[2024-01-24 12:06:14,050] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,053] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,053] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbb5025a-2210-4091-8ba6-df76c8236509/dqc_reference
[2024-01-24 12:06:15,518] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,519] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,519] [INFO] Running command: gunzip -c /var/lib/cwl/stg4450b486-4e2e-4064-94a3-3673ab5b7dcb/GCF_902168435.1_P3556_genomic.fna.gz | prodigal -d GCF_902168435.1_P3556_genomic.fna/cds.fna -a GCF_902168435.1_P3556_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:25,316] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:25,316] [INFO] Task started: HMMsearch
[2024-01-24 12:06:25,316] [INFO] Running command: hmmsearch --tblout GCF_902168435.1_P3556_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbb5025a-2210-4091-8ba6-df76c8236509/dqc_reference/reference_markers.hmm GCF_902168435.1_P3556_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:25,682] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:25,683] [INFO] Found 6/6 markers.
[2024-01-24 12:06:25,729] [INFO] Query marker FASTA was written to GCF_902168435.1_P3556_genomic.fna/markers.fasta
[2024-01-24 12:06:25,729] [INFO] Task started: Blastn
[2024-01-24 12:06:25,730] [INFO] Running command: blastn -query GCF_902168435.1_P3556_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbb5025a-2210-4091-8ba6-df76c8236509/dqc_reference/reference_markers.fasta -out GCF_902168435.1_P3556_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:26,390] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:26,393] [INFO] Selected 35 target genomes.
[2024-01-24 12:06:26,394] [INFO] Target genome list was writen to GCF_902168435.1_P3556_genomic.fna/target_genomes.txt
[2024-01-24 12:06:26,407] [INFO] Task started: fastANI
[2024-01-24 12:06:26,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg4450b486-4e2e-4064-94a3-3673ab5b7dcb/GCF_902168435.1_P3556_genomic.fna.gz --refList GCF_902168435.1_P3556_genomic.fna/target_genomes.txt --output GCF_902168435.1_P3556_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:55,272] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:55,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbb5025a-2210-4091-8ba6-df76c8236509/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:55,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbb5025a-2210-4091-8ba6-df76c8236509/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:55,304] [INFO] Found 33 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:55,304] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:55,305] [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 marasmi	strain=Marseille-P3556	GCA_902168435.1	1926279	1926279	type	True	100.0	1523	1523	95	conclusive
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	77.7813	84	1523	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.6917	153	1523	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	77.6498	159	1523	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	77.5886	142	1523	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	77.581	144	1523	95	below_threshold
Bacillus oleivorans	strain=JC228	GCA_900207585.1	1448271	1448271	type	True	77.5555	72	1523	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	77.5244	102	1523	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	77.4927	150	1523	95	below_threshold
Neobacillus thermocopriae	strain=SgZ-7	GCA_010975035.1	1215031	1215031	type	True	77.4693	126	1523	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	77.3929	138	1523	95	below_threshold
Mesobacillus boroniphilus	strain=JCM 21738	GCA_000517385.1	308892	308892	type	True	77.3754	91	1523	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	77.3525	134	1523	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	77.3284	95	1523	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	77.3221	141	1523	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	77.3133	137	1523	95	below_threshold
Mesobacillus boroniphilus	strain=JCM 21738	GCA_001315165.1	308892	308892	type	True	77.3065	90	1523	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	77.3015	122	1523	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	77.2794	52	1523	95	below_threshold
Neobacillus bataviensis	strain=LMG 21833	GCA_000307875.1	220685	220685	type	True	77.2645	141	1523	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.2351	154	1523	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	77.1288	136	1523	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	77.1283	186	1523	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	77.1019	125	1523	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	77.0991	148	1523	95	below_threshold
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	77.0826	76	1523	95	below_threshold
Peribacillus simplex	strain=DSM 1321	GCA_002243645.1	1478	1478	suspected-type	True	77.0214	101	1523	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	77.0121	98	1523	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.9376	114	1523	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	76.898	110	1523	95	below_threshold
Peribacillus faecalis	strain=AGMB 02131	GCA_014712675.1	2772559	2772559	type	True	76.8602	86	1523	95	below_threshold
Bacillus altitudinis	strain=41KF2b	GCA_000691145.1	293387	293387	type	True	76.7946	58	1523	95	below_threshold
Sutcliffiella cohnii	strain=NBRC 15565	GCA_001591425.1	33932	33932	type	True	76.4639	87	1523	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:55,307] [INFO] DFAST Taxonomy check result was written to GCF_902168435.1_P3556_genomic.fna/tc_result.tsv
[2024-01-24 12:06:55,308] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:55,308] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:55,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbb5025a-2210-4091-8ba6-df76c8236509/dqc_reference/checkm_data
[2024-01-24 12:06:55,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:55,356] [INFO] Task started: CheckM
[2024-01-24 12:06:55,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902168435.1_P3556_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902168435.1_P3556_genomic.fna/checkm_input GCF_902168435.1_P3556_genomic.fna/checkm_result
[2024-01-24 12:07:29,859] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:29,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:29,886] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:29,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:29,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902168435.1_P3556_genomic.fna/markers.fasta)
[2024-01-24 12:07:29,887] [INFO] Task started: Blastn
[2024-01-24 12:07:29,888] [INFO] Running command: blastn -query GCF_902168435.1_P3556_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbb5025a-2210-4091-8ba6-df76c8236509/dqc_reference/reference_markers_gtdb.fasta -out GCF_902168435.1_P3556_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:30,694] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:30,698] [INFO] Selected 28 target genomes.
[2024-01-24 12:07:30,698] [INFO] Target genome list was writen to GCF_902168435.1_P3556_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:30,724] [INFO] Task started: fastANI
[2024-01-24 12:07:30,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg4450b486-4e2e-4064-94a3-3673ab5b7dcb/GCF_902168435.1_P3556_genomic.fna.gz --refList GCF_902168435.1_P3556_genomic.fna/target_genomes_gtdb.txt --output GCF_902168435.1_P3556_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:54,799] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:54,826] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:54,827] [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_902168435.1	s__Bacillus_BU marasmi	100.0	1523	1523	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BU	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012843265.1	s__Bacillus_BU sp012843265	81.9682	907	1523	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242895.2	s__Bacillus_BU sp000242895	78.6526	383	1523	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013248975.1	s__Neobacillus endophyticus	77.6945	141	1523	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_002860255.1	s__Neobacillus cucumis_A	77.6508	166	1523	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_001636315.1	s__Neobacillus mesonae	77.6265	155	1523	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.98	98.98	0.94	0.94	2	-
GCF_001940785.1	s__Neobacillus sp001940785	77.6161	138	1523	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_018343515.1	s__Bacillus_AH sp018343515	77.6133	51	1523	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AH	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019219025.1	s__Neobacillus sp019219025	77.5238	140	1523	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_009917645.1	s__Robertmurraya sp009917645	77.5047	142	1523	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_014874135.1	s__Neobacillus sp014874135	77.4589	176	1523	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_018613415.1	s__Neobacillus sp018613415	77.4429	157	1523	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_018343665.1	s__Cytobacillus sp018343665	77.4277	144	1523	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_002585305.1	s__Neobacillus sp002585305	77.4273	162	1523	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_002567005.1	s__Neobacillus sp002567005	77.3753	158	1523	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_900115925.1	s__CL95 sp900115925	77.3471	130	1523	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_002860165.1	s__Bacillus_BJ sp002860165	77.3194	102	1523	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BJ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667825.1	s__Metabacillus litoralis_B	77.3055	107	1523	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_900103525.1	s__Neobacillus sp900103525	77.2303	161	1523	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_002860125.1	s__Bacillus_BJ canaveralius	77.2041	107	1523	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BJ	95.0	99.48	99.12	0.94	0.92	4	-
GCA_011524525.1	s__Robertmurraya sp011524525	77.1755	99	1523	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_002736105.1	s__Solibacillus sp002736105	77.1133	75	1523	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259415.1	s__Metabacillus sp003259415	77.1117	108	1523	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874625.1	s__Cytobacillus eiseniae	77.0937	149	1523	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_002250055.1	s__Sutcliffiella cohnii	76.9786	96	1523	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella	95.0	100.00	100.00	0.97	0.97	2	-
GCA_001938995.1	s__Bacillus pumilus_G	76.9402	57	1523	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000691145.1	s__Bacillus altitudinis	76.7946	58	1523	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.17	97.02	0.95	0.92	117	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	76.7499	108	1523	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	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:54,829] [INFO] GTDB search result was written to GCF_902168435.1_P3556_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:54,830] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:54,840] [INFO] DFAST_QC result json was written to GCF_902168435.1_P3556_genomic.fna/dqc_result.json
[2024-01-24 12:07:54,841] [INFO] DFAST_QC completed!
[2024-01-24 12:07:54,841] [INFO] Total running time: 0h1m41s