[2024-01-25 19:40:06,047] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:40:06,049] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:40:06,049] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc544b10-94b2-46ed-a826-402ed7c77a79/dqc_reference
[2024-01-25 19:40:07,159] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:40:07,160] [INFO] Task started: Prodigal
[2024-01-25 19:40:07,160] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b7c0dcc-dd0f-4319-8783-5dc91a91ce88/GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna.gz | prodigal -d GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/cds.fna -a GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:40:16,853] [INFO] Task succeeded: Prodigal
[2024-01-25 19:40:16,853] [INFO] Task started: HMMsearch
[2024-01-25 19:40:16,854] [INFO] Running command: hmmsearch --tblout GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc544b10-94b2-46ed-a826-402ed7c77a79/dqc_reference/reference_markers.hmm GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:40:17,162] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:40:17,163] [INFO] Found 6/6 markers.
[2024-01-25 19:40:17,210] [INFO] Query marker FASTA was written to GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/markers.fasta
[2024-01-25 19:40:17,210] [INFO] Task started: Blastn
[2024-01-25 19:40:17,210] [INFO] Running command: blastn -query GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc544b10-94b2-46ed-a826-402ed7c77a79/dqc_reference/reference_markers.fasta -out GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:17,767] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:17,770] [INFO] Selected 25 target genomes.
[2024-01-25 19:40:17,771] [INFO] Target genome list was writen to GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/target_genomes.txt
[2024-01-25 19:40:17,788] [INFO] Task started: fastANI
[2024-01-25 19:40:17,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b7c0dcc-dd0f-4319-8783-5dc91a91ce88/GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna.gz --refList GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/target_genomes.txt --output GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:40:39,305] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:39,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc544b10-94b2-46ed-a826-402ed7c77a79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:40:39,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc544b10-94b2-46ed-a826-402ed7c77a79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:40:39,318] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:40:39,319] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:40:39,319] [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 loiseleuriae	strain=FJAT-27997	GCA_001183985.1	1679170	1679170	type	True	87.2704	1257	1805	95	below_threshold
Peribacillus butanolivorans	strain=DSM 18926	GCA_001273755.1	421767	421767	type	True	79.0789	341	1805	95	below_threshold
Peribacillus simplex	strain=DSM 1321	GCA_002243645.1	1478	1478	suspected-type	True	78.6737	248	1805	95	below_threshold
Peribacillus muralis	strain=DSM 16288	GCA_001439925.1	264697	264697	type	True	78.2776	193	1805	95	below_threshold
Peribacillus simplex	strain=NBRC 15720	GCA_001591785.1	1478	1478	suspected-type	True	78.2691	235	1805	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	78.2517	230	1805	95	below_threshold
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	77.829	114	1805	95	below_threshold
Peribacillus psychrosaccharolyticus	strain=ATCC 23296	GCA_000305495.2	1407	1407	type	True	77.5371	208	1805	95	below_threshold
Lysinibacillus xylanilyticus	strain=DSM 23493	GCA_001183605.1	582475	582475	type	True	77.4637	105	1805	95	below_threshold
Bacillus benzoevorans	strain=DSM 5391	GCA_014207535.1	1456	1456	type	True	77.283	103	1805	95	below_threshold
Peribacillus saganii	strain=V47-23a	GCA_003429095.1	2303992	2303992	type	True	77.2021	142	1805	95	below_threshold
Bacillus tepidiphilus	strain=SYSU G01002	GCA_009466385.1	2652445	2652445	type	True	77.186	115	1805	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	77.0236	137	1805	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	76.9898	95	1805	95	below_threshold
Cytobacillus luteolus	strain=DSM 22388	GCA_017873715.1	682179	682179	type	True	76.9489	84	1805	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	76.8845	56	1805	95	below_threshold
Anaerobacillus alkaliphilus	strain=B16-10	GCA_004116265.1	1548597	1548597	type	True	76.848	62	1805	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.8203	101	1805	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.8078	93	1805	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.555	107	1805	95	below_threshold
Solibacillus isronensis	strain=B3W22	GCA_000298255.1	412383	412383	type	True	76.3194	75	1805	95	below_threshold
Solibacillus kalamii	strain=DSM 101595	GCA_016909025.1	1748298	1748298	type	True	76.2712	65	1805	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.2463	95	1805	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:40:39,320] [INFO] DFAST Taxonomy check result was written to GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/tc_result.tsv
[2024-01-25 19:40:39,321] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:40:39,321] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:40:39,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc544b10-94b2-46ed-a826-402ed7c77a79/dqc_reference/checkm_data
[2024-01-25 19:40:39,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:40:39,375] [INFO] Task started: CheckM
[2024-01-25 19:40:39,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/checkm_input GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/checkm_result
[2024-01-25 19:41:11,466] [INFO] Task succeeded: CheckM
[2024-01-25 19:41:11,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:41:11,484] [INFO] ===== Completeness check finished =====
[2024-01-25 19:41:11,485] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:41:11,485] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/markers.fasta)
[2024-01-25 19:41:11,485] [INFO] Task started: Blastn
[2024-01-25 19:41:11,485] [INFO] Running command: blastn -query GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc544b10-94b2-46ed-a826-402ed7c77a79/dqc_reference/reference_markers_gtdb.fasta -out GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:12,320] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:12,323] [INFO] Selected 15 target genomes.
[2024-01-25 19:41:12,323] [INFO] Target genome list was writen to GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:41:12,345] [INFO] Task started: fastANI
[2024-01-25 19:41:12,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b7c0dcc-dd0f-4319-8783-5dc91a91ce88/GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna.gz --refList GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/target_genomes_gtdb.txt --output GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:41:27,949] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:27,959] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:41:27,959] [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_014138605.1	s__Peribacillus huizhouensis	98.7202	1557	1805	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	conclusive
GCF_001510645.1	s__Peribacillus sp001510645	87.7969	1284	1805	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	87.3045	1252	1805	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_004006295.1	s__Peribacillus asahii_A	78.6358	277	1805	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_001578185.1	s__Peribacillus simplex_A	78.4414	255	1805	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	97.63	97.17	0.91	0.91	3	-
GCF_003570725.1	s__Peribacillus asahii	78.2582	228	1805	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_003073175.1	s__Bacillus_BN acanthi	77.8207	113	1805	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_900112495.1	s__Peribacillus sp900112495	77.8146	177	1805	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	95.26	95.26	0.85	0.85	2	-
GCF_000305495.1	s__Peribacillus psychrosaccharolyticus	77.5118	208	1805	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	77.2989	153	1805	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_002845985.1	s__Lysinibacillus fusiformis_D	77.2817	77	1805	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.12	98.25	0.94	0.92	9	-
GCF_000426085.1	s__URHB0009 sp000426085	77.1252	117	1805	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__URHB0009	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002734285.1	s__Fredinandcohnia onubensis_A	77.0334	109	1805	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_002871465.1	s__Metabacillus sp002871465	76.9419	130	1805	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.74	98.74	0.91	0.91	2	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	76.9209	144	1805	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:41:27,960] [INFO] GTDB search result was written to GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/result_gtdb.tsv
[2024-01-25 19:41:27,961] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:41:27,964] [INFO] DFAST_QC result json was written to GCF_000504145.1_SOAPdenovo_for_version2.04_of_Bacillus_sp._FJAT-14515_genome_genomic.fna/dqc_result.json
[2024-01-25 19:41:27,964] [INFO] DFAST_QC completed!
[2024-01-25 19:41:27,965] [INFO] Total running time: 0h1m22s