[2024-01-24 14:30:34,212] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:34,218] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:34,218] [INFO] DQC Reference Directory: /var/lib/cwl/stgac6e4159-6947-49d7-91b2-4f8b63fae032/dqc_reference
[2024-01-24 14:30:35,661] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:35,662] [INFO] Task started: Prodigal
[2024-01-24 14:30:35,662] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2f74660-c6df-4509-98a6-b8627115827d/GCF_002746455.1_ASM274645v1_genomic.fna.gz | prodigal -d GCF_002746455.1_ASM274645v1_genomic.fna/cds.fna -a GCF_002746455.1_ASM274645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:47,181] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:47,182] [INFO] Task started: HMMsearch
[2024-01-24 14:30:47,182] [INFO] Running command: hmmsearch --tblout GCF_002746455.1_ASM274645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac6e4159-6947-49d7-91b2-4f8b63fae032/dqc_reference/reference_markers.hmm GCF_002746455.1_ASM274645v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:47,531] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:47,532] [INFO] Found 6/6 markers.
[2024-01-24 14:30:47,587] [INFO] Query marker FASTA was written to GCF_002746455.1_ASM274645v1_genomic.fna/markers.fasta
[2024-01-24 14:30:47,587] [INFO] Task started: Blastn
[2024-01-24 14:30:47,587] [INFO] Running command: blastn -query GCF_002746455.1_ASM274645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac6e4159-6947-49d7-91b2-4f8b63fae032/dqc_reference/reference_markers.fasta -out GCF_002746455.1_ASM274645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:48,283] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:48,286] [INFO] Selected 23 target genomes.
[2024-01-24 14:30:48,287] [INFO] Target genome list was writen to GCF_002746455.1_ASM274645v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:00,653] [INFO] Task started: fastANI
[2024-01-24 14:31:00,655] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2f74660-c6df-4509-98a6-b8627115827d/GCF_002746455.1_ASM274645v1_genomic.fna.gz --refList GCF_002746455.1_ASM274645v1_genomic.fna/target_genomes.txt --output GCF_002746455.1_ASM274645v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:28,013] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:28,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac6e4159-6947-49d7-91b2-4f8b63fae032/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:28,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac6e4159-6947-49d7-91b2-4f8b63fae032/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:28,034] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:28,034] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:28,035] [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
Bacillus tropicus	strain=N24	GCA_001884035.1	2026188	2026188	type	True	93.809	1400	1806	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	93.4006	1438	1806	95	below_threshold
Bacillus pacificus	strain=EB422	GCA_001884025.1	2026187	2026187	type	True	93.3515	1408	1806	95	below_threshold
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	93.3504	1403	1806	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_000742895.1	1392	1392	type	True	93.3304	1443	1806	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_000167275.1	1392	1392	type	True	93.2971	1413	1806	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	93.2428	1255	1806	95	below_threshold
Bacillus anthracis	strain=A0488	GCA_000181835.1	1392	1392	type	True	93.1902	1394	1806	95	below_threshold
Bacillus cereus	strain=FSL M8-0473	GCA_002014665.1	1396	1396	suspected-type	True	91.7734	1334	1806	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_006094295.1	1396	1396	suspected-type	True	91.7088	1395	1806	95	below_threshold
Bacillus cereus	strain=NCTC2599	GCA_900445355.1	1396	1396	suspected-type	True	91.6785	1375	1806	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_000007825.1	1396	1396	suspected-type	True	91.6772	1389	1806	95	below_threshold
Bacillus luti	strain=TD41	GCA_001884105.1	2026191	2026191	type	True	91.5266	1331	1806	95	below_threshold
Bacillus thuringiensis	strain=ATCC 10792	GCA_000161615.1	1428	1428	suspected-type	True	91.432	1456	1806	95	below_threshold
Bacillus thuringiensis	strain=ATCC 10792	GCA_002119445.1	1428	1428	suspected-type	True	91.3751	1441	1806	95	below_threshold
Bacillus toyonensis	strain=BCT-7112	GCA_000496285.1	155322	155322	type	True	91.097	1340	1806	95	below_threshold
Bacillus nitratireducens	strain=4049	GCA_001884135.1	2026193	2026193	type	True	90.2629	1359	1806	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_000003925.1	1405	1405	type	True	89.7031	1372	1806	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	89.5854	1390	1806	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.7904	105	1806	95	below_threshold
Anoxybacillus kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	76.6209	72	1806	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:28,045] [INFO] DFAST Taxonomy check result was written to GCF_002746455.1_ASM274645v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:28,046] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:28,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:28,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac6e4159-6947-49d7-91b2-4f8b63fae032/dqc_reference/checkm_data
[2024-01-24 14:31:28,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:28,111] [INFO] Task started: CheckM
[2024-01-24 14:31:28,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002746455.1_ASM274645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002746455.1_ASM274645v1_genomic.fna/checkm_input GCF_002746455.1_ASM274645v1_genomic.fna/checkm_result
[2024-01-24 14:32:05,473] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:05,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:05,496] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:05,497] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:05,497] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002746455.1_ASM274645v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:05,498] [INFO] Task started: Blastn
[2024-01-24 14:32:05,498] [INFO] Running command: blastn -query GCF_002746455.1_ASM274645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac6e4159-6947-49d7-91b2-4f8b63fae032/dqc_reference/reference_markers_gtdb.fasta -out GCF_002746455.1_ASM274645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:06,305] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:06,308] [INFO] Selected 17 target genomes.
[2024-01-24 14:32:06,308] [INFO] Target genome list was writen to GCF_002746455.1_ASM274645v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:06,320] [INFO] Task started: fastANI
[2024-01-24 14:32:06,321] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2f74660-c6df-4509-98a6-b8627115827d/GCF_002746455.1_ASM274645v1_genomic.fna.gz --refList GCF_002746455.1_ASM274645v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002746455.1_ASM274645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:27,406] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:27,420] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:27,420] [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_002746455.1	s__Bacillus_A fungorum	100.0	1802	1806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.51	97.51	0.90	0.90	2	conclusive
GCF_001884035.1	s__Bacillus_A tropicus	93.809	1400	1806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.3658	96.52	95.65	0.91	0.83	109	-
GCF_006494425.1	s__Bacillus_A sp006494425	93.7774	1430	1806	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_001455345.1	s__Bacillus_A thuringiensis_N	93.7613	1431	1806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.23	95.30	0.91	0.84	24	-
GCF_001583695.1	s__Bacillus_A wiedmannii	93.4847	1403	1806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	96.52	95.09	0.90	0.85	225	-
GCF_900094905.1	s__Bacillus_A cereus_AG	93.3695	1388	1806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.51	99.13	0.92	0.90	3	-
GCF_000742895.1	s__Bacillus_A anthracis	93.3305	1443	1806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.2518	99.29	95.34	0.96	0.83	417	-
GCF_018332475.1	s__Bacillus_A sp018332475	93.2534	1254	1806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	95.31	95.31	0.87	0.87	2	-
GCF_001884045.1	s__Bacillus_A mobilis	93.2118	1421	1806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	96.91	95.80	0.85	0.81	33	-
GCF_008923725.1	s__Bacillus_A sp008923725	93.145	1433	1806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001884185.1	s__Bacillus_A albus	93.0409	1417	1806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.54	95.46	0.90	0.83	25	-
GCF_002571225.1	s__Bacillus_A sp002571225	92.8486	1415	1806	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_001884105.1	s__Bacillus_A luti	91.5266	1331	1806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.24	95.75	0.91	0.89	10	-
GCF_014932895.1	s__Bacillus_A thuringiensis_AA	90.4536	1391	1806	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_002564555.1	s__Bacillus_A cereus_K	90.39	1278	1806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	98.77	97.26	0.94	0.89	7	-
GCF_002578045.1	s__Bacillus_A cereus_AK	89.784	1081	1806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.93	99.93	0.97	0.97	2	-
GCF_002975175.1	s__Bacillus_A sp002975175	88.9853	1350	1806	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	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:27,422] [INFO] GTDB search result was written to GCF_002746455.1_ASM274645v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:27,423] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:27,427] [INFO] DFAST_QC result json was written to GCF_002746455.1_ASM274645v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:27,427] [INFO] DFAST_QC completed!
[2024-01-24 14:32:27,427] [INFO] Total running time: 0h1m53s