[2024-01-24 12:05:26,626] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:26,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:26,628] [INFO] DQC Reference Directory: /var/lib/cwl/stgf096b904-c0d1-4841-9139-a48111452085/dqc_reference
[2024-01-24 12:05:30,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:30,678] [INFO] Task started: Prodigal
[2024-01-24 12:05:30,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg58027fce-1f26-4682-8a69-28fe4c8f05c9/GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/cds.fna -a GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:05:43,579] [INFO] Task succeeded: Prodigal
[2024-01-24 12:05:43,579] [INFO] Task started: HMMsearch
[2024-01-24 12:05:43,579] [INFO] Running command: hmmsearch --tblout GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf096b904-c0d1-4841-9139-a48111452085/dqc_reference/reference_markers.hmm GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:05:43,912] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:05:43,913] [INFO] Found 6/6 markers.
[2024-01-24 12:05:43,964] [INFO] Query marker FASTA was written to GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:05:43,964] [INFO] Task started: Blastn
[2024-01-24 12:05:43,964] [INFO] Running command: blastn -query GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf096b904-c0d1-4841-9139-a48111452085/dqc_reference/reference_markers.fasta -out GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:05:44,898] [INFO] Task succeeded: Blastn
[2024-01-24 12:05:44,902] [INFO] Selected 15 target genomes.
[2024-01-24 12:05:44,903] [INFO] Target genome list was writen to GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:05:44,908] [INFO] Task started: fastANI
[2024-01-24 12:05:44,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg58027fce-1f26-4682-8a69-28fe4c8f05c9/GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna.gz --refList GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:01,011] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:01,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf096b904-c0d1-4841-9139-a48111452085/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:01,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf096b904-c0d1-4841-9139-a48111452085/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:01,024] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:01,025] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:01,025] [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 oryziphila	strain=REICA_142	GCA_900094795.1	1005667	1005667	type	True	100.0	1532	1540	95	conclusive
Kosakonia arachidis	strain=Ah-143	GCA_900116535.1	551989	551989	type	True	93.3414	1316	1540	95	below_threshold
Kosakonia oryzae	strain=CGMCC 1.7012	GCA_900112145.1	497725	497725	type	True	93.0148	1296	1540	95	below_threshold
Kosakonia oryzae	strain=Ola 51	GCA_001658025.2	497725	497725	type	True	92.955	1303	1540	95	below_threshold
Kosakonia sacchari	strain=CGMCC 1.12102	GCA_900100995.1	1158459	1158459	type	True	84.33	1129	1540	95	below_threshold
Kosakonia sacchari	strain=SP1	GCA_000300455.4	1158459	1158459	type	True	84.283	1132	1540	95	below_threshold
Kosakonia oryzendophytica	strain=REICA_082	GCA_900094925.1	1005665	1005665	type	True	83.4222	1109	1540	95	below_threshold
Kosakonia cowanii	strain=888-76	GCA_001975225.1	208223	208223	type	True	82.8853	1025	1540	95	below_threshold
Enterobacter soli		GCA_900185935.1	885040	885040	type	True	81.0902	824	1540	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.0126	806	1540	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	81.001	843	1540	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	80.9861	818	1540	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.9106	811	1540	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	80.8812	817	1540	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	78.0663	118	1540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:01,028] [INFO] DFAST Taxonomy check result was written to GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:06:01,029] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:01,029] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:01,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf096b904-c0d1-4841-9139-a48111452085/dqc_reference/checkm_data
[2024-01-24 12:06:01,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:01,083] [INFO] Task started: CheckM
[2024-01-24 12:06:01,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/checkm_input GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:06:42,266] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:42,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:42,296] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:42,296] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:42,297] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:06:42,297] [INFO] Task started: Blastn
[2024-01-24 12:06:42,297] [INFO] Running command: blastn -query GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf096b904-c0d1-4841-9139-a48111452085/dqc_reference/reference_markers_gtdb.fasta -out GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:43,515] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:43,518] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:43,518] [INFO] Target genome list was writen to GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:43,530] [INFO] Task started: fastANI
[2024-01-24 12:06:43,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg58027fce-1f26-4682-8a69-28fe4c8f05c9/GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna.gz --refList GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:06:56,984] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:57,000] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:06:57,000] [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_900094795.1	s__Kosakonia oryziphila	100.0	1532	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018261615.1	s__Kosakonia sp018261615	94.472	1271	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900109485.1	s__Kosakonia sacchari_B	93.3548	1304	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7228	98.05	98.05	0.93	0.93	2	-
GCF_900116535.1	s__Kosakonia arachidis	93.3329	1317	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000280495.2	s__Kosakonia radicincitans	93.2034	1338	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	99.26	99.13	0.95	0.93	14	-
GCF_001658025.2	s__Kosakonia oryzae	92.955	1303	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	98.47	96.95	0.97	0.93	3	-
GCF_000410515.1	s__Kosakonia sp000410515	84.3828	1140	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	98.63	98.59	0.96	0.95	5	-
GCF_001975225.1	s__Kosakonia cowanii	82.8895	1024	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	97.51	95.65	0.94	0.87	21	-
GCF_001521715.1	s__Enterobacter asburiae	81.0864	817	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.42	96.92	0.89	0.84	32	-
GCF_013375935.1	s__Enterobacter cloacae_O	80.8539	800	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.68	98.59	0.94	0.92	6	-
GCF_001729765.1	s__Enterobacter kobei	80.7336	806	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.81	98.45	0.89	0.85	141	-
--------------------------------------------------------------------------------
[2024-01-24 12:06:57,003] [INFO] GTDB search result was written to GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:06:57,003] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:06:57,008] [INFO] DFAST_QC result json was written to GCF_900094795.1_IMG-taxon_2616644846_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:06:57,008] [INFO] DFAST_QC completed!
[2024-01-24 12:06:57,009] [INFO] Total running time: 0h1m30s