[2024-01-25 19:53:35,554] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:35,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:35,556] [INFO] DQC Reference Directory: /var/lib/cwl/stgc223904a-aa10-4e88-aff4-7c59ca9c800a/dqc_reference
[2024-01-25 19:53:36,658] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:36,659] [INFO] Task started: Prodigal
[2024-01-25 19:53:36,659] [INFO] Running command: gunzip -c /var/lib/cwl/stgf769a697-c50c-415f-9534-ddfaee7b3dbd/GCF_030813235.1_ASM3081323v1_genomic.fna.gz | prodigal -d GCF_030813235.1_ASM3081323v1_genomic.fna/cds.fna -a GCF_030813235.1_ASM3081323v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:46,635] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:46,635] [INFO] Task started: HMMsearch
[2024-01-25 19:53:46,636] [INFO] Running command: hmmsearch --tblout GCF_030813235.1_ASM3081323v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc223904a-aa10-4e88-aff4-7c59ca9c800a/dqc_reference/reference_markers.hmm GCF_030813235.1_ASM3081323v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:46,897] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:46,898] [INFO] Found 6/6 markers.
[2024-01-25 19:53:46,938] [INFO] Query marker FASTA was written to GCF_030813235.1_ASM3081323v1_genomic.fna/markers.fasta
[2024-01-25 19:53:46,938] [INFO] Task started: Blastn
[2024-01-25 19:53:46,938] [INFO] Running command: blastn -query GCF_030813235.1_ASM3081323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc223904a-aa10-4e88-aff4-7c59ca9c800a/dqc_reference/reference_markers.fasta -out GCF_030813235.1_ASM3081323v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:47,490] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:47,493] [INFO] Selected 27 target genomes.
[2024-01-25 19:53:47,493] [INFO] Target genome list was writen to GCF_030813235.1_ASM3081323v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:47,525] [INFO] Task started: fastANI
[2024-01-25 19:53:47,525] [INFO] Running command: fastANI --query /var/lib/cwl/stgf769a697-c50c-415f-9534-ddfaee7b3dbd/GCF_030813235.1_ASM3081323v1_genomic.fna.gz --refList GCF_030813235.1_ASM3081323v1_genomic.fna/target_genomes.txt --output GCF_030813235.1_ASM3081323v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:08,153] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:08,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc223904a-aa10-4e88-aff4-7c59ca9c800a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:08,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc223904a-aa10-4e88-aff4-7c59ca9c800a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:08,167] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:54:08,168] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:54:08,168] [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
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	79.7224	699	1814	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	78.4476	304	1814	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	78.1483	255	1814	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	77.8301	248	1814	95	below_threshold
Robertmurraya siralis	strain=171544	GCA_005502275.1	77777	77777	type	True	77.6802	141	1814	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	77.6619	99	1814	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	77.6	207	1814	95	below_threshold
Bacillus mesophilus	strain=DSM 101000	GCA_016908955.1	1808955	1808955	type	True	77.5605	61	1814	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	77.4247	223	1814	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	77.4037	146	1814	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	77.3795	100	1814	95	below_threshold
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	77.3737	150	1814	95	below_threshold
Peribacillus frigoritolerans	strain=FJAT-2396	GCA_001636405.1	450367	450367	type	True	77.2831	103	1814	95	below_threshold
Bacillus cytotoxicus	strain=NVH 391-98	GCA_000017425.1	580165	580165	type	True	77.1764	60	1814	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	77.1696	115	1814	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	77.152	61	1814	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_019915265.1	2672567	2672567	type	True	77.1033	106	1814	95	below_threshold
Bacillus tepidiphilus	strain=SYSU G01002	GCA_009466385.1	2652445	2652445	type	True	77.0811	98	1814	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	77.0426	128	1814	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_011008855.1	2672567	2672567	type	True	76.9848	107	1814	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	76.9467	100	1814	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	76.8885	89	1814	95	below_threshold
Metabacillus mangrovi	strain=KCTC 33872	GCA_009711125.1	1491830	1491830	type	True	76.8397	53	1814	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	76.4842	82	1814	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:08,169] [INFO] DFAST Taxonomy check result was written to GCF_030813235.1_ASM3081323v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:08,170] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:08,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:08,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc223904a-aa10-4e88-aff4-7c59ca9c800a/dqc_reference/checkm_data
[2024-01-25 19:54:08,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:08,226] [INFO] Task started: CheckM
[2024-01-25 19:54:08,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030813235.1_ASM3081323v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030813235.1_ASM3081323v1_genomic.fna/checkm_input GCF_030813235.1_ASM3081323v1_genomic.fna/checkm_result
[2024-01-25 19:54:41,742] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:41,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:41,765] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:41,765] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:41,766] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030813235.1_ASM3081323v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:41,766] [INFO] Task started: Blastn
[2024-01-25 19:54:41,766] [INFO] Running command: blastn -query GCF_030813235.1_ASM3081323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc223904a-aa10-4e88-aff4-7c59ca9c800a/dqc_reference/reference_markers_gtdb.fasta -out GCF_030813235.1_ASM3081323v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:42,556] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:42,560] [INFO] Selected 29 target genomes.
[2024-01-25 19:54:42,560] [INFO] Target genome list was writen to GCF_030813235.1_ASM3081323v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:42,580] [INFO] Task started: fastANI
[2024-01-25 19:54:42,580] [INFO] Running command: fastANI --query /var/lib/cwl/stgf769a697-c50c-415f-9534-ddfaee7b3dbd/GCF_030813235.1_ASM3081323v1_genomic.fna.gz --refList GCF_030813235.1_ASM3081323v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030813235.1_ASM3081323v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:14,100] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:14,118] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:55:14,119] [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_002835735.1	s__Cytobacillus horneckiae	79.7148	700	1814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.87	98.22	0.90	0.90	3	-
GCF_014836495.1	s__Cytobacillus sp014836495	78.4476	304	1814	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_003182355.1	s__Cytobacillus oceanisediminis_A	78.2913	224	1814	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_000518885.1	s__Cytobacillus sp000518885	78.2258	220	1814	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_001420595.1	s__Cytobacillus solani	78.1768	253	1814	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_001636345.1	s__Cytobacillus gottheilii	78.1047	230	1814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	96.50	95.11	0.87	0.87	3	-
GCF_000294775.2	s__Cytobacillus oceanisediminis_B	78.0553	240	1814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.75	98.26	0.86	0.83	6	-
GCF_900166665.1	s__Cytobacillus gottheilii_A	77.9971	236	1814	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_014773385.1	s__IB182487 sp014773385	77.9459	96	1814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__IB182487	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001439605.1	s__Cytobacillus praedii	77.8121	251	1814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.20	99.20	0.93	0.93	2	-
GCF_006546985.1	s__VATK01 sp006546985	77.7423	138	1814	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_005502275.1	s__Robertmurraya siralis	77.7223	142	1814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	99.13	99.00	0.93	0.92	3	-
GCF_900199725.1	s__Cytobacillus massiliigabonensis	77.6424	272	1814	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_007273535.1	s__Niallia circulans_B	77.6134	108	1814	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_004341175.1	s__Neobacillus sp004341175	77.5245	139	1814	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_017874625.1	s__Cytobacillus eiseniae	77.4115	224	1814	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_004358205.1	s__Neobacillus salipaludis	77.4098	148	1814	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_018613055.1	s__Mesobacillus sp018613055	77.3595	98	1814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900103525.1	s__Neobacillus sp900103525	77.2872	144	1814	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_014960805.1	s__Bacillus_BV sp014960805	77.2111	95	1814	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_000482325.1	s__Neobacillus sp000482325	77.196	139	1814	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_013248975.1	s__Neobacillus endophyticus	77.1696	115	1814	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_009466385.1	s__Bacillus_BN tepidiphilus	77.0966	100	1814	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_002835805.1	s__Niallia nealsonii	77.0426	128	1814	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_016107705.1	s__Neobacillus cucumis_B	77.0222	158	1814	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	76.9698	100	1814	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_013200995.1	s__Gottfriedia sp002556365	76.884	74	1814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	95.58	95.58	0.84	0.83	3	-
GCF_002844575.1	s__Margalitia camelliae	76.8279	89	1814	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_002584535.1	s__Bacillus_A cereus_AW	76.4879	82	1814	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	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:14,120] [INFO] GTDB search result was written to GCF_030813235.1_ASM3081323v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:14,121] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:14,125] [INFO] DFAST_QC result json was written to GCF_030813235.1_ASM3081323v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:14,125] [INFO] DFAST_QC completed!
[2024-01-25 19:55:14,125] [INFO] Total running time: 0h1m39s