[2024-01-24 13:32:18,008] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:18,010] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:18,011] [INFO] DQC Reference Directory: /var/lib/cwl/stg4160f0fe-50fc-4769-a09e-e92f7c974e49/dqc_reference
[2024-01-24 13:32:19,468] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:19,469] [INFO] Task started: Prodigal
[2024-01-24 13:32:19,469] [INFO] Running command: gunzip -c /var/lib/cwl/stg9268a998-d5b1-45c1-b056-690d365069e8/GCF_014218705.1_ASM1421870v1_genomic.fna.gz | prodigal -d GCF_014218705.1_ASM1421870v1_genomic.fna/cds.fna -a GCF_014218705.1_ASM1421870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:33,914] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:33,914] [INFO] Task started: HMMsearch
[2024-01-24 13:32:33,915] [INFO] Running command: hmmsearch --tblout GCF_014218705.1_ASM1421870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4160f0fe-50fc-4769-a09e-e92f7c974e49/dqc_reference/reference_markers.hmm GCF_014218705.1_ASM1421870v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:34,242] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:34,244] [INFO] Found 6/6 markers.
[2024-01-24 13:32:34,298] [INFO] Query marker FASTA was written to GCF_014218705.1_ASM1421870v1_genomic.fna/markers.fasta
[2024-01-24 13:32:34,299] [INFO] Task started: Blastn
[2024-01-24 13:32:34,299] [INFO] Running command: blastn -query GCF_014218705.1_ASM1421870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4160f0fe-50fc-4769-a09e-e92f7c974e49/dqc_reference/reference_markers.fasta -out GCF_014218705.1_ASM1421870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:35,212] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:35,216] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:35,216] [INFO] Target genome list was writen to GCF_014218705.1_ASM1421870v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:35,222] [INFO] Task started: fastANI
[2024-01-24 13:32:35,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg9268a998-d5b1-45c1-b056-690d365069e8/GCF_014218705.1_ASM1421870v1_genomic.fna.gz --refList GCF_014218705.1_ASM1421870v1_genomic.fna/target_genomes.txt --output GCF_014218705.1_ASM1421870v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:00,385] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:00,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4160f0fe-50fc-4769-a09e-e92f7c974e49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:00,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4160f0fe-50fc-4769-a09e-e92f7c974e49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:00,401] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:00,401] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:00,402] [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 sichuanensis	strain=090646	GCA_014218705.1	2725494	2725494	type	True	100.0	1780	1783	95	conclusive
Kluyvera ascorbata	strain=ATCC 33433	GCA_000735365.1	51288	51288	suspected-type	True	91.0849	1253	1783	95	below_threshold
Kluyvera georgiana	strain=ATCC 51603	GCA_001654985.1	73098	73098	type	True	87.4784	1251	1783	95	below_threshold
Kluyvera cryocrescens	strain=NBRC 102467	GCA_001571285.1	580	580	type	True	85.7582	1258	1783	95	below_threshold
Kluyvera intermedia	strain=NCTC12125	GCA_900635475.1	61648	61648	suspected-type	True	85.5137	1201	1783	95	below_threshold
Kluyvera intermedia	strain=NBRC 102594	GCA_001598315.1	61648	61648	suspected-type	True	85.4123	1171	1783	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	83.2153	1022	1783	95	below_threshold
Pseudocitrobacter vendiensis	strain=type strain: CPO20170097	GCA_943590815.1	2488306	2488306	type	True	83.0952	1009	1783	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	82.6135	911	1783	95	below_threshold
Enterobacter asburiae	strain=FDAARGOS_892	GCA_016027695.1	61645	61645	type	True	82.453	877	1783	95	below_threshold
Enterobacter asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	82.4265	881	1783	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	82.2453	935	1783	95	below_threshold
Klebsiella aerogenes	strain=KCTC 2190	GCA_000215745.1	548	548	type	True	81.9688	937	1783	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.9583	895	1783	95	below_threshold
Kosakonia oryzae	strain=Ola 51	GCA_001658025.2	497725	497725	type	True	80.949	821	1783	95	below_threshold
Kosakonia oryzae	strain=CGMCC 1.7012	GCA_900112145.1	497725	497725	type	True	80.9426	826	1783	95	below_threshold
Kosakonia arachidis	strain=Ah-143	GCA_900116535.1	551989	551989	type	True	80.4622	751	1783	95	below_threshold
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	79.1896	539	1783	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	78.7409	514	1783	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:00,403] [INFO] DFAST Taxonomy check result was written to GCF_014218705.1_ASM1421870v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:00,404] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:00,404] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:00,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4160f0fe-50fc-4769-a09e-e92f7c974e49/dqc_reference/checkm_data
[2024-01-24 13:33:00,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:00,458] [INFO] Task started: CheckM
[2024-01-24 13:33:00,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014218705.1_ASM1421870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014218705.1_ASM1421870v1_genomic.fna/checkm_input GCF_014218705.1_ASM1421870v1_genomic.fna/checkm_result
[2024-01-24 13:33:46,557] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:46,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:46,581] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:46,582] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:46,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014218705.1_ASM1421870v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:46,582] [INFO] Task started: Blastn
[2024-01-24 13:33:46,583] [INFO] Running command: blastn -query GCF_014218705.1_ASM1421870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4160f0fe-50fc-4769-a09e-e92f7c974e49/dqc_reference/reference_markers_gtdb.fasta -out GCF_014218705.1_ASM1421870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:47,856] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:47,860] [INFO] Selected 13 target genomes.
[2024-01-24 13:33:47,861] [INFO] Target genome list was writen to GCF_014218705.1_ASM1421870v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:47,883] [INFO] Task started: fastANI
[2024-01-24 13:33:47,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg9268a998-d5b1-45c1-b056-690d365069e8/GCF_014218705.1_ASM1421870v1_genomic.fna.gz --refList GCF_014218705.1_ASM1421870v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014218705.1_ASM1421870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:02,380] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:02,400] [INFO] Found 13 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:34:02,400] [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_014218705.1	s__Kluyvera sichuanensis	100.0	1780	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_009929615.1	s__Frisingicoccus sp009929615	96.263	64	1783	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.91	99.91	0.88	0.88	2	inconclusive
GCF_000735365.1	s__Kluyvera ascorbata	91.0744	1253	1783	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	90.9911	744	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001654985.1	s__Kluyvera georgiana	87.513	1247	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.06	98.06	0.84	0.84	2	-
GCF_014168815.1	s__Kluyvera ascorbata_B	87.2789	1283	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.36	99.08	0.90	0.88	9	-
GCA_002211745.1	s__Kluyvera georgiana_A	87.0092	1239	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.12	98.12	0.89	0.89	2	-
GCF_001571285.1	s__Kluyvera cryocrescens	85.7587	1259	1783	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	85.7157	1194	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900635475.1	s__Kluyvera intermedia	85.5099	1202	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.24	98.87	0.94	0.90	4	-
GCA_902363335.1	s__Kluyvera sp902363335	85.3901	1148	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006711645.1	s__Klebsiella electrica	83.0066	992	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.88	98.54	0.89	0.85	7	-
GCF_000280495.2	s__Kosakonia radicincitans	82.292	906	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	99.26	99.13	0.95	0.93	14	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:02,402] [INFO] GTDB search result was written to GCF_014218705.1_ASM1421870v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:02,403] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:02,407] [INFO] DFAST_QC result json was written to GCF_014218705.1_ASM1421870v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:02,407] [INFO] DFAST_QC completed!
[2024-01-24 13:34:02,408] [INFO] Total running time: 0h1m44s