976	105	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002261155.1	s__FJAT-46582 sp002261155	76.7889	108	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002975175.1	s__Bacillus_A sp002975175	76.6929	110	1403	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_001757995.1	s__Bacillus_A mycoides_B	76.6876	110	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.94	99.86	0.98	0.98	4	-
GCF_001591585.1	s__Niallia circulans	76.6805	113	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.18	98.58	0.93	0.91	9	-
GCF_000307855.1	s__Calidifontibacillus azotoformans	76.5244	79	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	97.05	97.05	0.89	0.89	2	-
GCF_016909075.1	s__Priestia iocasae	76.4667	105	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:55,048] [INFO] GTDB search result was written to GCF_003570725.1_ASM357072v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:55,049] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:55,053] [INFO] DFAST_QC result json was written to GCF_003570725.1_ASM357072v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:55,054] [INFO] DFAST_QC completed!
[2024-01-24 13:42:55,054] [INFO] Total running time: 0h1m14s