[2024-01-25 17:50:50,697] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:50:50,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:50:50,703] [INFO] DQC Reference Directory: /var/lib/cwl/stg01f93e78-c255-4cfb-987a-cc232514cef3/dqc_reference
[2024-01-25 17:50:51,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:50:51,863] [INFO] Task started: Prodigal
[2024-01-25 17:50:51,863] [INFO] Running command: gunzip -c /var/lib/cwl/stg729075ed-4e7e-4b69-9b95-2a341ca3eb23/GCF_012933555.1_ASM1293355v1_genomic.fna.gz | prodigal -d GCF_012933555.1_ASM1293355v1_genomic.fna/cds.fna -a GCF_012933555.1_ASM1293355v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:00,849] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:00,850] [INFO] Task started: HMMsearch
[2024-01-25 17:51:00,850] [INFO] Running command: hmmsearch --tblout GCF_012933555.1_ASM1293355v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01f93e78-c255-4cfb-987a-cc232514cef3/dqc_reference/reference_markers.hmm GCF_012933555.1_ASM1293355v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:01,112] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:01,113] [INFO] Found 6/6 markers.
[2024-01-25 17:51:01,151] [INFO] Query marker FASTA was written to GCF_012933555.1_ASM1293355v1_genomic.fna/markers.fasta
[2024-01-25 17:51:01,152] [INFO] Task started: Blastn
[2024-01-25 17:51:01,152] [INFO] Running command: blastn -query GCF_012933555.1_ASM1293355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01f93e78-c255-4cfb-987a-cc232514cef3/dqc_reference/reference_markers.fasta -out GCF_012933555.1_ASM1293355v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:01,703] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:01,707] [INFO] Selected 19 target genomes.
[2024-01-25 17:51:01,707] [INFO] Target genome list was writen to GCF_012933555.1_ASM1293355v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:01,714] [INFO] Task started: fastANI
[2024-01-25 17:51:01,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg729075ed-4e7e-4b69-9b95-2a341ca3eb23/GCF_012933555.1_ASM1293355v1_genomic.fna.gz --refList GCF_012933555.1_ASM1293355v1_genomic.fna/target_genomes.txt --output GCF_012933555.1_ASM1293355v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:20,748] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:20,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01f93e78-c255-4cfb-987a-cc232514cef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:20,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01f93e78-c255-4cfb-987a-cc232514cef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:20,759] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:51:20,759] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:20,759] [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 alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	100.0	1741	1746	95	conclusive
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	84.4885	1165	1746	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_003055085.1	46224	46224	type	True	79.0436	116	1746	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_016785185.1	46224	46224	type	True	79.0308	137	1746	95	below_threshold
Bacillus methanolicus	strain=PB1	GCA_000262755.1	1471	1471	suspected-type	True	78.9727	93	1746	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	78.7447	373	1746	95	below_threshold
Niallia taxi	strain=M5HDSG1-1	GCA_004005475.1	2499688	2499688	type	True	78.7141	306	1746	95	below_threshold
Bacillus massilionigeriensis	strain=Marseille-P2384	GCA_900117315.1	1805475	1805475	type	True	78.6301	146	1746	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	78.5409	123	1746	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	78.4614	103	1746	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	78.3292	168	1746	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	77.5958	140	1746	95	below_threshold
Bacillus marasmi	strain=Marseille-P3556	GCA_902168435.1	1926279	1926279	type	True	77.1414	119	1746	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	76.6694	126	1746	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	76.4784	128	1746	95	below_threshold
Saliterribacillus persicus	strain=DSM 27696	GCA_003337485.1	930114	930114	type	True	76.273	65	1746	95	below_threshold
Anoxybacillus kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	76.2628	53	1746	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:20,763] [INFO] DFAST Taxonomy check result was written to GCF_012933555.1_ASM1293355v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:20,764] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:20,764] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:20,764] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01f93e78-c255-4cfb-987a-cc232514cef3/dqc_reference/checkm_data
[2024-01-25 17:51:20,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:20,818] [INFO] Task started: CheckM
[2024-01-25 17:51:20,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012933555.1_ASM1293355v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012933555.1_ASM1293355v1_genomic.fna/checkm_input GCF_012933555.1_ASM1293355v1_genomic.fna/checkm_result
[2024-01-25 17:51:51,724] [INFO] Task succeeded: CheckM
[2024-01-25 17:51:51,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:51:51,749] [INFO] ===== Completeness check finished =====
[2024-01-25 17:51:51,749] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:51:51,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012933555.1_ASM1293355v1_genomic.fna/markers.fasta)
[2024-01-25 17:51:51,750] [INFO] Task started: Blastn
[2024-01-25 17:51:51,750] [INFO] Running command: blastn -query GCF_012933555.1_ASM1293355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01f93e78-c255-4cfb-987a-cc232514cef3/dqc_reference/reference_markers_gtdb.fasta -out GCF_012933555.1_ASM1293355v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:52,564] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:52,569] [INFO] Selected 7 target genomes.
[2024-01-25 17:51:52,569] [INFO] Target genome list was writen to GCF_012933555.1_ASM1293355v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:52,575] [INFO] Task started: fastANI
[2024-01-25 17:51:52,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg729075ed-4e7e-4b69-9b95-2a341ca3eb23/GCF_012933555.1_ASM1293355v1_genomic.fna.gz --refList GCF_012933555.1_ASM1293355v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012933555.1_ASM1293355v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:02,967] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:02,973] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:02,973] [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
GCA_900199695.1	s__Niallia sp900199695	98.3954	1412	1746	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	conclusive
GCF_001076885.1	s__Niallia sp001076885	84.9981	1079	1746	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_003726095.1	s__Niallia circulans_A	84.7445	1196	1746	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_001591585.1	s__Niallia circulans	84.4894	1165	1746	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_009183415.1	s__Niallia sp009183415	79.9957	563	1746	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_007273535.1	s__Niallia circulans_B	78.9382	305	1746	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_000380245.2	s__Bacillus_AD massiliogorillae	76.6694	126	1746	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	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:02,975] [INFO] GTDB search result was written to GCF_012933555.1_ASM1293355v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:02,975] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:02,979] [INFO] DFAST_QC result json was written to GCF_012933555.1_ASM1293355v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:02,979] [INFO] DFAST_QC completed!
[2024-01-25 17:52:02,979] [INFO] Total running time: 0h1m12s