[2024-01-25 18:11:20,516] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:20,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:20,519] [INFO] DQC Reference Directory: /var/lib/cwl/stg539ee9b1-a12e-4c3c-9589-a9191fbf44a3/dqc_reference
[2024-01-25 18:11:21,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:21,646] [INFO] Task started: Prodigal
[2024-01-25 18:11:21,646] [INFO] Running command: gunzip -c /var/lib/cwl/stg49b80705-aee2-4d15-b404-6c905952801f/GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna.gz | prodigal -d GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/cds.fna -a GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:32,259] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:32,259] [INFO] Task started: HMMsearch
[2024-01-25 18:11:32,259] [INFO] Running command: hmmsearch --tblout GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg539ee9b1-a12e-4c3c-9589-a9191fbf44a3/dqc_reference/reference_markers.hmm GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:32,487] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:32,488] [INFO] Found 6/6 markers.
[2024-01-25 18:11:32,527] [INFO] Query marker FASTA was written to GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/markers.fasta
[2024-01-25 18:11:32,527] [INFO] Task started: Blastn
[2024-01-25 18:11:32,527] [INFO] Running command: blastn -query GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg539ee9b1-a12e-4c3c-9589-a9191fbf44a3/dqc_reference/reference_markers.fasta -out GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:33,415] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:33,419] [INFO] Selected 16 target genomes.
[2024-01-25 18:11:33,420] [INFO] Target genome list was writen to GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/target_genomes.txt
[2024-01-25 18:11:33,423] [INFO] Task started: fastANI
[2024-01-25 18:11:33,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg49b80705-aee2-4d15-b404-6c905952801f/GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna.gz --refList GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/target_genomes.txt --output GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:48,808] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:48,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg539ee9b1-a12e-4c3c-9589-a9191fbf44a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:48,809] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg539ee9b1-a12e-4c3c-9589-a9191fbf44a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:48,818] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:11:48,818] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:11:48,818] [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
Franconibacter helveticus	strain=LMG 23732	GCA_000463115.2	357240	357240	type	True	100.0	1484	1484	95	conclusive
Franconibacter helveticus	strain=513	GCA_000485945.1	357240	357240	type	True	99.8189	1289	1484	95	conclusive
Franconibacter daqui	strain=CGMCC 1.15944	GCA_014644275.1	2047724	2047724	type	True	88.0377	1272	1484	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000409325.1	535744	535744	type	True	82.8738	974	1484	95	below_threshold
Cronobacter dublinensis subsp. lausannensis	strain=LMG 23824	GCA_000409365.1	413500	413497	type	True	82.8635	971	1484	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_900447325.1	535744	535744	type	True	82.8069	994	1484	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000319325.1	535744	535744	type	True	82.7883	967	1484	95	below_threshold
Cronobacter dublinensis subsp. lactaridi	strain=LMG 23825	GCA_000409345.1	413499	413497	type	True	82.763	991	1484	95	below_threshold
Cronobacter dublinensis subsp. dublinensis	strain=LMG 23823	GCA_000409225.1	413498	413497	type	True	82.7438	976	1484	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_001277195.1	413501	413501	type	True	82.7009	998	1484	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_000409285.1	413501	413501	type	True	82.6967	976	1484	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	82.6435	903	1484	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	80.699	813	1484	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	80.6592	804	1484	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	80.6055	785	1484	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	80.2515	723	1484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:48,820] [INFO] DFAST Taxonomy check result was written to GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/tc_result.tsv
[2024-01-25 18:11:48,820] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:48,820] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:48,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg539ee9b1-a12e-4c3c-9589-a9191fbf44a3/dqc_reference/checkm_data
[2024-01-25 18:11:48,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:48,862] [INFO] Task started: CheckM
[2024-01-25 18:11:48,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/checkm_input GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/checkm_result
[2024-01-25 18:12:22,835] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:22,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:22,865] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:22,865] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:22,866] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/markers.fasta)
[2024-01-25 18:12:22,866] [INFO] Task started: Blastn
[2024-01-25 18:12:22,867] [INFO] Running command: blastn -query GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg539ee9b1-a12e-4c3c-9589-a9191fbf44a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:24,358] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:24,361] [INFO] Selected 8 target genomes.
[2024-01-25 18:12:24,361] [INFO] Target genome list was writen to GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:24,369] [INFO] Task started: fastANI
[2024-01-25 18:12:24,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg49b80705-aee2-4d15-b404-6c905952801f/GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna.gz --refList GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:32,648] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:32,655] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:32,655] [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_000463115.2	s__Franconibacter helveticus	100.0	1484	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Franconibacter	95.0	99.42	99.04	0.94	0.92	6	conclusive
GCA_000621185.1	s__Franconibacter pulveris	88.038	1271	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Franconibacter	95.0	98.43	96.71	0.95	0.93	7	-
GCF_001277175.1	s__Cronobacter universalis	82.8492	1002	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.87	99.62	0.99	0.98	4	-
GCF_001277215.2	s__Cronobacter malonaticus	82.8172	984	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.86	98.11	0.94	0.89	62	-
GCF_001277235.1	s__Cronobacter dublinensis	82.7339	996	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.74	96.92	0.93	0.89	42	-
GCF_001277195.1	s__Cronobacter muytjensii	82.7248	995	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.13	98.83	0.94	0.91	9	-
GCA_000027065.2	s__Cronobacter turicensis	82.7212	996	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.17	96.06	0.93	0.89	18	-
GCF_000982825.1	s__Cronobacter sakazakii	82.6964	981	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.00	97.39	0.92	0.86	440	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:32,656] [INFO] GTDB search result was written to GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:32,657] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:32,660] [INFO] DFAST_QC result json was written to GCF_000463115.2_CroHelLMG23732_1.0_genomic.fna/dqc_result.json
[2024-01-25 18:12:32,660] [INFO] DFAST_QC completed!
[2024-01-25 18:12:32,660] [INFO] Total running time: 0h1m12s