[2024-01-24 14:06:14,917] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:14,919] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:14,919] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0933bfd-83a8-4b17-a4e9-daa62113eaf0/dqc_reference
[2024-01-24 14:06:16,285] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:16,286] [INFO] Task started: Prodigal
[2024-01-24 14:06:16,286] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a4f8410-e23f-46b7-a76c-6b528141146f/GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna.gz | prodigal -d GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/cds.fna -a GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:30,148] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:30,148] [INFO] Task started: HMMsearch
[2024-01-24 14:06:30,148] [INFO] Running command: hmmsearch --tblout GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0933bfd-83a8-4b17-a4e9-daa62113eaf0/dqc_reference/reference_markers.hmm GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:30,458] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:30,459] [INFO] Found 6/6 markers.
[2024-01-24 14:06:30,508] [INFO] Query marker FASTA was written to GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/markers.fasta
[2024-01-24 14:06:30,508] [INFO] Task started: Blastn
[2024-01-24 14:06:30,509] [INFO] Running command: blastn -query GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0933bfd-83a8-4b17-a4e9-daa62113eaf0/dqc_reference/reference_markers.fasta -out GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:31,403] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:31,407] [INFO] Selected 19 target genomes.
[2024-01-24 14:06:31,407] [INFO] Target genome list was writen to GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:31,427] [INFO] Task started: fastANI
[2024-01-24 14:06:31,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a4f8410-e23f-46b7-a76c-6b528141146f/GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna.gz --refList GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/target_genomes.txt --output GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:50,350] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:50,351] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0933bfd-83a8-4b17-a4e9-daa62113eaf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:50,351] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0933bfd-83a8-4b17-a4e9-daa62113eaf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:50,365] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:50,366] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:50,366] [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
Kluyvera georgiana	strain=ATCC 51603	GCA_001654985.1	73098	73098	type	True	100.0	1611	1618	95	conclusive
Kluyvera sichuanensis	strain=090646	GCA_014218705.1	2725494	2725494	type	True	87.5345	1223	1618	95	below_threshold
Kluyvera ascorbata	strain=ATCC 33433	GCA_000735365.1	51288	51288	suspected-type	True	87.2219	1140	1618	95	below_threshold
Kluyvera cryocrescens	strain=NBRC 102467	GCA_001571285.1	580	580	type	True	85.6117	1160	1618	95	below_threshold
Kluyvera intermedia	strain=NBRC 102594	GCA_001598315.1	61648	61648	suspected-type	True	85.1039	1105	1618	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	83.1042	994	1618	95	below_threshold
Pseudocitrobacter vendiensis	strain=type strain: CPO20170097	GCA_943590815.1	2488306	2488306	type	True	82.9697	953	1618	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	82.431	870	1618	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	82.0573	886	1618	95	below_threshold
Enterobacter hormaechei subsp. steigerwaltii	strain=DSM 16691	GCA_001729725.1	299766	158836	type	True	82.0152	865	1618	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.9644	843	1618	95	below_threshold
Salmonella enterica subsp. enterica	strain=LT2	GCA_002289225.1	59201	28901	type	True	81.6825	724	1618	95	below_threshold
Salmonella enterica	strain=FDAARGOS_768	GCA_006365335.1	28901	28901	type	True	81.6792	737	1618	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	81.6522	736	1618	95	below_threshold
Enterobacter ludwigii	strain=EN-119	GCA_001750725.1	299767	299767	type	True	81.5638	846	1618	95	below_threshold
Shewanella cyperi	strain=FJAT-53720	GCA_017354985.1	2814292	2814292	type	True	76.5905	70	1618	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:50,369] [INFO] DFAST Taxonomy check result was written to GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:50,370] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:50,370] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:50,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0933bfd-83a8-4b17-a4e9-daa62113eaf0/dqc_reference/checkm_data
[2024-01-24 14:06:50,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:50,428] [INFO] Task started: CheckM
[2024-01-24 14:06:50,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/checkm_input GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/checkm_result
[2024-01-24 14:07:31,848] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:31,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:31,874] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:31,875] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:31,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/markers.fasta)
[2024-01-24 14:07:31,876] [INFO] Task started: Blastn
[2024-01-24 14:07:31,876] [INFO] Running command: blastn -query GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0933bfd-83a8-4b17-a4e9-daa62113eaf0/dqc_reference/reference_markers_gtdb.fasta -out GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:33,079] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:33,082] [INFO] Selected 14 target genomes.
[2024-01-24 14:07:33,082] [INFO] Target genome list was writen to GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:33,094] [INFO] Task started: fastANI
[2024-01-24 14:07:33,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a4f8410-e23f-46b7-a76c-6b528141146f/GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna.gz --refList GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/target_genomes_gtdb.txt --output GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:47,869] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:47,881] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:47,881] [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_001654985.1	s__Kluyvera georgiana	100.0	1611	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.06	98.06	0.84	0.84	2	conclusive
GCA_002211745.1	s__Kluyvera georgiana_A	94.5806	1341	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.12	98.12	0.89	0.89	2	-
GCF_014168815.1	s__Kluyvera ascorbata_B	88.0703	1255	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.36	99.08	0.90	0.88	9	-
GCF_014218705.1	s__Kluyvera sichuanensis	87.5345	1223	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735365.1	s__Kluyvera ascorbata	87.2219	1140	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.94	97.70	0.94	0.89	5	-
GCA_016939855.1	s__Kluyvera ascorbata_C	86.7566	670	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571285.1	s__Kluyvera cryocrescens	85.6117	1160	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.35	99.12	0.95	0.93	4	-
GCF_001266615.1	s__Kluyvera cryocrescens_A	85.4385	1122	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363335.1	s__Kluyvera sp902363335	85.233	1071	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015234305.1	s__Superficieibacter sp900766525	81.7489	834	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Superficieibacter	95.0	96.26	96.26	0.86	0.86	2	-
GCA_002470465.1	s__Scandinavium sp002470465	81.5772	828	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002915575.1	s__Superficieibacter electus	81.5079	767	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Superficieibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002953195.1	s__Mixta gaviniae	79.968	558	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.91	99.91	0.99	0.99	2	-
GCF_002858805.1	s__Chimaeribacter arupi	79.9177	485	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chimaeribacter	95.0	99.29	99.19	0.95	0.94	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:47,883] [INFO] GTDB search result was written to GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:47,883] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:47,887] [INFO] DFAST_QC result json was written to GCF_001654985.1_Kge51603_DRAFTv1_genomic.fna/dqc_result.json
[2024-01-24 14:07:47,887] [INFO] DFAST_QC completed!
[2024-01-24 14:07:47,887] [INFO] Total running time: 0h1m33s