[2024-01-24 13:31:57,786] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,788] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,788] [INFO] DQC Reference Directory: /var/lib/cwl/stg876bd51e-5f22-4e38-9c43-689c20640f8b/dqc_reference
[2024-01-24 13:31:59,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:59,099] [INFO] Task started: Prodigal
[2024-01-24 13:31:59,100] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b1a7cb5-7541-4a92-84b2-288bbf288dfa/GCF_006364295.1_ASM636429v1_genomic.fna.gz | prodigal -d GCF_006364295.1_ASM636429v1_genomic.fna/cds.fna -a GCF_006364295.1_ASM636429v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:14,342] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:14,342] [INFO] Task started: HMMsearch
[2024-01-24 13:32:14,342] [INFO] Running command: hmmsearch --tblout GCF_006364295.1_ASM636429v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg876bd51e-5f22-4e38-9c43-689c20640f8b/dqc_reference/reference_markers.hmm GCF_006364295.1_ASM636429v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:14,608] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:14,609] [INFO] Found 6/6 markers.
[2024-01-24 13:32:14,657] [INFO] Query marker FASTA was written to GCF_006364295.1_ASM636429v1_genomic.fna/markers.fasta
[2024-01-24 13:32:14,657] [INFO] Task started: Blastn
[2024-01-24 13:32:14,657] [INFO] Running command: blastn -query GCF_006364295.1_ASM636429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg876bd51e-5f22-4e38-9c43-689c20640f8b/dqc_reference/reference_markers.fasta -out GCF_006364295.1_ASM636429v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:15,641] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:15,647] [INFO] Selected 10 target genomes.
[2024-01-24 13:32:15,648] [INFO] Target genome list was writen to GCF_006364295.1_ASM636429v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:15,651] [INFO] Task started: fastANI
[2024-01-24 13:32:15,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b1a7cb5-7541-4a92-84b2-288bbf288dfa/GCF_006364295.1_ASM636429v1_genomic.fna.gz --refList GCF_006364295.1_ASM636429v1_genomic.fna/target_genomes.txt --output GCF_006364295.1_ASM636429v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:28,041] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:28,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg876bd51e-5f22-4e38-9c43-689c20640f8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:28,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg876bd51e-5f22-4e38-9c43-689c20640f8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:28,053] [INFO] Found 10 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 13:32:28,053] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:28,054] [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
Klebsiella pneumoniae	strain=FDAARGOS_775	GCA_006364295.1	573	573	type	True	100.0	1854	1856	95	conclusive
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	99.9982	1848	1856	95	conclusive
Klebsiella pneumoniae	strain=ATCC 13883	GCA_000742135.1	573	573	type	True	99.9859	1842	1856	95	conclusive
Klebsiella pneumoniae subsp. pneumoniae	strain=DSM 30104	GCA_000281755.1	72407	573	type	True	99.9745	1820	1856	95	conclusive
Klebsiella pneumoniae	strain=DSM 30104	GCA_020115495.1	573	573	type	True	99.9478	1774	1856	95	conclusive
Klebsiella pneumoniae subsp. pneumoniae	strain=NBRC 14940	GCA_001590945.1	72407	573	type	True	99.9467	1753	1856	95	conclusive
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	82.0715	922	1856	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.9588	923	1856	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	81.9019	897	1856	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.7593	917	1856	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:28,058] [INFO] DFAST Taxonomy check result was written to GCF_006364295.1_ASM636429v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:28,059] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:28,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:28,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg876bd51e-5f22-4e38-9c43-689c20640f8b/dqc_reference/checkm_data
[2024-01-24 13:32:28,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:28,112] [INFO] Task started: CheckM
[2024-01-24 13:32:28,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006364295.1_ASM636429v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006364295.1_ASM636429v1_genomic.fna/checkm_input GCF_006364295.1_ASM636429v1_genomic.fna/checkm_result
[2024-01-24 13:33:16,173] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:16,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:16,195] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:16,196] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:16,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006364295.1_ASM636429v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:16,197] [INFO] Task started: Blastn
[2024-01-24 13:33:16,197] [INFO] Running command: blastn -query GCF_006364295.1_ASM636429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg876bd51e-5f22-4e38-9c43-689c20640f8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_006364295.1_ASM636429v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:17,693] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:17,696] [INFO] Selected 6 target genomes.
[2024-01-24 13:33:17,697] [INFO] Target genome list was writen to GCF_006364295.1_ASM636429v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:17,709] [INFO] Task started: fastANI
[2024-01-24 13:33:17,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b1a7cb5-7541-4a92-84b2-288bbf288dfa/GCF_006364295.1_ASM636429v1_genomic.fna.gz --refList GCF_006364295.1_ASM636429v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006364295.1_ASM636429v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:26,438] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:26,446] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:33:26,446] [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_000742135.1	s__Klebsiella pneumoniae	99.9859	1842	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	98.97	95.97	0.88	0.77	11294	inconclusive
GCF_900978845.1	s__Klebsiella africana	95.2615	1509	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	95.65	95.27	0.93	0.90	27	inconclusive
GCF_000828055.2	s__Klebsiella variicola	94.8063	1551	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.94	96.87	0.93	0.84	528	-
GCF_000751755.1	s__Klebsiella quasipneumoniae	93.704	1527	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.20	95.71	0.90	0.83	644	-
GCF_000215745.1	s__Klebsiella aerogenes	86.289	1219	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.40	95.78	0.92	0.85	341	-
GCA_002211745.1	s__Kluyvera georgiana_A	82.1857	934	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.12	98.12	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:26,448] [INFO] GTDB search result was written to GCF_006364295.1_ASM636429v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:26,448] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:26,451] [INFO] DFAST_QC result json was written to GCF_006364295.1_ASM636429v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:26,451] [INFO] DFAST_QC completed!
[2024-01-24 13:33:26,451] [INFO] Total running time: 0h1m29s