[2024-01-25 19:49:20,693] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:20,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:20,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a47814e-95b2-4629-8e1c-6dde0c97084c/dqc_reference
[2024-01-25 19:49:21,822] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:21,823] [INFO] Task started: Prodigal
[2024-01-25 19:49:21,823] [INFO] Running command: gunzip -c /var/lib/cwl/stg49e2a70e-c798-4028-95db-56c4ed99f100/GCF_002835735.1_ASM283573v1_genomic.fna.gz | prodigal -d GCF_002835735.1_ASM283573v1_genomic.fna/cds.fna -a GCF_002835735.1_ASM283573v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:31,452] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:31,452] [INFO] Task started: HMMsearch
[2024-01-25 19:49:31,452] [INFO] Running command: hmmsearch --tblout GCF_002835735.1_ASM283573v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a47814e-95b2-4629-8e1c-6dde0c97084c/dqc_reference/reference_markers.hmm GCF_002835735.1_ASM283573v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:31,800] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:31,802] [INFO] Found 6/6 markers.
[2024-01-25 19:49:31,848] [INFO] Query marker FASTA was written to GCF_002835735.1_ASM283573v1_genomic.fna/markers.fasta
[2024-01-25 19:49:31,849] [INFO] Task started: Blastn
[2024-01-25 19:49:31,849] [INFO] Running command: blastn -query GCF_002835735.1_ASM283573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a47814e-95b2-4629-8e1c-6dde0c97084c/dqc_reference/reference_markers.fasta -out GCF_002835735.1_ASM283573v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:32,413] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:32,415] [INFO] Selected 22 target genomes.
[2024-01-25 19:49:32,416] [INFO] Target genome list was writen to GCF_002835735.1_ASM283573v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:32,428] [INFO] Task started: fastANI
[2024-01-25 19:49:32,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg49e2a70e-c798-4028-95db-56c4ed99f100/GCF_002835735.1_ASM283573v1_genomic.fna.gz --refList GCF_002835735.1_ASM283573v1_genomic.fna/target_genomes.txt --output GCF_002835735.1_ASM283573v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:50,598] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:50,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a47814e-95b2-4629-8e1c-6dde0c97084c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:50,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a47814e-95b2-4629-8e1c-6dde0c97084c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:50,612] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:49:50,612] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:50,612] [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
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	100.0	1775	1783	95	conclusive
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	78.6204	366	1783	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	78.1396	220	1783	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	78.0069	243	1783	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	77.8248	250	1783	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	77.6622	233	1783	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	77.5737	120	1783	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	77.5151	128	1783	95	below_threshold
Priestia abyssalis	strain=DSM 25875	GCA_002019595.1	1221450	1221450	type	True	77.4821	94	1783	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	77.4214	158	1783	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	77.3541	147	1783	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	77.2521	127	1783	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	77.2325	128	1783	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	77.1881	101	1783	95	below_threshold
Bacillus mesophilus	strain=SA4	GCA_011008845.1	1808955	1808955	type	True	77.0683	73	1783	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	77.0554	148	1783	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	76.9828	147	1783	95	below_threshold
Bacillus mesophilus	strain=DSM 101000	GCA_016908955.1	1808955	1808955	type	True	76.9796	72	1783	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	76.6998	107	1783	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:50,626] [INFO] DFAST Taxonomy check result was written to GCF_002835735.1_ASM283573v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:50,627] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:50,627] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:50,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a47814e-95b2-4629-8e1c-6dde0c97084c/dqc_reference/checkm_data
[2024-01-25 19:49:50,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:50,682] [INFO] Task started: CheckM
[2024-01-25 19:49:50,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002835735.1_ASM283573v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002835735.1_ASM283573v1_genomic.fna/checkm_input GCF_002835735.1_ASM283573v1_genomic.fna/checkm_result
[2024-01-25 19:50:23,217] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:23,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:23,246] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:23,246] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:23,247] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002835735.1_ASM283573v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:23,247] [INFO] Task started: Blastn
[2024-01-25 19:50:23,247] [INFO] Running command: blastn -query GCF_002835735.1_ASM283573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a47814e-95b2-4629-8e1c-6dde0c97084c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002835735.1_ASM283573v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:24,028] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:24,030] [INFO] Selected 25 target genomes.
[2024-01-25 19:50:24,031] [INFO] Target genome list was writen to GCF_002835735.1_ASM283573v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:24,044] [INFO] Task started: fastANI
[2024-01-25 19:50:24,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg49e2a70e-c798-4028-95db-56c4ed99f100/GCF_002835735.1_ASM283573v1_genomic.fna.gz --refList GCF_002835735.1_ASM283573v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002835735.1_ASM283573v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:46,815] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:46,829] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:46,829] [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_002835735.1	s__Cytobacillus horneckiae	100.0	1775	1783	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	conclusive
GCF_002276165.1	s__Cytobacillus kochii	78.7698	385	1783	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_014836495.1	s__Cytobacillus sp014836495	78.6298	367	1783	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_003182355.1	s__Cytobacillus oceanisediminis_A	78.2117	228	1783	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_000518885.1	s__Cytobacillus sp000518885	78.1688	225	1783	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_002871465.1	s__Metabacillus sp002871465	78.1663	123	1783	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.74	98.74	0.91	0.91	2	-
GCF_017874625.1	s__Cytobacillus eiseniae	78.1253	221	1783	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_004366035.1	s__Cytobacillus oceanisediminis_C	78.1058	224	1783	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_007830235.1	s__Cytobacillus oceanisediminis	78.0831	231	1783	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_900199725.1	s__Cytobacillus massiliigabonensis	78.0053	235	1783	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_001420595.1	s__Cytobacillus solani	78.0007	244	1783	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_001636345.1	s__Cytobacillus gottheilii	77.8675	230	1783	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_001439605.1	s__Cytobacillus praedii	77.8174	250	1783	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.20	99.20	0.93	0.93	2	-
GCF_001509555.1	s__Cytobacillus sp001509555	77.8098	212	1783	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_008923245.1	s__Cytobacillus depressus	77.6525	232	1783	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_000759675.1	s__Neobacillus niacini_A	77.6139	155	1783	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	77.5737	120	1783	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	95.47	95.47	0.86	0.86	2	-
GCF_004358205.1	s__Neobacillus salipaludis	77.4251	157	1783	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	77.3959	142	1783	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	77.3391	142	1783	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_016107705.1	s__Neobacillus cucumis_B	77.1848	148	1783	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_018343535.1	s__Neobacillus sp018343535	77.0457	146	1783	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.05	99.05	0.95	0.95	2	-
GCF_001591665.1	s__Neobacillus soli	76.9522	149	1783	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_016908395.1	s__Metabacillus crassostreae	76.6434	106	1783	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:46,831] [INFO] GTDB search result was written to GCF_002835735.1_ASM283573v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:46,832] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:46,841] [INFO] DFAST_QC result json was written to GCF_002835735.1_ASM283573v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:46,841] [INFO] DFAST_QC completed!
[2024-01-25 19:50:46,841] [INFO] Total running time: 0h1m26s