[2024-01-24 13:49:19,455] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,457] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,457] [INFO] DQC Reference Directory: /var/lib/cwl/stg18b30a94-4feb-4ebc-a38f-0864b725560a/dqc_reference
[2024-01-24 13:49:20,770] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,771] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,771] [INFO] Running command: gunzip -c /var/lib/cwl/stg4db6462c-4ae9-4dc4-ba4d-4c2d08831701/GCF_004331415.1_ASM433141v1_genomic.fna.gz | prodigal -d GCF_004331415.1_ASM433141v1_genomic.fna/cds.fna -a GCF_004331415.1_ASM433141v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:36,011] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:36,012] [INFO] Task started: HMMsearch
[2024-01-24 13:49:36,012] [INFO] Running command: hmmsearch --tblout GCF_004331415.1_ASM433141v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18b30a94-4feb-4ebc-a38f-0864b725560a/dqc_reference/reference_markers.hmm GCF_004331415.1_ASM433141v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:36,338] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:36,339] [INFO] Found 6/6 markers.
[2024-01-24 13:49:36,398] [INFO] Query marker FASTA was written to GCF_004331415.1_ASM433141v1_genomic.fna/markers.fasta
[2024-01-24 13:49:36,399] [INFO] Task started: Blastn
[2024-01-24 13:49:36,399] [INFO] Running command: blastn -query GCF_004331415.1_ASM433141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18b30a94-4feb-4ebc-a38f-0864b725560a/dqc_reference/reference_markers.fasta -out GCF_004331415.1_ASM433141v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:37,352] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:37,355] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:37,355] [INFO] Target genome list was writen to GCF_004331415.1_ASM433141v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:37,359] [INFO] Task started: fastANI
[2024-01-24 13:49:37,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg4db6462c-4ae9-4dc4-ba4d-4c2d08831701/GCF_004331415.1_ASM433141v1_genomic.fna.gz --refList GCF_004331415.1_ASM433141v1_genomic.fna/target_genomes.txt --output GCF_004331415.1_ASM433141v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:51,855] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:51,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18b30a94-4feb-4ebc-a38f-0864b725560a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:51,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18b30a94-4feb-4ebc-a38f-0864b725560a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:51,866] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:51,866] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:51,867] [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 quasisacchari	strain=WCHEs120001	GCA_004331415.1	2529380	2529380	type	True	100.0	1675	1677	95	conclusive
Kosakonia sacchari	strain=CGMCC 1.12102	GCA_900100995.1	1158459	1158459	type	True	93.2546	1494	1677	95	below_threshold
Kosakonia sacchari	strain=SP1	GCA_000300455.4	1158459	1158459	type	True	93.2383	1499	1677	95	below_threshold
Kosakonia pseudosacchari	strain=JM-387	GCA_900184035.1	1646340	1646340	type	True	92.6853	1499	1677	95	below_threshold
Kosakonia oryzae	strain=Ola 51	GCA_001658025.2	497725	497725	type	True	84.7896	1305	1677	95	below_threshold
Kosakonia oryzendophytica	strain=REICA_082	GCA_900094925.1	1005665	1005665	type	True	84.1207	1209	1677	95	below_threshold
Kosakonia cowanii	strain=888-76	GCA_001975225.1	208223	208223	type	True	83.6293	1133	1677	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.32	850	1677	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.2848	836	1677	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.1988	832	1677	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.1924	846	1677	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.1648	875	1677	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:51,869] [INFO] DFAST Taxonomy check result was written to GCF_004331415.1_ASM433141v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:51,870] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:51,870] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:51,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18b30a94-4feb-4ebc-a38f-0864b725560a/dqc_reference/checkm_data
[2024-01-24 13:49:51,872] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:51,923] [INFO] Task started: CheckM
[2024-01-24 13:49:51,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004331415.1_ASM433141v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004331415.1_ASM433141v1_genomic.fna/checkm_input GCF_004331415.1_ASM433141v1_genomic.fna/checkm_result
[2024-01-24 13:50:39,191] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:39,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:39,208] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:39,209] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:39,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004331415.1_ASM433141v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:39,210] [INFO] Task started: Blastn
[2024-01-24 13:50:39,210] [INFO] Running command: blastn -query GCF_004331415.1_ASM433141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18b30a94-4feb-4ebc-a38f-0864b725560a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004331415.1_ASM433141v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:40,614] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:40,619] [INFO] Selected 7 target genomes.
[2024-01-24 13:50:40,619] [INFO] Target genome list was writen to GCF_004331415.1_ASM433141v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:40,626] [INFO] Task started: fastANI
[2024-01-24 13:50:40,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg4db6462c-4ae9-4dc4-ba4d-4c2d08831701/GCF_004331415.1_ASM433141v1_genomic.fna.gz --refList GCF_004331415.1_ASM433141v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004331415.1_ASM433141v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:49,374] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:49,380] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:49,381] [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_004331415.1	s__Kosakonia quasisacchari	100.0	1675	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000300455.3	s__Kosakonia sacchari	93.2383	1499	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	98.35	95.81	0.96	0.92	5	-
GCF_000410515.1	s__Kosakonia sp000410515	93.0182	1522	1677	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	92.683	1500	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	98.43	98.39	0.94	0.93	3	-
GCF_000814905.1	s__Kosakonia sp000814905	86.2104	1180	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000280495.2	s__Kosakonia radicincitans	84.8119	1308	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	99.26	99.13	0.95	0.93	14	-
GCF_001975225.1	s__Kosakonia cowanii	83.6314	1132	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	97.51	95.65	0.94	0.87	21	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:49,382] [INFO] GTDB search result was written to GCF_004331415.1_ASM433141v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:49,383] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:49,385] [INFO] DFAST_QC result json was written to GCF_004331415.1_ASM433141v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:49,386] [INFO] DFAST_QC completed!
[2024-01-24 13:50:49,386] [INFO] Total running time: 0h1m30s