[2024-01-24 14:22:31,938] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:31,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:31,940] [INFO] DQC Reference Directory: /var/lib/cwl/stgd705aff9-b8e0-4d84-b8c2-7de2427307d2/dqc_reference
[2024-01-24 14:22:36,011] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:36,012] [INFO] Task started: Prodigal
[2024-01-24 14:22:36,013] [INFO] Running command: gunzip -c /var/lib/cwl/stg301975b5-ca8c-4386-80ad-b8c275c5464e/GCF_001658025.2_ASM165802v2_genomic.fna.gz | prodigal -d GCF_001658025.2_ASM165802v2_genomic.fna/cds.fna -a GCF_001658025.2_ASM165802v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:51,748] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:51,749] [INFO] Task started: HMMsearch
[2024-01-24 14:22:51,749] [INFO] Running command: hmmsearch --tblout GCF_001658025.2_ASM165802v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd705aff9-b8e0-4d84-b8c2-7de2427307d2/dqc_reference/reference_markers.hmm GCF_001658025.2_ASM165802v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:52,236] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:52,238] [INFO] Found 6/6 markers.
[2024-01-24 14:22:52,285] [INFO] Query marker FASTA was written to GCF_001658025.2_ASM165802v2_genomic.fna/markers.fasta
[2024-01-24 14:22:52,285] [INFO] Task started: Blastn
[2024-01-24 14:22:52,286] [INFO] Running command: blastn -query GCF_001658025.2_ASM165802v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd705aff9-b8e0-4d84-b8c2-7de2427307d2/dqc_reference/reference_markers.fasta -out GCF_001658025.2_ASM165802v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:59,582] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:59,589] [INFO] Selected 13 target genomes.
[2024-01-24 14:22:59,590] [INFO] Target genome list was writen to GCF_001658025.2_ASM165802v2_genomic.fna/target_genomes.txt
[2024-01-24 14:22:59,607] [INFO] Task started: fastANI
[2024-01-24 14:22:59,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg301975b5-ca8c-4386-80ad-b8c275c5464e/GCF_001658025.2_ASM165802v2_genomic.fna.gz --refList GCF_001658025.2_ASM165802v2_genomic.fna/target_genomes.txt --output GCF_001658025.2_ASM165802v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:18,302] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:18,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd705aff9-b8e0-4d84-b8c2-7de2427307d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:18,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd705aff9-b8e0-4d84-b8c2-7de2427307d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:18,316] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:23:18,316] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:18,316] [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 oryzae	strain=Ola 51	GCA_001658025.2	497725	497725	type	True	100.0	1805	1805	95	conclusive
Kosakonia oryzae	strain=CGMCC 1.7012	GCA_900112145.1	497725	497725	type	True	99.9912	1785	1805	95	conclusive
Kosakonia oryziphila	strain=REICA_142	GCA_900094795.1	1005667	1005667	type	True	93.0139	1296	1805	95	below_threshold
Kosakonia arachidis	strain=Ah-143	GCA_900116535.1	551989	551989	type	True	92.5916	1445	1805	95	below_threshold
Kosakonia sacchari	strain=SP1	GCA_000300455.4	1158459	1158459	type	True	85.1977	1276	1805	95	below_threshold
Kosakonia sacchari	strain=CGMCC 1.12102	GCA_900100995.1	1158459	1158459	type	True	85.0284	1258	1805	95	below_threshold
Kosakonia oryzendophytica	strain=REICA_082	GCA_900094925.1	1005665	1005665	type	True	84.1192	1244	1805	95	below_threshold
Kosakonia cowanii	strain=888-76	GCA_001975225.1	208223	208223	type	True	83.8096	1129	1805	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.4697	920	1805	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.45	912	1805	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.3462	905	1805	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	81.2147	906	1805	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.1743	917	1805	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:18,326] [INFO] DFAST Taxonomy check result was written to GCF_001658025.2_ASM165802v2_genomic.fna/tc_result.tsv
[2024-01-24 14:23:18,327] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:18,327] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:18,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd705aff9-b8e0-4d84-b8c2-7de2427307d2/dqc_reference/checkm_data
[2024-01-24 14:23:18,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:18,420] [INFO] Task started: CheckM
[2024-01-24 14:23:18,420] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001658025.2_ASM165802v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001658025.2_ASM165802v2_genomic.fna/checkm_input GCF_001658025.2_ASM165802v2_genomic.fna/checkm_result
[2024-01-24 14:24:15,769] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:15,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:15,791] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:15,791] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:15,792] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001658025.2_ASM165802v2_genomic.fna/markers.fasta)
[2024-01-24 14:24:15,792] [INFO] Task started: Blastn
[2024-01-24 14:24:15,793] [INFO] Running command: blastn -query GCF_001658025.2_ASM165802v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd705aff9-b8e0-4d84-b8c2-7de2427307d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_001658025.2_ASM165802v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:18,204] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:18,207] [INFO] Selected 7 target genomes.
[2024-01-24 14:24:18,207] [INFO] Target genome list was writen to GCF_001658025.2_ASM165802v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:18,214] [INFO] Task started: fastANI
[2024-01-24 14:24:18,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg301975b5-ca8c-4386-80ad-b8c275c5464e/GCF_001658025.2_ASM165802v2_genomic.fna.gz --refList GCF_001658025.2_ASM165802v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001658025.2_ASM165802v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:28,612] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:28,689] [INFO] Found 7 fastANI hits (3 hits with ANI > circumscription radius)
[2024-01-24 14:24:28,689] [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_001658025.2	s__Kosakonia oryzae	100.0	1805	1805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	98.47	96.95	0.97	0.93	3	inconclusive
GCA_900109485.1	s__Kosakonia sacchari_B	95.7325	1635	1805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7228	98.05	98.05	0.93	0.93	2	inconclusive
GCF_000280495.2	s__Kosakonia radicincitans	95.7301	1697	1805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	99.26	99.13	0.95	0.93	14	inconclusive
GCA_018261615.1	s__Kosakonia sp018261615	93.3891	1300	1805	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	93.0139	1296	1805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116535.1	s__Kosakonia arachidis	92.6041	1444	1805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000300455.3	s__Kosakonia sacchari	85.2009	1275	1805	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	98.35	95.81	0.96	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:28,691] [INFO] GTDB search result was written to GCF_001658025.2_ASM165802v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:28,691] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:28,694] [INFO] DFAST_QC result json was written to GCF_001658025.2_ASM165802v2_genomic.fna/dqc_result.json
[2024-01-24 14:24:28,694] [INFO] DFAST_QC completed!
[2024-01-24 14:24:28,694] [INFO] Total running time: 0h1m57s