[2024-01-24 13:57:56,403] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:56,405] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:56,405] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc6e9afb-1510-4ba5-b508-49075c93fe6c/dqc_reference
[2024-01-24 13:57:57,808] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,810] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,810] [INFO] Running command: gunzip -c /var/lib/cwl/stgf47069f4-819d-4286-aa57-5bb3c56af407/GCF_917563885.1_JJ-79_genomic.fna.gz | prodigal -d GCF_917563885.1_JJ-79_genomic.fna/cds.fna -a GCF_917563885.1_JJ-79_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:07,251] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:07,251] [INFO] Task started: HMMsearch
[2024-01-24 13:58:07,251] [INFO] Running command: hmmsearch --tblout GCF_917563885.1_JJ-79_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc6e9afb-1510-4ba5-b508-49075c93fe6c/dqc_reference/reference_markers.hmm GCF_917563885.1_JJ-79_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:07,618] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:07,619] [INFO] Found 6/6 markers.
[2024-01-24 13:58:07,671] [INFO] Query marker FASTA was written to GCF_917563885.1_JJ-79_genomic.fna/markers.fasta
[2024-01-24 13:58:07,672] [INFO] Task started: Blastn
[2024-01-24 13:58:07,672] [INFO] Running command: blastn -query GCF_917563885.1_JJ-79_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc6e9afb-1510-4ba5-b508-49075c93fe6c/dqc_reference/reference_markers.fasta -out GCF_917563885.1_JJ-79_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:08,310] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:08,318] [INFO] Selected 29 target genomes.
[2024-01-24 13:58:08,319] [INFO] Target genome list was writen to GCF_917563885.1_JJ-79_genomic.fna/target_genomes.txt
[2024-01-24 13:58:08,332] [INFO] Task started: fastANI
[2024-01-24 13:58:08,332] [INFO] Running command: fastANI --query /var/lib/cwl/stgf47069f4-819d-4286-aa57-5bb3c56af407/GCF_917563885.1_JJ-79_genomic.fna.gz --refList GCF_917563885.1_JJ-79_genomic.fna/target_genomes.txt --output GCF_917563885.1_JJ-79_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:31,305] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:31,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc6e9afb-1510-4ba5-b508-49075c93fe6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:31,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc6e9afb-1510-4ba5-b508-49075c93fe6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:31,332] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:31,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:31,332] [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
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	100.0	1522	1525	95	conclusive
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	77.7888	201	1525	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	77.6321	213	1525	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	77.4742	200	1525	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	77.4679	136	1525	95	below_threshold
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	77.4536	120	1525	95	below_threshold
Bacillus massilionigeriensis	strain=Marseille-P2384	GCA_900117315.1	1805475	1805475	type	True	77.3787	152	1525	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	77.2941	120	1525	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	77.2881	194	1525	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	77.2543	169	1525	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	77.1897	161	1525	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	77.1875	122	1525	95	below_threshold
Ectobacillus panaciterrae	strain=DSM 19096	GCA_000430785.1	363872	363872	type	True	77.1805	65	1525	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	77.179	166	1525	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	77.16	118	1525	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	77.1474	165	1525	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	77.1032	86	1525	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.0454	197	1525	95	below_threshold
Gottfriedia acidiceleris	strain=NRRL B-41736	GCA_002156925.1	371036	371036	type	True	76.9881	100	1525	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.9781	158	1525	95	below_threshold
Gottfriedia acidiceleris	strain=DSM 18954	GCA_002128425.1	371036	371036	type	True	76.8909	98	1525	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_019915265.1	2672567	2672567	type	True	76.8499	109	1525	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.7847	123	1525	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	76.7839	111	1525	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_011008855.1	2672567	2672567	type	True	76.7467	111	1525	95	below_threshold
Solibacillus cecembensis	strain=DSM 21993	GCA_001439635.1	459347	459347	type	True	76.7072	64	1525	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_000007825.1	1396	1396	suspected-type	True	76.5455	99	1525	95	below_threshold
Bacillus cereus	strain=FSL M8-0473	GCA_002014665.1	1396	1396	suspected-type	True	76.2539	95	1525	95	below_threshold
Bacillus thuringiensis	strain=ATCC 10792	GCA_002119445.1	1428	1428	suspected-type	True	76.1966	92	1525	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:31,334] [INFO] DFAST Taxonomy check result was written to GCF_917563885.1_JJ-79_genomic.fna/tc_result.tsv
[2024-01-24 13:58:31,335] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:31,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:31,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc6e9afb-1510-4ba5-b508-49075c93fe6c/dqc_reference/checkm_data
[2024-01-24 13:58:31,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:31,388] [INFO] Task started: CheckM
[2024-01-24 13:58:31,388] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_917563885.1_JJ-79_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_917563885.1_JJ-79_genomic.fna/checkm_input GCF_917563885.1_JJ-79_genomic.fna/checkm_result
[2024-01-24 13:59:06,528] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:06,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:06,549] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:06,550] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:06,550] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_917563885.1_JJ-79_genomic.fna/markers.fasta)
[2024-01-24 13:59:06,551] [INFO] Task started: Blastn
[2024-01-24 13:59:06,551] [INFO] Running command: blastn -query GCF_917563885.1_JJ-79_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc6e9afb-1510-4ba5-b508-49075c93fe6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_917563885.1_JJ-79_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:07,399] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:07,403] [INFO] Selected 35 target genomes.
[2024-01-24 13:59:07,403] [INFO] Target genome list was writen to GCF_917563885.1_JJ-79_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:07,436] [INFO] Task started: fastANI
[2024-01-24 13:59:07,437] [INFO] Running command: fastANI --query /var/lib/cwl/stgf47069f4-819d-4286-aa57-5bb3c56af407/GCF_917563885.1_JJ-79_genomic.fna.gz --refList GCF_917563885.1_JJ-79_genomic.fna/target_genomes_gtdb.txt --output GCF_917563885.1_JJ-79_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:36,366] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:36,405] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:36,405] [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_000759675.1	s__Neobacillus niacini_A	77.694	240	1525	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_003073175.1	s__Bacillus_BN acanthi	77.6054	118	1525	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	-
GCA_009917645.1	s__Robertmurraya sp009917645	77.5268	154	1525	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_002860255.1	s__Neobacillus cucumis_A	77.5031	197	1525	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	-
GCA_019219025.1	s__Neobacillus sp019219025	77.4736	210	1525	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_002585305.1	s__Neobacillus sp002585305	77.4722	197	1525	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_001591665.1	s__Neobacillus soli	77.4629	200	1525	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900103525.1	s__Neobacillus sp900103525	77.4335	197	1525	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_001866655.1	s__Neobacillus sp001866655	77.4315	191	1525	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_014217835.1	s__Metabacillus litoralis_A	77.416	132	1525	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_002567005.1	s__Neobacillus sp002567005	77.3971	192	1525	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_000686805.1	s__Neobacillus sp000686805	77.3798	213	1525	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_900117315.1	s__Bacillus_BE massilionigeriensis	77.3787	152	1525	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BE	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001509555.1	s__Cytobacillus sp001509555	77.3196	173	1525	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_900115925.1	s__CL95 sp900115925	77.2858	148	1525	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__CL95	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017497975.1	s__Metabacillus sp017497975	77.2808	158	1525	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177675.1	s__Neobacillus sp900177675	77.2764	206	1525	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_017874625.1	s__Cytobacillus eiseniae	77.2557	168	1525	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_000482325.1	s__Neobacillus sp000482325	77.25	183	1525	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_002019635.1	s__Metabacillus halosaccharovorans	77.2361	129	1525	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	95.47	95.47	0.86	0.86	2	-
GCF_002835735.1	s__Cytobacillus horneckiae	77.16	118	1525	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_009928415.1	s__Neobacillus sp009928415	77.1232	166	1525	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_002844575.1	s__Margalitia camelliae	77.1032	86	1525	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_018613065.1	s__Neobacillus sp018613065	77.0907	214	1525	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_001420595.1	s__Cytobacillus solani	77.0769	193	1525	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_010975035.1	s__Neobacillus thermocopriae	77.0622	144	1525	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.41	95.38	0.92	0.91	3	-
GCF_011250555.1	s__Neobacillus sp011250555	77.0608	190	1525	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_009183415.1	s__Niallia sp009183415	77.0276	123	1525	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_016908835.1	s__Bacillus_AD endoradicis	77.0236	109	1525	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_002577655.1	s__Metabacillus sp002577655	76.9832	121	1525	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011008855.1	s__Bacillus_BT aquiflavi	76.7275	112	1525	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BT	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016464375.1	s__Neobacillus renqingensis	76.3652	105	1525	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:36,407] [INFO] GTDB search result was written to GCF_917563885.1_JJ-79_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:36,408] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:36,414] [INFO] DFAST_QC result json was written to GCF_917563885.1_JJ-79_genomic.fna/dqc_result.json
[2024-01-24 13:59:36,414] [INFO] DFAST_QC completed!
[2024-01-24 13:59:36,414] [INFO] Total running time: 0h1m40s