[2024-01-24 12:45:09,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:09,802] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:09,802] [INFO] DQC Reference Directory: /var/lib/cwl/stg438fb84a-958d-42a3-83ff-58b84a5c53f2/dqc_reference
[2024-01-24 12:45:13,081] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,082] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,082] [INFO] Running command: gunzip -c /var/lib/cwl/stgca53c653-2366-4405-a2ea-2db857d9bdd2/GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna.gz | prodigal -d GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/cds.fna -a GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:24,630] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:24,631] [INFO] Task started: HMMsearch
[2024-01-24 12:45:24,631] [INFO] Running command: hmmsearch --tblout GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg438fb84a-958d-42a3-83ff-58b84a5c53f2/dqc_reference/reference_markers.hmm GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:24,912] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:24,913] [INFO] Found 6/6 markers.
[2024-01-24 12:45:24,950] [INFO] Query marker FASTA was written to GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/markers.fasta
[2024-01-24 12:45:24,951] [INFO] Task started: Blastn
[2024-01-24 12:45:24,951] [INFO] Running command: blastn -query GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg438fb84a-958d-42a3-83ff-58b84a5c53f2/dqc_reference/reference_markers.fasta -out GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:25,921] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:25,925] [INFO] Selected 22 target genomes.
[2024-01-24 12:45:25,926] [INFO] Target genome list was writen to GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/target_genomes.txt
[2024-01-24 12:45:25,947] [INFO] Task started: fastANI
[2024-01-24 12:45:25,947] [INFO] Running command: fastANI --query /var/lib/cwl/stgca53c653-2366-4405-a2ea-2db857d9bdd2/GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna.gz --refList GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/target_genomes.txt --output GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:46,426] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:46,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg438fb84a-958d-42a3-83ff-58b84a5c53f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:46,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg438fb84a-958d-42a3-83ff-58b84a5c53f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:46,444] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:46,444] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:46,445] [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
Siccibacter turicensis	strain=LMG 23730	GCA_000463155.2	357233	357233	type	True	100.0	1391	1396	95	conclusive
Siccibacter colletis	strain=1383	GCA_000696575.1	1505757	1505757	type	True	86.5018	1169	1396	95	below_threshold
Cronobacter dublinensis subsp. lactaridi	strain=LMG 23825	GCA_000409345.1	413499	413497	type	True	81.904	902	1396	95	below_threshold
Cronobacter dublinensis subsp. lausannensis	strain=LMG 23824	GCA_000409365.1	413500	413497	type	True	81.844	907	1396	95	below_threshold
Cronobacter malonaticus	strain=LMG 23826	GCA_000409305.1	413503	413503	type	True	81.7895	907	1396	95	below_threshold
Cronobacter malonaticus	strain=LMG 23826	GCA_001277215.2	413503	413503	type	True	81.7557	940	1396	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	81.5371	850	1396	95	below_threshold
Cronobacter dublinensis subsp. dublinensis	strain=LMG 23823	GCA_000409225.1	413498	413497	type	True	81.4936	923	1396	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_001277195.1	413501	413501	type	True	81.4442	891	1396	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_000409285.1	413501	413501	type	True	81.4371	879	1396	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.3618	856	1396	95	below_threshold
Enterobacter asburiae	strain=FDAARGOS_892	GCA_016027695.1	61645	61645	type	True	81.3273	804	1396	95	below_threshold
Enterobacter asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	81.2983	810	1396	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.2867	831	1396	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.2076	837	1396	95	below_threshold
Pluralibacter gergoviae	strain=NBRC 105706	GCA_001598855.1	61647	61647	type	True	81.1995	802	1396	95	below_threshold
Franconibacter helveticus	strain=LMG 23732	GCA_000463115.2	357240	357240	type	True	81.1407	827	1396	95	below_threshold
Franconibacter helveticus	strain=513	GCA_000485945.1	357240	357240	type	True	81.0844	771	1396	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.8607	810	1396	95	below_threshold
Yokenella regensburgei	strain=NCTC11966	GCA_900460805.1	158877	158877	type	True	80.704	724	1396	95	below_threshold
Atlantibacter hermannii	strain=FDAARGOS_888	GCA_016027855.1	565	565	type	True	80.6717	735	1396	95	below_threshold
Yokenella regensburgei	strain=ATCC 49455	GCA_000735455.1	158877	158877	type	True	80.5859	719	1396	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:46,448] [INFO] DFAST Taxonomy check result was written to GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/tc_result.tsv
[2024-01-24 12:45:46,449] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:46,449] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:46,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg438fb84a-958d-42a3-83ff-58b84a5c53f2/dqc_reference/checkm_data
[2024-01-24 12:45:46,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:46,498] [INFO] Task started: CheckM
[2024-01-24 12:45:46,498] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/checkm_input GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/checkm_result
[2024-01-24 12:46:23,629] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:23,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:23,653] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:23,653] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:23,654] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/markers.fasta)
[2024-01-24 12:46:23,654] [INFO] Task started: Blastn
[2024-01-24 12:46:23,654] [INFO] Running command: blastn -query GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg438fb84a-958d-42a3-83ff-58b84a5c53f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:25,135] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:25,140] [INFO] Selected 17 target genomes.
[2024-01-24 12:46:25,140] [INFO] Target genome list was writen to GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:25,169] [INFO] Task started: fastANI
[2024-01-24 12:46:25,169] [INFO] Running command: fastANI --query /var/lib/cwl/stgca53c653-2366-4405-a2ea-2db857d9bdd2/GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna.gz --refList GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:41,546] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:41,566] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:41,567] [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_000463155.2	s__Siccibacter turicensis	100.0	1389	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Siccibacter	95.0	98.74	97.87	0.95	0.92	6	conclusive
GCF_000696575.1	s__Siccibacter colletis	86.52	1167	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Siccibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000027065.2	s__Cronobacter turicensis	81.9113	913	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.17	96.06	0.93	0.89	18	-
GCF_001277175.1	s__Cronobacter universalis	81.8682	920	1396	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	81.7679	939	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.86	98.11	0.94	0.89	62	-
GCF_000982825.1	s__Cronobacter sakazakii	81.7298	919	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.00	97.39	0.92	0.86	440	-
GCF_002208095.1	s__Enterobacter cloacae_M	81.3747	832	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.7528	98.28	96.89	0.91	0.85	84	-
GCF_007570865.1	s__Atlantibacter subterranea	81.2927	794	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.55	98.44	0.93	0.91	8	-
GCF_000164865.1	s__Enterobacter_B lignolyticus	81.2247	799	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_B	95.0	98.80	98.80	0.94	0.94	2	-
GCF_014193285.1	s__Atlantibacter sp002345315	81.213	790	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.54	98.53	0.93	0.90	4	-
GCF_009907385.1	s__Atlantibacter hermannii_A	81.204	786	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598855.1	s__Pluralibacter gergoviae	81.2039	803	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pluralibacter	95.0	98.81	98.03	0.90	0.85	23	-
GCF_000463115.2	s__Franconibacter helveticus	81.1219	829	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Franconibacter	95.0	99.42	99.04	0.94	0.92	6	-
GCF_000321045.1	s__Phytobacter massiliensis	80.9207	784	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002469605.1	s__UBA7405 sp002469605	80.8677	631	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019237635.1	s__Enterobacter_B sp019237635	80.8101	702	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900635495.1	s__Atlantibacter hermannii	80.7069	726	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.95	98.59	0.96	0.90	28	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:41,568] [INFO] GTDB search result was written to GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:41,570] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:41,578] [INFO] DFAST_QC result json was written to GCF_000463155.2_CroZurLMG23730T_1.0_genomic.fna/dqc_result.json
[2024-01-24 12:46:41,578] [INFO] DFAST_QC completed!
[2024-01-24 12:46:41,578] [INFO] Total running time: 0h1m32s