[2024-01-24 13:41:10,495] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg302f729d-9f94-4efb-af26-5d38e475caeb/dqc_reference
[2024-01-24 13:41:11,868] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:11,869] [INFO] Task started: Prodigal
[2024-01-24 13:41:11,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b048306-c529-4a73-996a-89bf6e6dfd3e/GCF_000215745.1_ASM21574v1_genomic.fna.gz | prodigal -d GCF_000215745.1_ASM21574v1_genomic.fna/cds.fna -a GCF_000215745.1_ASM21574v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:25,912] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:25,912] [INFO] Task started: HMMsearch
[2024-01-24 13:41:25,912] [INFO] Running command: hmmsearch --tblout GCF_000215745.1_ASM21574v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg302f729d-9f94-4efb-af26-5d38e475caeb/dqc_reference/reference_markers.hmm GCF_000215745.1_ASM21574v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:26,234] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:26,235] [INFO] Found 6/6 markers.
[2024-01-24 13:41:26,281] [INFO] Query marker FASTA was written to GCF_000215745.1_ASM21574v1_genomic.fna/markers.fasta
[2024-01-24 13:41:26,281] [INFO] Task started: Blastn
[2024-01-24 13:41:26,281] [INFO] Running command: blastn -query GCF_000215745.1_ASM21574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg302f729d-9f94-4efb-af26-5d38e475caeb/dqc_reference/reference_markers.fasta -out GCF_000215745.1_ASM21574v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:27,307] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:27,310] [INFO] Selected 18 target genomes.
[2024-01-24 13:41:27,311] [INFO] Target genome list was writen to GCF_000215745.1_ASM21574v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:27,317] [INFO] Task started: fastANI
[2024-01-24 13:41:27,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b048306-c529-4a73-996a-89bf6e6dfd3e/GCF_000215745.1_ASM21574v1_genomic.fna.gz --refList GCF_000215745.1_ASM21574v1_genomic.fna/target_genomes.txt --output GCF_000215745.1_ASM21574v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:50,980] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:50,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg302f729d-9f94-4efb-af26-5d38e475caeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:50,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg302f729d-9f94-4efb-af26-5d38e475caeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:50,995] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:50,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:50,996] [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 aerogenes	strain=KCTC 2190	GCA_000215745.1	548	548	type	True	100.0	1759	1760	95	conclusive
Klebsiella aerogenes	strain=FDAARGOS 1442	GCA_019048125.1	548	548	type	True	99.9958	1753	1760	95	conclusive
Klebsiella variicola	strain=DSM 15968	GCA_000828055.2	244366	244366	type	True	86.4176	1228	1760	95	below_threshold
Klebsiella variicola	strain=F2R9	GCA_017638945.1	244366	244366	type	True	86.335	1255	1760	95	below_threshold
Klebsiella variicola	strain=type strain: F2R9	GCA_900978195.1	244366	244366	type	True	86.2387	1221	1760	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	86.1343	1220	1760	95	below_threshold
Klebsiella pneumoniae	strain=ATCC 13883	GCA_000742135.1	573	573	type	True	86.1108	1217	1760	95	below_threshold
Klebsiella pneumoniae subsp. pneumoniae	strain=NBRC 14940	GCA_001590945.1	72407	573	type	True	86.0126	1180	1760	95	below_threshold
Klebsiella pneumoniae subsp. pneumoniae	strain=ATCC 13883	GCA_000788015.1	72407	573	type	True	85.9851	1232	1760	95	below_threshold
Klebsiella michiganensis	strain=DSM 25444	GCA_002925905.1	1134687	1134687	type	True	84.2437	1229	1760	95	below_threshold
Klebsiella grimontii	strain=06D021	GCA_900200035.1	2058152	2058152	type	True	84.1612	1203	1760	95	below_threshold
Klebsiella pasteurii		GCA_902158725.1	2587529	2587529	type	True	84.1468	1210	1760	95	below_threshold
Klebsiella michiganensis	strain=CCUG 66515	GCA_009173485.1	1134687	1134687	type	True	84.1252	1226	1760	95	below_threshold
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	84.0599	1199	1760	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.791	880	1760	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.7436	905	1760	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	81.6654	881	1760	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.5838	894	1760	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:50,998] [INFO] DFAST Taxonomy check result was written to GCF_000215745.1_ASM21574v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:50,999] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:50,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:50,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg302f729d-9f94-4efb-af26-5d38e475caeb/dqc_reference/checkm_data
[2024-01-24 13:41:51,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:51,053] [INFO] Task started: CheckM
[2024-01-24 13:41:51,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000215745.1_ASM21574v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000215745.1_ASM21574v1_genomic.fna/checkm_input GCF_000215745.1_ASM21574v1_genomic.fna/checkm_result
[2024-01-24 13:42:34,194] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:34,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:34,222] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:34,222] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:34,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000215745.1_ASM21574v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:34,223] [INFO] Task started: Blastn
[2024-01-24 13:42:34,223] [INFO] Running command: blastn -query GCF_000215745.1_ASM21574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg302f729d-9f94-4efb-af26-5d38e475caeb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000215745.1_ASM21574v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:35,828] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:35,831] [INFO] Selected 14 target genomes.
[2024-01-24 13:42:35,831] [INFO] Target genome list was writen to GCF_000215745.1_ASM21574v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:35,854] [INFO] Task started: fastANI
[2024-01-24 13:42:35,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b048306-c529-4a73-996a-89bf6e6dfd3e/GCF_000215745.1_ASM21574v1_genomic.fna.gz --refList GCF_000215745.1_ASM21574v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000215745.1_ASM21574v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:53,549] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:53,569] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:53,570] [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_000215745.1	s__Klebsiella aerogenes	100.0	1760	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.40	95.78	0.92	0.85	341	conclusive
GCF_000828055.2	s__Klebsiella variicola	86.4172	1226	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.94	96.87	0.93	0.84	528	-
GCF_000742135.1	s__Klebsiella pneumoniae	86.1069	1218	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	98.97	95.97	0.88	0.77	11294	-
GCF_900978845.1	s__Klebsiella africana	85.9749	1210	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	95.65	95.27	0.93	0.90	27	-
GCF_000751755.1	s__Klebsiella quasipneumoniae	85.7787	1213	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.20	95.71	0.90	0.83	644	-
GCF_002925905.1	s__Klebsiella michiganensis	84.244	1227	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.53	97.41	0.90	0.83	291	-
GCF_900200035.1	s__Klebsiella grimontii	84.1809	1200	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.56	95.68	0.89	0.83	175	-
GCF_001598695.1	s__Klebsiella oxytoca	84.0641	1199	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.31	98.97	0.94	0.89	181	-
GCF_009707385.1	s__Klebsiella oxytoca_C	83.9849	1170	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014298075.1	s__Klebsiella sp003752615	83.8872	1225	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.02	98.38	0.93	0.91	5	-
GCF_902158555.1	s__Klebsiella spallanzanii	83.7877	1144	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.75	98.01	0.91	0.88	4	-
GCF_000735435.1	s__Klebsiella planticola	83.7641	1185	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.7194	99.21	98.49	0.93	0.89	44	-
GCF_003261575.2	s__Klebsiella huaxiensis	83.6979	1149	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	96.95	95.21	0.89	0.84	9	-
GCA_900759445.1	s__Klebsiella sp900759445	82.9592	672	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:53,572] [INFO] GTDB search result was written to GCF_000215745.1_ASM21574v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:53,572] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:53,577] [INFO] DFAST_QC result json was written to GCF_000215745.1_ASM21574v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:53,577] [INFO] DFAST_QC completed!
[2024-01-24 13:42:53,577] [INFO] Total running time: 0h1m43s