[2024-01-24 11:44:23,772] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,776] [INFO] DQC Reference Directory: /var/lib/cwl/stgff03a85f-d917-4cb2-89ee-4c5d41e8cd4d/dqc_reference
[2024-01-24 11:44:26,338] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,340] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,340] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a3365a2-8e40-42c8-abf4-692efa3115f2/GCF_004005475.1_ASM400547v1_genomic.fna.gz | prodigal -d GCF_004005475.1_ASM400547v1_genomic.fna/cds.fna -a GCF_004005475.1_ASM400547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:38,793] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:38,794] [INFO] Task started: HMMsearch
[2024-01-24 11:44:38,794] [INFO] Running command: hmmsearch --tblout GCF_004005475.1_ASM400547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff03a85f-d917-4cb2-89ee-4c5d41e8cd4d/dqc_reference/reference_markers.hmm GCF_004005475.1_ASM400547v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:39,109] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:39,111] [INFO] Found 6/6 markers.
[2024-01-24 11:44:39,162] [INFO] Query marker FASTA was written to GCF_004005475.1_ASM400547v1_genomic.fna/markers.fasta
[2024-01-24 11:44:39,162] [INFO] Task started: Blastn
[2024-01-24 11:44:39,162] [INFO] Running command: blastn -query GCF_004005475.1_ASM400547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff03a85f-d917-4cb2-89ee-4c5d41e8cd4d/dqc_reference/reference_markers.fasta -out GCF_004005475.1_ASM400547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:39,769] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:39,773] [INFO] Selected 25 target genomes.
[2024-01-24 11:44:39,773] [INFO] Target genome list was writen to GCF_004005475.1_ASM400547v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:39,791] [INFO] Task started: fastANI
[2024-01-24 11:44:39,791] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a3365a2-8e40-42c8-abf4-692efa3115f2/GCF_004005475.1_ASM400547v1_genomic.fna.gz --refList GCF_004005475.1_ASM400547v1_genomic.fna/target_genomes.txt --output GCF_004005475.1_ASM400547v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:58,657] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:58,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff03a85f-d917-4cb2-89ee-4c5d41e8cd4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:58,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff03a85f-d917-4cb2-89ee-4c5d41e8cd4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:58,679] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:58,680] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:58,680] [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
Niallia taxi	strain=M5HDSG1-1	GCA_004005475.1	2499688	2499688	type	True	100.0	1902	1903	95	conclusive
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	78.6554	303	1903	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	78.4649	306	1903	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	78.2353	352	1903	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.7011	137	1903	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	77.527	138	1903	95	below_threshold
Bacillus massilionigeriensis	strain=Marseille-P2384	GCA_900117315.1	1805475	1805475	type	True	77.5042	102	1903	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	77.4891	117	1903	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	77.3156	98	1903	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	77.259	108	1903	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	77.2116	113	1903	95	below_threshold
Mesobacillus boroniphilus	strain=JCM 21738	GCA_001315165.1	308892	308892	type	True	77.1009	84	1903	95	below_threshold
Mesobacillus boroniphilus	strain=JCM 21738	GCA_000517385.1	308892	308892	type	True	77.1008	84	1903	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	77.0106	91	1903	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	76.987	137	1903	95	below_threshold
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	76.8498	69	1903	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.845	71	1903	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	76.8369	124	1903	95	below_threshold
Neobacillus drentensis	strain=NBRC 102427	GCA_001591445.1	220684	220684	type	True	76.8244	95	1903	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	76.7928	69	1903	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	76.7908	92	1903	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	76.7713	108	1903	95	below_threshold
Metabacillus fastidiosus	strain=NBRC 101226	GCA_001591625.1	1458	1458	type	True	76.7338	89	1903	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.34	108	1903	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:58,682] [INFO] DFAST Taxonomy check result was written to GCF_004005475.1_ASM400547v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:58,682] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:58,682] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:58,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff03a85f-d917-4cb2-89ee-4c5d41e8cd4d/dqc_reference/checkm_data
[2024-01-24 11:44:58,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:58,749] [INFO] Task started: CheckM
[2024-01-24 11:44:58,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004005475.1_ASM400547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004005475.1_ASM400547v1_genomic.fna/checkm_input GCF_004005475.1_ASM400547v1_genomic.fna/checkm_result
[2024-01-24 11:45:38,495] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:38,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:38,517] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:38,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:38,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004005475.1_ASM400547v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:38,519] [INFO] Task started: Blastn
[2024-01-24 11:45:38,519] [INFO] Running command: blastn -query GCF_004005475.1_ASM400547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff03a85f-d917-4cb2-89ee-4c5d41e8cd4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004005475.1_ASM400547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:39,351] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:39,355] [INFO] Selected 14 target genomes.
[2024-01-24 11:45:39,356] [INFO] Target genome list was writen to GCF_004005475.1_ASM400547v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:39,368] [INFO] Task started: fastANI
[2024-01-24 11:45:39,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a3365a2-8e40-42c8-abf4-692efa3115f2/GCF_004005475.1_ASM400547v1_genomic.fna.gz --refList GCF_004005475.1_ASM400547v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004005475.1_ASM400547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:53,998] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:54,014] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:54,014] [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_004005475.1	s__Niallia taxi	100.0	1902	1903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	97.90	96.11	0.92	0.86	5	conclusive
GCF_007273535.1	s__Niallia circulans_B	92.6873	1573	1903	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	-
GCA_011524565.1	s__Niallia sp011524565	83.0929	1209	1903	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	-
GCA_900199695.1	s__Niallia sp900199695	79.0322	298	1903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	98.49	98.15	0.84	0.82	5	-
GCF_003726095.1	s__Niallia circulans_A	78.4388	317	1903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.27	98.85	0.92	0.89	8	-
GCF_001076885.1	s__Niallia sp001076885	78.3018	305	1903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.59	99.45	0.92	0.91	4	-
GCF_002835805.1	s__Niallia nealsonii	78.2248	353	1903	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_900177675.1	s__Neobacillus sp900177675	77.7933	142	1903	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_003182355.1	s__Cytobacillus oceanisediminis_A	77.341	123	1903	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_017874625.1	s__Cytobacillus eiseniae	77.188	114	1903	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_001274725.1	s__Cytobacillus globisporus	77.1465	140	1903	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_006546985.1	s__VATK01 sp006546985	76.844	127	1903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__VATK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591445.1	s__Neobacillus drentensis	76.8244	95	1903	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	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:54,016] [INFO] GTDB search result was written to GCF_004005475.1_ASM400547v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:54,017] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:54,022] [INFO] DFAST_QC result json was written to GCF_004005475.1_ASM400547v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:54,022] [INFO] DFAST_QC completed!
[2024-01-24 11:45:54,022] [INFO] Total running time: 0h1m30s