[2024-01-24 11:43:51,876] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:51,878] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:51,878] [INFO] DQC Reference Directory: /var/lib/cwl/stg612779cc-8f36-4fac-b8a5-218e5876631d/dqc_reference
[2024-01-24 11:43:53,104] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:53,105] [INFO] Task started: Prodigal
[2024-01-24 11:43:53,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg70c1a1dc-877b-4813-821f-850fc6560c94/GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/cds.fna -a GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:06,723] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:06,724] [INFO] Task started: HMMsearch
[2024-01-24 11:44:06,724] [INFO] Running command: hmmsearch --tblout GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg612779cc-8f36-4fac-b8a5-218e5876631d/dqc_reference/reference_markers.hmm GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:06,973] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:06,974] [INFO] Found 6/6 markers.
[2024-01-24 11:44:07,013] [INFO] Query marker FASTA was written to GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:44:07,013] [INFO] Task started: Blastn
[2024-01-24 11:44:07,013] [INFO] Running command: blastn -query GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg612779cc-8f36-4fac-b8a5-218e5876631d/dqc_reference/reference_markers.fasta -out GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:07,960] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:07,963] [INFO] Selected 18 target genomes.
[2024-01-24 11:44:07,964] [INFO] Target genome list was writen to GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:44:07,970] [INFO] Task started: fastANI
[2024-01-24 11:44:07,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg70c1a1dc-877b-4813-821f-850fc6560c94/GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna.gz --refList GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:25,873] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:25,873] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg612779cc-8f36-4fac-b8a5-218e5876631d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:25,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg612779cc-8f36-4fac-b8a5-218e5876631d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:25,888] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:25,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:25,888] [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
Kosakonia oryzendophytica	strain=REICA_082	GCA_900094925.1	1005665	1005665	type	True	100.0	1594	1597	95	conclusive
Kosakonia pseudosacchari	strain=JM-387	GCA_900184035.1	1646340	1646340	type	True	84.365	1210	1597	95	below_threshold
Kosakonia sacchari	strain=SP1	GCA_000300455.4	1158459	1158459	type	True	84.3538	1218	1597	95	below_threshold
Kosakonia sacchari	strain=CGMCC 1.12102	GCA_900100995.1	1158459	1158459	type	True	84.3515	1197	1597	95	below_threshold
Kosakonia oryzae	strain=CGMCC 1.7012	GCA_900112145.1	497725	497725	type	True	84.1763	1240	1597	95	below_threshold
Kosakonia oryzae	strain=Ola 51	GCA_001658025.2	497725	497725	type	True	84.1718	1233	1597	95	below_threshold
Kosakonia quasisacchari	strain=WCHEs120001	GCA_004331415.1	2529380	2529380	type	True	83.9976	1223	1597	95	below_threshold
Kosakonia oryziphila	strain=REICA_142	GCA_900094795.1	1005667	1005667	type	True	83.5227	1099	1597	95	below_threshold
Kosakonia cowanii	strain=888-76	GCA_001975225.1	208223	208223	type	True	82.7721	1068	1597	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.1071	815	1597	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.0656	821	1597	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	80.9323	849	1597	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.9088	843	1597	95	below_threshold
Klebsiella africana	strain=SB5857	GCA_900978845.1	2489010	2489010	type	True	80.5963	754	1597	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	80.5652	814	1597	95	below_threshold
Klebsiella africana	strain=200023	GCA_020526085.1	2489010	2489010	type	True	80.5347	774	1597	95	below_threshold
Klebsiella pneumoniae	strain=ATCC 13883	GCA_000742135.1	573	573	type	True	80.5066	777	1597	95	below_threshold
Klebsiella pneumoniae subsp. pneumoniae	strain=NBRC 14940	GCA_001590945.1	72407	573	type	True	80.4772	747	1597	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:25,890] [INFO] DFAST Taxonomy check result was written to GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:44:25,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:25,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:25,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg612779cc-8f36-4fac-b8a5-218e5876631d/dqc_reference/checkm_data
[2024-01-24 11:44:25,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:25,936] [INFO] Task started: CheckM
[2024-01-24 11:44:25,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/checkm_input GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:45:07,353] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:07,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:07,373] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:07,373] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:07,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:45:07,374] [INFO] Task started: Blastn
[2024-01-24 11:45:07,374] [INFO] Running command: blastn -query GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg612779cc-8f36-4fac-b8a5-218e5876631d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:08,808] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:08,811] [INFO] Selected 16 target genomes.
[2024-01-24 11:45:08,812] [INFO] Target genome list was writen to GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:08,822] [INFO] Task started: fastANI
[2024-01-24 11:45:08,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg70c1a1dc-877b-4813-821f-850fc6560c94/GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna.gz --refList GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:27,219] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:27,231] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:27,232] [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_900094925.1	s__Kosakonia oryzendophytica	100.0	1594	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	99.59	99.37	0.98	0.97	4	conclusive
GCA_002886105.1	s__Kosakonia sp002886105	93.6811	1483	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000410515.1	s__Kosakonia sp000410515	84.3936	1257	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	98.63	98.59	0.96	0.95	5	-
GCF_900184035.1	s__Kosakonia pseudosacchari	84.3624	1211	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	98.43	98.39	0.94	0.93	3	-
GCF_000300455.3	s__Kosakonia sacchari	84.3456	1219	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	98.35	95.81	0.96	0.92	5	-
GCA_900109485.1	s__Kosakonia sacchari_B	84.2148	1223	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7228	98.05	98.05	0.93	0.93	2	-
GCF_001658025.2	s__Kosakonia oryzae	84.1598	1235	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	98.47	96.95	0.97	0.93	3	-
GCF_000280495.2	s__Kosakonia radicincitans	84.1495	1252	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	99.26	99.13	0.95	0.93	14	-
GCF_004331415.1	s__Kosakonia quasisacchari	83.9975	1223	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094795.1	s__Kosakonia oryziphila	83.5401	1098	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814905.1	s__Kosakonia sp000814905	83.4395	1053	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975225.1	s__Kosakonia cowanii	82.7786	1066	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	97.51	95.65	0.94	0.87	21	-
GCF_014490785.1	s__Kosakonia sp014490785	82.6378	1061	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000321045.1	s__Phytobacter massiliensis	81.53	919	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019218745.1	s__Enterobacter_D sp019218745	81.2821	837	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902985.1	s__Leclercia sp002902985	80.945	841	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.13	96.37	0.93	0.86	16	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:27,251] [INFO] GTDB search result was written to GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:27,251] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:27,255] [INFO] DFAST_QC result json was written to GCF_900094925.1_IMG-taxon_2617270737_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:45:27,255] [INFO] DFAST_QC completed!
[2024-01-24 11:45:27,255] [INFO] Total running time: 0h1m35s