[2024-01-24 15:02:03,506] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:03,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:03,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fbd9513-45f5-4d17-a584-56bf0282ea98/dqc_reference
[2024-01-24 15:02:06,127] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:06,128] [INFO] Task started: Prodigal
[2024-01-24 15:02:06,129] [INFO] Running command: gunzip -c /var/lib/cwl/stgace1a877-e8f5-4bc7-badc-e54fcdf088da/GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/cds.fna -a GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:15,541] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:15,541] [INFO] Task started: HMMsearch
[2024-01-24 15:02:15,542] [INFO] Running command: hmmsearch --tblout GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fbd9513-45f5-4d17-a584-56bf0282ea98/dqc_reference/reference_markers.hmm GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:15,855] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:15,856] [INFO] Found 6/6 markers.
[2024-01-24 15:02:15,895] [INFO] Query marker FASTA was written to GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:02:15,896] [INFO] Task started: Blastn
[2024-01-24 15:02:15,896] [INFO] Running command: blastn -query GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fbd9513-45f5-4d17-a584-56bf0282ea98/dqc_reference/reference_markers.fasta -out GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:16,525] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:16,528] [INFO] Selected 30 target genomes.
[2024-01-24 15:02:16,528] [INFO] Target genome list was writen to GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:02:16,557] [INFO] Task started: fastANI
[2024-01-24 15:02:16,558] [INFO] Running command: fastANI --query /var/lib/cwl/stgace1a877-e8f5-4bc7-badc-e54fcdf088da/GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna.gz --refList GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:37,414] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:37,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fbd9513-45f5-4d17-a584-56bf0282ea98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:37,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fbd9513-45f5-4d17-a584-56bf0282ea98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:37,431] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:37,431] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:37,431] [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 oleivorans	strain=JC228	GCA_900207585.1	1448271	1448271	type	True	100.0	1489	1491	95	conclusive
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	78.3401	100	1491	95	below_threshold
Bacillus gaemokensis	strain=KCTC 13318	GCA_001590835.1	574375	574375	type	True	78.092	65	1491	95	below_threshold
Bacillus massilionigeriensis	strain=Marseille-P2384	GCA_900117315.1	1805475	1805475	type	True	77.6479	77	1491	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	77.6306	60	1491	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	77.4389	70	1491	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.425	101	1491	95	below_threshold
Metabacillus idriensis	strain=DSM-19097	GCA_904423875.1	324768	324768	type	True	77.4228	68	1491	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	77.3845	104	1491	95	below_threshold
Mesobacillus foraminis	strain=CV53	GCA_013618915.1	279826	279826	type	True	77.3526	70	1491	95	below_threshold
Bacillus pakistanensis	strain=DSM 24834	GCA_016908495.1	992288	992288	type	True	77.2795	105	1491	95	below_threshold
Bacillus methanolicus	strain=PB1	GCA_000262755.1	1471	1471	suspected-type	True	77.0801	88	1491	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	77.0716	116	1491	95	below_threshold
Mesobacillus foraminis	strain=CV53	GCA_004340465.1	279826	279826	type	True	76.9962	70	1491	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	76.995	77	1491	95	below_threshold
Bacillus coahuilensis	strain=m4-4	GCA_000171615.1	408580	408580	type	True	76.9873	55	1491	95	below_threshold
Cytobacillus luteolus	strain=DSM 22388	GCA_017873715.1	682179	682179	type	True	76.8977	70	1491	95	below_threshold
Cytobacillus luteolus	strain=YIM 93174	GCA_014982515.1	682179	682179	type	True	76.7928	71	1491	95	below_threshold
Metabacillus fastidiosus	strain=NBRC 101226	GCA_001591625.1	1458	1458	type	True	76.7289	73	1491	95	below_threshold
Gottfriedia acidiceleris	strain=DSM 18954	GCA_002128425.1	371036	371036	type	True	76.5564	69	1491	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	76.5443	98	1491	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	76.5295	84	1491	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:37,433] [INFO] DFAST Taxonomy check result was written to GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:02:37,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:37,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:37,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fbd9513-45f5-4d17-a584-56bf0282ea98/dqc_reference/checkm_data
[2024-01-24 15:02:37,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:37,502] [INFO] Task started: CheckM
[2024-01-24 15:02:37,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/checkm_input GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:03:11,380] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:11,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:11,406] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:11,406] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:11,407] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:03:11,407] [INFO] Task started: Blastn
[2024-01-24 15:03:11,407] [INFO] Running command: blastn -query GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fbd9513-45f5-4d17-a584-56bf0282ea98/dqc_reference/reference_markers_gtdb.fasta -out GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:12,279] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:12,282] [INFO] Selected 28 target genomes.
[2024-01-24 15:03:12,283] [INFO] Target genome list was writen to GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:12,301] [INFO] Task started: fastANI
[2024-01-24 15:03:12,301] [INFO] Running command: fastANI --query /var/lib/cwl/stgace1a877-e8f5-4bc7-badc-e54fcdf088da/GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna.gz --refList GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:35,034] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:35,054] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:35,055] [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_900207585.1	s__Bacillus_BF oleivorans	100.0	1489	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__JC228;f__JC228;g__Bacillus_BF	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001048695.1	s__Neobacillus massiliamazoniensis	78.301	101	1491	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_001590835.1	s__Bacillus_A gaemokensis	78.092	65	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.98	99.98	1.00	1.00	2	-
GCF_009720625.1	s__Metabacillus sp004801455	77.7224	98	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900117315.1	s__Bacillus_BE massilionigeriensis	77.6479	77	1491	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_000724485.1	s__Bacillus_Z methanolicus_A	77.6325	81	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_Z	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002860255.1	s__Neobacillus cucumis_A	77.4686	97	1491	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_001420595.1	s__Cytobacillus solani	77.3868	100	1491	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_008923245.1	s__Cytobacillus depressus	77.3845	104	1491	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_900112415.1	s__Bacillus_A sp900112415	77.3791	63	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.00	99.00	0.93	0.93	2	-
GCF_004341175.1	s__Neobacillus sp004341175	77.3129	90	1491	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_000482325.1	s__Neobacillus sp000482325	77.1302	114	1491	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_000262755.1	s__Bacillus_Z methanolicus	77.0573	88	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107705.1	s__Neobacillus cucumis_B	76.9974	111	1491	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_000380245.2	s__Bacillus_AD massiliogorillae	76.995	77	1491	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_000171615.1	s__Bacillus_T coahuilensis	76.9898	56	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_K;g__Bacillus_T	95.0	98.94	98.61	0.92	0.90	3	-
GCF_003944835.1	s__HMF5848 sp003944835	76.9224	50	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__HMF5848;g__HMF5848	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002574545.1	s__Gottfriedia sp002574545	76.9195	58	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873715.1	s__Bacillus_BV luteolus	76.8977	70	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Bacillus_BV	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013396335.1	s__Neobacillus sp013396335	76.8637	106	1491	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_000712595.1	s__Bacillus_A manliponensis	76.8229	51	1491	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_001636345.1	s__Cytobacillus gottheilii	76.6977	96	1491	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_900104555.1	s__Litchfieldia salsa	76.4617	84	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524525.1	s__Robertmurraya sp011524525	76.4381	51	1491	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_004138285.1	s__Gottfriedia acidiceleris_A	76.0933	56	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:35,057] [INFO] GTDB search result was written to GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:35,057] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:35,063] [INFO] DFAST_QC result json was written to GCF_900207585.1_IMG-taxon_2740891863_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:03:35,064] [INFO] DFAST_QC completed!
[2024-01-24 15:03:35,064] [INFO] Total running time: 0h1m32s