[2024-01-24 12:21:44,575] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,577] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,577] [INFO] DQC Reference Directory: /var/lib/cwl/stg49eea199-972a-4eaa-80b3-927aa364c92c/dqc_reference
[2024-01-24 12:21:45,993] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:45,993] [INFO] Task started: Prodigal
[2024-01-24 12:21:45,994] [INFO] Running command: gunzip -c /var/lib/cwl/stg00abf5e4-387d-49af-af68-a04ae6099cba/GCF_003935895.2_ASM393589v2_genomic.fna.gz | prodigal -d GCF_003935895.2_ASM393589v2_genomic.fna/cds.fna -a GCF_003935895.2_ASM393589v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:59,994] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:59,995] [INFO] Task started: HMMsearch
[2024-01-24 12:21:59,995] [INFO] Running command: hmmsearch --tblout GCF_003935895.2_ASM393589v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49eea199-972a-4eaa-80b3-927aa364c92c/dqc_reference/reference_markers.hmm GCF_003935895.2_ASM393589v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:00,403] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:00,405] [INFO] Found 6/6 markers.
[2024-01-24 12:22:00,459] [INFO] Query marker FASTA was written to GCF_003935895.2_ASM393589v2_genomic.fna/markers.fasta
[2024-01-24 12:22:00,460] [INFO] Task started: Blastn
[2024-01-24 12:22:00,460] [INFO] Running command: blastn -query GCF_003935895.2_ASM393589v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg49eea199-972a-4eaa-80b3-927aa364c92c/dqc_reference/reference_markers.fasta -out GCF_003935895.2_ASM393589v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:01,459] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:01,463] [INFO] Selected 31 target genomes.
[2024-01-24 12:22:01,463] [INFO] Target genome list was writen to GCF_003935895.2_ASM393589v2_genomic.fna/target_genomes.txt
[2024-01-24 12:22:01,474] [INFO] Task started: fastANI
[2024-01-24 12:22:01,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg00abf5e4-387d-49af-af68-a04ae6099cba/GCF_003935895.2_ASM393589v2_genomic.fna.gz --refList GCF_003935895.2_ASM393589v2_genomic.fna/target_genomes.txt --output GCF_003935895.2_ASM393589v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:32,828] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:32,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49eea199-972a-4eaa-80b3-927aa364c92c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:32,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49eea199-972a-4eaa-80b3-927aa364c92c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:32,852] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:32,852] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:32,853] [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
Yokenella regensburgei	strain=NCTC11966	GCA_900460805.1	158877	158877	type	True	81.9364	912	1570	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.8499	944	1570	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.8241	897	1570	95	below_threshold
Lelliottia nimipressuralis	strain=CCUG 25894	GCA_004115925.1	69220	69220	type	True	81.8218	920	1570	95	below_threshold
Enterobacter cancerogenus	strain=FDAARGOS 1428	GCA_019047785.1	69218	69218	type	True	81.8218	932	1570	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.8094	945	1570	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.7733	932	1570	95	below_threshold
Yokenella regensburgei	strain=ATCC 49455	GCA_000735455.1	158877	158877	type	True	81.7481	888	1570	95	below_threshold
Kluyvera sichuanensis	strain=090646	GCA_014218705.1	2725494	2725494	type	True	81.7439	887	1570	95	below_threshold
Enterobacter mori	strain=LMG 25706	GCA_000211415.1	539813	539813	type	True	81.7205	901	1570	95	below_threshold
Enterobacter cancerogenus		GCA_900185905.1	69218	69218	type	True	81.7119	909	1570	95	below_threshold
Kluyvera georgiana	strain=ATCC 51603	GCA_001654985.1	73098	73098	type	True	81.6769	828	1570	95	below_threshold
Kluyvera ascorbata	strain=ATCC 33433	GCA_000735365.1	51288	51288	suspected-type	True	81.6691	854	1570	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	81.5565	897	1570	95	below_threshold
Leclercia adecarboxylata	strain=FDAARGOS_1505	GCA_020097395.1	83655	83655	suspected-type	True	81.5527	903	1570	95	below_threshold
Pseudocitrobacter vendiensis	strain=type strain: CPO20170097	GCA_943590815.1	2488306	2488306	type	True	81.4795	903	1570	95	below_threshold
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030T	GCA_020525925.1	1667327	1463165	type	True	81.4574	890	1570	95	below_threshold
Raoultella terrigena	strain=NBRC 14941	GCA_006539725.1	577	577	type	True	81.4172	895	1570	95	below_threshold
Leclercia adecarboxylata	strain=NBRC 102595	GCA_001515505.1	83655	83655	suspected-type	True	81.3959	873	1570	95	below_threshold
Klebsiella pneumoniae subsp. rhinoscleromatis	strain=ATCC 13884	GCA_000163455.1	39831	573	type	True	81.3339	821	1570	95	below_threshold
Klebsiella pneumoniae	strain=ATCC 13883	GCA_000742135.1	573	573	type	True	81.3165	872	1570	95	below_threshold
Kluyvera cryocrescens	strain=NBRC 102467	GCA_001571285.1	580	580	type	True	81.1715	874	1570	95	below_threshold
Klebsiella oxytoca	strain=NCTC13727	GCA_900636985.1	571	571	type	True	81.1294	861	1570	95	below_threshold
Kluyvera intermedia	strain=NCTC12125	GCA_900635475.1	61648	61648	suspected-type	True	81.086	845	1570	95	below_threshold
Klebsiella spallanzanii		GCA_902158555.1	2587528	2587528	type	True	81.0244	848	1570	95	below_threshold
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	80.9871	842	1570	95	below_threshold
Klebsiella oxytoca	strain=DSM 5175	GCA_020115535.1	571	571	type	True	80.9495	842	1570	95	below_threshold
Kluyvera intermedia	strain=NBRC 102594	GCA_001598315.1	61648	61648	suspected-type	True	80.9305	819	1570	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	80.9016	851	1570	95	below_threshold
Citrobacter rodentium	strain=NBRC 105723	GCA_000759815.1	67825	67825	type	True	80.8226	811	1570	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_015965555.1	67825	67825	type	True	80.7782	811	1570	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:32,855] [INFO] DFAST Taxonomy check result was written to GCF_003935895.2_ASM393589v2_genomic.fna/tc_result.tsv
[2024-01-24 12:22:32,855] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:32,856] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:32,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49eea199-972a-4eaa-80b3-927aa364c92c/dqc_reference/checkm_data
[2024-01-24 12:22:32,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:32,903] [INFO] Task started: CheckM
[2024-01-24 12:22:32,903] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003935895.2_ASM393589v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003935895.2_ASM393589v2_genomic.fna/checkm_input GCF_003935895.2_ASM393589v2_genomic.fna/checkm_result
[2024-01-24 12:23:17,524] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:17,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:17,555] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:17,556] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:17,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003935895.2_ASM393589v2_genomic.fna/markers.fasta)
[2024-01-24 12:23:17,557] [INFO] Task started: Blastn
[2024-01-24 12:23:17,557] [INFO] Running command: blastn -query GCF_003935895.2_ASM393589v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg49eea199-972a-4eaa-80b3-927aa364c92c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003935895.2_ASM393589v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:19,049] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:19,052] [INFO] Selected 8 target genomes.
[2024-01-24 12:23:19,052] [INFO] Target genome list was writen to GCF_003935895.2_ASM393589v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:19,058] [INFO] Task started: fastANI
[2024-01-24 12:23:19,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg00abf5e4-387d-49af-af68-a04ae6099cba/GCF_003935895.2_ASM393589v2_genomic.fna.gz --refList GCF_003935895.2_ASM393589v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003935895.2_ASM393589v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:29,530] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:29,543] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:29,543] [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_003935895.2	s__Scandinavium goeteborgense	100.0	1568	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	97.59	96.23	0.90	0.88	4	conclusive
GCF_902706235.1	s__Scandinavium sp902706235	93.0143	1301	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902706205.1	s__Scandinavium sp902706205	92.2546	1318	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215375.1	s__Scandinavium sp900215375	85.4445	1144	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002470465.1	s__Scandinavium sp002470465	85.0181	1087	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014156375.1	s__Scandinavium sp014156375	84.5055	1084	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009668205.1	s__Scandinavium sp009668205	83.9341	1100	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901456055.1	s__Phytobacter ursingii	80.6149	796	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	97.10	96.01	0.86	0.80	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:29,545] [INFO] GTDB search result was written to GCF_003935895.2_ASM393589v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:29,546] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:29,550] [INFO] DFAST_QC result json was written to GCF_003935895.2_ASM393589v2_genomic.fna/dqc_result.json
[2024-01-24 12:23:29,551] [INFO] DFAST_QC completed!
[2024-01-24 12:23:29,551] [INFO] Total running time: 0h1m45s