[2024-01-24 12:13:55,724] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:55,728] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:55,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg97ff193e-1a94-4cfe-9bba-46b8120a5cde/dqc_reference
[2024-01-24 12:13:57,518] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:57,519] [INFO] Task started: Prodigal
[2024-01-24 12:13:57,520] [INFO] Running command: gunzip -c /var/lib/cwl/stg1905ddfa-7e1c-4c0b-a203-8d36f4657bd8/GCF_006539725.1_ASM653972v1_genomic.fna.gz | prodigal -d GCF_006539725.1_ASM653972v1_genomic.fna/cds.fna -a GCF_006539725.1_ASM653972v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:12,074] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:12,075] [INFO] Task started: HMMsearch
[2024-01-24 12:14:12,075] [INFO] Running command: hmmsearch --tblout GCF_006539725.1_ASM653972v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97ff193e-1a94-4cfe-9bba-46b8120a5cde/dqc_reference/reference_markers.hmm GCF_006539725.1_ASM653972v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:12,488] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:12,489] [INFO] Found 6/6 markers.
[2024-01-24 12:14:12,537] [INFO] Query marker FASTA was written to GCF_006539725.1_ASM653972v1_genomic.fna/markers.fasta
[2024-01-24 12:14:12,538] [INFO] Task started: Blastn
[2024-01-24 12:14:12,538] [INFO] Running command: blastn -query GCF_006539725.1_ASM653972v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97ff193e-1a94-4cfe-9bba-46b8120a5cde/dqc_reference/reference_markers.fasta -out GCF_006539725.1_ASM653972v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:13,525] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:13,530] [INFO] Selected 20 target genomes.
[2024-01-24 12:14:13,530] [INFO] Target genome list was writen to GCF_006539725.1_ASM653972v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:13,545] [INFO] Task started: fastANI
[2024-01-24 12:14:13,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg1905ddfa-7e1c-4c0b-a203-8d36f4657bd8/GCF_006539725.1_ASM653972v1_genomic.fna.gz --refList GCF_006539725.1_ASM653972v1_genomic.fna/target_genomes.txt --output GCF_006539725.1_ASM653972v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:36,510] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:36,511] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97ff193e-1a94-4cfe-9bba-46b8120a5cde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:36,511] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97ff193e-1a94-4cfe-9bba-46b8120a5cde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:36,527] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:36,527] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:36,527] [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
Raoultella terrigena	strain=NBRC 14941	GCA_006539725.1	577	577	type	True	100.0	1814	1815	95	conclusive
Raoultella ornithinolytica	strain=NBRC 105727	GCA_001598295.1	54291	54291	type	True	86.0476	1403	1815	95	below_threshold
Raoultella electrica	strain=DSM 102253	GCA_006711645.1	1259973	1259973	type	True	85.9474	1325	1815	95	below_threshold
Raoultella planticola	strain=ATCC 33531	GCA_000735435.1	575	575	type	True	85.9247	1400	1815	95	below_threshold
Klebsiella michiganensis	strain=DSM 25444	GCA_002925905.1	1134687	1134687	type	True	85.0292	1330	1815	95	below_threshold
Klebsiella grimontii	strain=06D021	GCA_900200035.1	2058152	2058152	type	True	85.0159	1329	1815	95	below_threshold
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	84.6068	1296	1815	95	below_threshold
Klebsiella oxytoca	strain=NCTC13727	GCA_900636985.1	571	571	type	True	84.5695	1298	1815	95	below_threshold
Klebsiella oxytoca	strain=DSM 5175	GCA_020115535.1	571	571	type	True	84.55	1290	1815	95	below_threshold
Klebsiella pneumoniae subsp. pneumoniae	strain=NBRC 14940	GCA_001590945.1	72407	573	type	True	84.125	1225	1815	95	below_threshold
Klebsiella pneumoniae subsp. pneumoniae	strain=DSM 30104	GCA_000281755.1	72407	573	type	True	84.0974	1236	1815	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	84.0835	1255	1815	95	below_threshold
Klebsiella pneumoniae	strain=ATCC 13883	GCA_000742135.1	573	573	type	True	84.064	1245	1815	95	below_threshold
Klebsiella pneumoniae	strain=FDAARGOS_775	GCA_006364295.1	573	573	type	True	84.0432	1251	1815	95	below_threshold
Klebsiella africana	strain=SB5857	GCA_900978845.1	2489010	2489010	type	True	83.993	1225	1815	95	below_threshold
Klebsiella africana	strain=200023	GCA_020526085.1	2489010	2489010	type	True	83.9083	1230	1815	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	82.0306	961	1815	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.9197	924	1815	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	81.6206	885	1815	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.551	924	1815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:36,529] [INFO] DFAST Taxonomy check result was written to GCF_006539725.1_ASM653972v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:36,532] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:36,532] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:36,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97ff193e-1a94-4cfe-9bba-46b8120a5cde/dqc_reference/checkm_data
[2024-01-24 12:14:36,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:36,593] [INFO] Task started: CheckM
[2024-01-24 12:14:36,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539725.1_ASM653972v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539725.1_ASM653972v1_genomic.fna/checkm_input GCF_006539725.1_ASM653972v1_genomic.fna/checkm_result
[2024-01-24 12:15:19,445] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:19,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:19,488] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:19,488] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:19,489] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539725.1_ASM653972v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:19,489] [INFO] Task started: Blastn
[2024-01-24 12:15:19,490] [INFO] Running command: blastn -query GCF_006539725.1_ASM653972v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97ff193e-1a94-4cfe-9bba-46b8120a5cde/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539725.1_ASM653972v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:21,018] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:21,023] [INFO] Selected 12 target genomes.
[2024-01-24 12:15:21,024] [INFO] Target genome list was writen to GCF_006539725.1_ASM653972v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:21,049] [INFO] Task started: fastANI
[2024-01-24 12:15:21,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg1905ddfa-7e1c-4c0b-a203-8d36f4657bd8/GCF_006539725.1_ASM653972v1_genomic.fna.gz --refList GCF_006539725.1_ASM653972v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539725.1_ASM653972v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:35,714] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:35,728] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:35,728] [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_006539725.1	s__Klebsiella terrigena	100.0	1814	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.25	96.63	0.88	0.85	68	conclusive
GCF_002270295.1	s__Klebsiella sp002270295	94.133	1568	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004342285.1	s__Klebsiella sp004342285	86.5703	1365	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598295.1	s__Klebsiella ornithinolytica	86.0393	1404	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.7194	99.42	99.16	0.93	0.81	95	-
GCF_006711645.1	s__Klebsiella electrica	85.9527	1324	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.88	98.54	0.89	0.85	7	-
GCF_000735435.1	s__Klebsiella planticola	85.9247	1400	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.7194	99.21	98.49	0.93	0.89	44	-
GCF_014298075.1	s__Klebsiella sp003752615	85.7438	1358	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.02	98.38	0.93	0.91	5	-
GCF_002925905.1	s__Klebsiella michiganensis	85.037	1329	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.53	97.41	0.90	0.83	291	-
GCA_900759445.1	s__Klebsiella sp900759445	84.9076	715	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598695.1	s__Klebsiella oxytoca	84.5854	1299	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.31	98.97	0.94	0.89	181	-
GCF_000742135.1	s__Klebsiella pneumoniae	84.0803	1242	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	98.97	95.97	0.88	0.77	11294	-
GCF_900021175.1	s__Enterobacter_A timonensis	81.5762	890	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:35,729] [INFO] GTDB search result was written to GCF_006539725.1_ASM653972v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:35,730] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:35,734] [INFO] DFAST_QC result json was written to GCF_006539725.1_ASM653972v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:35,734] [INFO] DFAST_QC completed!
[2024-01-24 12:15:35,735] [INFO] Total running time: 0h1m40s