[2024-01-24 12:14:33,129] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,131] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,131] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a299b45-f3b6-4fac-b0aa-016f4cdabb93/dqc_reference
[2024-01-24 12:14:34,348] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:34,349] [INFO] Task started: Prodigal
[2024-01-24 12:14:34,349] [INFO] Running command: gunzip -c /var/lib/cwl/stg28bbc421-3752-4bc2-845d-a1c020741acf/GCF_002128405.1_ASM212840v1_genomic.fna.gz | prodigal -d GCF_002128405.1_ASM212840v1_genomic.fna/cds.fna -a GCF_002128405.1_ASM212840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:42,357] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:42,358] [INFO] Task started: HMMsearch
[2024-01-24 12:14:42,358] [INFO] Running command: hmmsearch --tblout GCF_002128405.1_ASM212840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a299b45-f3b6-4fac-b0aa-016f4cdabb93/dqc_reference/reference_markers.hmm GCF_002128405.1_ASM212840v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:42,631] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:42,632] [INFO] Found 6/6 markers.
[2024-01-24 12:14:42,672] [INFO] Query marker FASTA was written to GCF_002128405.1_ASM212840v1_genomic.fna/markers.fasta
[2024-01-24 12:14:42,672] [INFO] Task started: Blastn
[2024-01-24 12:14:42,672] [INFO] Running command: blastn -query GCF_002128405.1_ASM212840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a299b45-f3b6-4fac-b0aa-016f4cdabb93/dqc_reference/reference_markers.fasta -out GCF_002128405.1_ASM212840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:43,269] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:43,272] [INFO] Selected 13 target genomes.
[2024-01-24 12:14:43,272] [INFO] Target genome list was writen to GCF_002128405.1_ASM212840v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:43,276] [INFO] Task started: fastANI
[2024-01-24 12:14:43,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg28bbc421-3752-4bc2-845d-a1c020741acf/GCF_002128405.1_ASM212840v1_genomic.fna.gz --refList GCF_002128405.1_ASM212840v1_genomic.fna/target_genomes.txt --output GCF_002128405.1_ASM212840v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:54,456] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:54,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a299b45-f3b6-4fac-b0aa-016f4cdabb93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:54,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a299b45-f3b6-4fac-b0aa-016f4cdabb93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:54,466] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:54,466] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:54,466] [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
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	100.0	1448	1450	95	conclusive
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	99.9974	1450	1450	95	conclusive
Gottfriedia luciferensis	strain=DSM 18845	GCA_002156865.1	178774	178774	type	True	81.5534	771	1450	95	below_threshold
Gottfriedia acidiceleris	strain=DSM 18954	GCA_002128425.1	371036	371036	type	True	81.2515	760	1450	95	below_threshold
Gottfriedia acidiceleris	strain=NRRL B-41736	GCA_002156925.1	371036	371036	type	True	81.1623	765	1450	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	78.9421	361	1450	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	77.172	92	1450	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	77.0168	149	1450	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.9863	134	1450	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.8874	139	1450	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	76.4613	103	1450	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	76.2413	54	1450	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:54,468] [INFO] DFAST Taxonomy check result was written to GCF_002128405.1_ASM212840v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:54,468] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:54,469] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:54,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a299b45-f3b6-4fac-b0aa-016f4cdabb93/dqc_reference/checkm_data
[2024-01-24 12:14:54,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:54,512] [INFO] Task started: CheckM
[2024-01-24 12:14:54,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002128405.1_ASM212840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002128405.1_ASM212840v1_genomic.fna/checkm_input GCF_002128405.1_ASM212840v1_genomic.fna/checkm_result
[2024-01-24 12:15:23,548] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:23,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:23,572] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:23,572] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:23,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002128405.1_ASM212840v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:23,573] [INFO] Task started: Blastn
[2024-01-24 12:15:23,573] [INFO] Running command: blastn -query GCF_002128405.1_ASM212840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a299b45-f3b6-4fac-b0aa-016f4cdabb93/dqc_reference/reference_markers_gtdb.fasta -out GCF_002128405.1_ASM212840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:24,406] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:24,410] [INFO] Selected 12 target genomes.
[2024-01-24 12:15:24,411] [INFO] Target genome list was writen to GCF_002128405.1_ASM212840v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:24,423] [INFO] Task started: fastANI
[2024-01-24 12:15:24,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg28bbc421-3752-4bc2-845d-a1c020741acf/GCF_002128405.1_ASM212840v1_genomic.fna.gz --refList GCF_002128405.1_ASM212840v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002128405.1_ASM212840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:36,217] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:36,231] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:36,231] [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_002128405.1	s__Gottfriedia solisilvae	100.0	1448	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	98.14	96.28	0.93	0.87	3	conclusive
GCF_003053645.1	s__Gottfriedia sp003053645	86.3027	1105	1450	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_002156875.1	s__Gottfriedia sp002156875	82.2601	894	1450	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_002559405.1	s__Gottfriedia sp002559405	81.6809	649	1450	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_002156865.1	s__Gottfriedia luciferensis	81.5537	768	1450	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_002564465.1	s__Gottfriedia sp002564465	81.3823	750	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	95.47	95.21	0.86	0.86	4	-
GCF_002577195.1	s__Gottfriedia sp002577195	81.3807	734	1450	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_001712755.1	s__Gottfriedia luciferensis_B	81.3613	755	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	99.30	99.28	0.95	0.93	3	-
GCF_001420605.1	s__Gottfriedia sp001420605	81.2877	764	1450	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_002574545.1	s__Gottfriedia sp002574545	81.2118	699	1450	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_013200995.1	s__Gottfriedia sp002556365	81.1528	728	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	95.58	95.58	0.84	0.83	3	-
GCF_004340305.1	s__Gottfriedia sp004340305	80.4246	653	1450	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 12:15:36,233] [INFO] GTDB search result was written to GCF_002128405.1_ASM212840v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:36,234] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:36,239] [INFO] DFAST_QC result json was written to GCF_002128405.1_ASM212840v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:36,239] [INFO] DFAST_QC completed!
[2024-01-24 12:15:36,239] [INFO] Total running time: 0h1m3s