[2024-01-24 10:47:06,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,555] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,555] [INFO] DQC Reference Directory: /var/lib/cwl/stga9308d1d-ecae-4eee-813b-45ceaf426691/dqc_reference
[2024-01-24 10:47:11,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,909] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,910] [INFO] Running command: gunzip -c /var/lib/cwl/stg08d21b44-2961-4e95-8098-b2403feb1190/GCF_900445485.1_49386_G02_genomic.fna.gz | prodigal -d GCF_900445485.1_49386_G02_genomic.fna/cds.fna -a GCF_900445485.1_49386_G02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:23,962] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:23,962] [INFO] Task started: HMMsearch
[2024-01-24 10:47:23,962] [INFO] Running command: hmmsearch --tblout GCF_900445485.1_49386_G02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9308d1d-ecae-4eee-813b-45ceaf426691/dqc_reference/reference_markers.hmm GCF_900445485.1_49386_G02_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:24,310] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:24,311] [INFO] Found 6/6 markers.
[2024-01-24 10:47:24,362] [INFO] Query marker FASTA was written to GCF_900445485.1_49386_G02_genomic.fna/markers.fasta
[2024-01-24 10:47:24,362] [INFO] Task started: Blastn
[2024-01-24 10:47:24,362] [INFO] Running command: blastn -query GCF_900445485.1_49386_G02_genomic.fna/markers.fasta -db /var/lib/cwl/stga9308d1d-ecae-4eee-813b-45ceaf426691/dqc_reference/reference_markers.fasta -out GCF_900445485.1_49386_G02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:24,984] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:24,988] [INFO] Selected 15 target genomes.
[2024-01-24 10:47:24,988] [INFO] Target genome list was writen to GCF_900445485.1_49386_G02_genomic.fna/target_genomes.txt
[2024-01-24 10:47:25,086] [INFO] Task started: fastANI
[2024-01-24 10:47:25,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg08d21b44-2961-4e95-8098-b2403feb1190/GCF_900445485.1_49386_G02_genomic.fna.gz --refList GCF_900445485.1_49386_G02_genomic.fna/target_genomes.txt --output GCF_900445485.1_49386_G02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:42,735] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:42,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9308d1d-ecae-4eee-813b-45ceaf426691/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:42,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9308d1d-ecae-4eee-813b-45ceaf426691/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:42,753] [INFO] Found 15 fastANI hits (7 hits with ANI > threshold)
[2024-01-24 10:47:42,753] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:47:42,754] [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
Priestia megaterium	strain=NCTC10342	GCA_900445485.1	1404	1404	type	True	100.0	1921	1922	95	inconclusive
Priestia megaterium	strain=ATCC 14581	GCA_000832985.1	1404	1404	type	True	99.9988	1902	1922	95	inconclusive
Priestia megaterium	strain=ATCC 14581	GCA_006094495.1	1404	1404	type	True	99.9966	1900	1922	95	inconclusive
Priestia megaterium	strain=ATCC 14581	GCA_017086525.1	1404	1404	type	True	99.9963	1902	1922	95	inconclusive
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	99.9849	1802	1922	95	inconclusive
Priestia megaterium	strain=ATCC 14581	GCA_900113355.1	1404	1404	suspected-type	True	97.8078	1635	1922	95	inconclusive
Priestia aryabhattai	strain=B8W22	GCA_000956595.1	412384	412384	type	True	95.3787	1520	1922	95	inconclusive
Mangrovibacillus cuniculi	strain=R1DC41	GCA_015482585.1	2593652	2593652	type	True	79.2336	78	1922	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	78.595	69	1922	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	78.4223	278	1922	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	77.33	95	1922	95	below_threshold
Gottfriedia luciferensis	strain=DSM 18845	GCA_002156865.1	178774	178774	type	True	77.1964	112	1922	95	below_threshold
Anaerobacillus arseniciselenatis	strain=DSM 15340	GCA_001865995.1	85682	85682	type	True	76.7639	65	1922	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	76.7312	121	1922	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.5647	93	1922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:42,755] [INFO] DFAST Taxonomy check result was written to GCF_900445485.1_49386_G02_genomic.fna/tc_result.tsv
[2024-01-24 10:47:42,756] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:42,756] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:42,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9308d1d-ecae-4eee-813b-45ceaf426691/dqc_reference/checkm_data
[2024-01-24 10:47:42,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:42,818] [INFO] Task started: CheckM
[2024-01-24 10:47:42,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445485.1_49386_G02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445485.1_49386_G02_genomic.fna/checkm_input GCF_900445485.1_49386_G02_genomic.fna/checkm_result
[2024-01-24 10:48:22,979] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:22,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:23,005] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:23,005] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:23,006] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445485.1_49386_G02_genomic.fna/markers.fasta)
[2024-01-24 10:48:23,006] [INFO] Task started: Blastn
[2024-01-24 10:48:23,006] [INFO] Running command: blastn -query GCF_900445485.1_49386_G02_genomic.fna/markers.fasta -db /var/lib/cwl/stga9308d1d-ecae-4eee-813b-45ceaf426691/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445485.1_49386_G02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:23,871] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:23,875] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:23,875] [INFO] Target genome list was writen to GCF_900445485.1_49386_G02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:23,910] [INFO] Task started: fastANI
[2024-01-24 10:48:23,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg08d21b44-2961-4e95-8098-b2403feb1190/GCF_900445485.1_49386_G02_genomic.fna.gz --refList GCF_900445485.1_49386_G02_genomic.fna/target_genomes_gtdb.txt --output GCF_900445485.1_49386_G02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:34,881] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:34,901] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:34,902] [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_000832985.1	s__Priestia megaterium	99.9987	1903	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.5311	96.82	95.69	0.88	0.73	151	conclusive
GCF_000956595.1	s__Priestia aryabhattai	95.3543	1522	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	96.022	97.07	96.58	0.92	0.91	12	-
GCF_009497655.1	s__Priestia megaterium_A	95.2151	1545	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	96.022	98.08	96.36	0.92	0.89	34	-
GCF_008180335.1	s__Priestia megaterium_B	79.6917	526	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591565.1	s__Priestia flexa	79.5569	421	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	99.12	98.83	0.89	0.87	15	-
GCF_002265635.1	s__Priestia aryabhattai_A	79.3442	463	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	98.53	98.16	0.94	0.93	4	-
GCF_016909075.1	s__Priestia iocasae	78.4223	278	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591585.1	s__Niallia circulans	77.0156	96	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.18	98.58	0.93	0.91	9	-
GCF_900116295.1	s__Bacillus_A sp900116295	76.9582	146	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003570725.1	s__Peribacillus asahii	76.9117	131	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509555.1	s__Cytobacillus sp001509555	76.7484	98	1922	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	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:34,903] [INFO] GTDB search result was written to GCF_900445485.1_49386_G02_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:34,905] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:34,909] [INFO] DFAST_QC result json was written to GCF_900445485.1_49386_G02_genomic.fna/dqc_result.json
[2024-01-24 10:48:34,909] [INFO] DFAST_QC completed!
[2024-01-24 10:48:34,909] [INFO] Total running time: 0h1m28s