[2024-01-24 13:56:27,244] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:27,246] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:27,246] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ff551ac-0273-44d8-8c83-e15725df1c80/dqc_reference
[2024-01-24 13:56:28,499] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:28,500] [INFO] Task started: Prodigal
[2024-01-24 13:56:28,500] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cd4ff1b-96e1-4689-839e-1da5f82c18fd/GCF_003574475.2_ASM357447v2_genomic.fna.gz | prodigal -d GCF_003574475.2_ASM357447v2_genomic.fna/cds.fna -a GCF_003574475.2_ASM357447v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:31,373] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:31,374] [INFO] Task started: HMMsearch
[2024-01-24 13:56:31,374] [INFO] Running command: hmmsearch --tblout GCF_003574475.2_ASM357447v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ff551ac-0273-44d8-8c83-e15725df1c80/dqc_reference/reference_markers.hmm GCF_003574475.2_ASM357447v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:31,594] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:31,595] [INFO] Found 6/6 markers.
[2024-01-24 13:56:31,615] [INFO] Query marker FASTA was written to GCF_003574475.2_ASM357447v2_genomic.fna/markers.fasta
[2024-01-24 13:56:31,615] [INFO] Task started: Blastn
[2024-01-24 13:56:31,615] [INFO] Running command: blastn -query GCF_003574475.2_ASM357447v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ff551ac-0273-44d8-8c83-e15725df1c80/dqc_reference/reference_markers.fasta -out GCF_003574475.2_ASM357447v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:32,253] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:32,257] [INFO] Selected 14 target genomes.
[2024-01-24 13:56:32,258] [INFO] Target genome list was writen to GCF_003574475.2_ASM357447v2_genomic.fna/target_genomes.txt
[2024-01-24 13:56:32,286] [INFO] Task started: fastANI
[2024-01-24 13:56:32,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cd4ff1b-96e1-4689-839e-1da5f82c18fd/GCF_003574475.2_ASM357447v2_genomic.fna.gz --refList GCF_003574475.2_ASM357447v2_genomic.fna/target_genomes.txt --output GCF_003574475.2_ASM357447v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:37,027] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:37,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ff551ac-0273-44d8-8c83-e15725df1c80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:37,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ff551ac-0273-44d8-8c83-e15725df1c80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:37,043] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:56:37,043] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:56:37,043] [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
Francisella philomiragia	strain=O#319L	GCA_000833455.1	28110	28110	type	True	78.4735	164	598	95	below_threshold
Francisella philomiragia	strain=ATCC 25015	GCA_000156715.1	28110	28110	type	True	78.4083	168	598	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001885235.1	622488	622488	type	True	78.1244	152	598	95	below_threshold
Allofrancisella frigidaquae	strain=SYSU 10HL1970	GCA_012222825.1	1085644	1085644	type	True	78.1169	129	598	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001608445.1	622488	622488	type	True	78.0929	149	598	95	below_threshold
Francisella salina	strain=TX07-7308	GCA_000219045.1	573569	573569	type	True	78.0795	167	598	95	below_threshold
Francisella uliginis	strain=TX07-7310	GCA_001895265.1	573570	573570	type	True	77.7196	214	598	95	below_threshold
Allofrancisella inopinata	strain=SYSU YG23	GCA_012222965.1	1085647	1085647	type	True	77.6913	147	598	95	below_threshold
Allofrancisella inopinata	strain=DSM 101834	GCA_004365555.1	1085647	1085647	type	True	77.6683	146	598	95	below_threshold
Allofrancisella guangzhouensis	strain=08HL01032	GCA_000815225.1	594679	594679	type	True	77.6582	139	598	95	below_threshold
Francisella adeliensis	strain=FDC440	GCA_003290445.1	2007306	2007306	type	True	77.5543	131	598	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:37,045] [INFO] DFAST Taxonomy check result was written to GCF_003574475.2_ASM357447v2_genomic.fna/tc_result.tsv
[2024-01-24 13:56:37,046] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:37,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:37,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ff551ac-0273-44d8-8c83-e15725df1c80/dqc_reference/checkm_data
[2024-01-24 13:56:37,047] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:37,069] [INFO] Task started: CheckM
[2024-01-24 13:56:37,069] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003574475.2_ASM357447v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003574475.2_ASM357447v2_genomic.fna/checkm_input GCF_003574475.2_ASM357447v2_genomic.fna/checkm_result
[2024-01-24 13:56:53,939] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:53,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:53,965] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:53,965] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:53,966] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003574475.2_ASM357447v2_genomic.fna/markers.fasta)
[2024-01-24 13:56:53,966] [INFO] Task started: Blastn
[2024-01-24 13:56:53,966] [INFO] Running command: blastn -query GCF_003574475.2_ASM357447v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ff551ac-0273-44d8-8c83-e15725df1c80/dqc_reference/reference_markers_gtdb.fasta -out GCF_003574475.2_ASM357447v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:54,949] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:54,953] [INFO] Selected 16 target genomes.
[2024-01-24 13:56:54,953] [INFO] Target genome list was writen to GCF_003574475.2_ASM357447v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:54,965] [INFO] Task started: fastANI
[2024-01-24 13:56:54,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cd4ff1b-96e1-4689-839e-1da5f82c18fd/GCF_003574475.2_ASM357447v2_genomic.fna.gz --refList GCF_003574475.2_ASM357447v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003574475.2_ASM357447v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:00,166] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:00,176] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:00,177] [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_003574475.2	s__Pseudofrancisella aestuarii	100.0	598	598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Pseudofrancisella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001880225.1	s__Pseudofrancisella frigiditurris	93.3988	535	598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Pseudofrancisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156715.1	s__Francisella philomiragia	78.4083	168	598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	97.81	97.38	0.91	0.88	49	-
GCF_001885235.1	s__Francisella hispaniensis	78.1007	153	598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	98.55	97.74	0.95	0.92	4	-
GCF_012222825.1	s__Allofrancisella frigidaquae	78.089	130	598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Allofrancisella	95.0	98.33	98.33	0.93	0.93	2	-
GCF_012222965.1	s__Allofrancisella inopinata	77.7362	145	598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Allofrancisella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001895265.1	s__Francisella uliginis	77.7196	214	598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008711465.1	s__Francisella sp008711465	77.7179	187	598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000815225.1	s__Allofrancisella guangzhouensis	77.6316	138	598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Allofrancisella	95.0	99.92	99.90	0.98	0.96	4	-
GCF_012224145.1	s__Francisella sp012224145	77.6083	191	598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003290445.1	s__Francisella_A adeliensis	77.5305	132	598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella_A	95.0	98.86	95.45	0.98	0.93	5	-
GCF_000008985.1	s__Francisella tularensis	77.4968	151	598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.28	97.47	0.99	0.89	860	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:00,179] [INFO] GTDB search result was written to GCF_003574475.2_ASM357447v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:00,180] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:00,184] [INFO] DFAST_QC result json was written to GCF_003574475.2_ASM357447v2_genomic.fna/dqc_result.json
[2024-01-24 13:57:00,185] [INFO] DFAST_QC completed!
[2024-01-24 13:57:00,185] [INFO] Total running time: 0h0m33s