[2024-01-24 14:37:45,830] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:37:45,834] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:37:45,834] [INFO] DQC Reference Directory: /var/lib/cwl/stgf886c92f-40f8-44c2-b650-0d8d7f9830eb/dqc_reference
[2024-01-24 14:37:49,297] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:37:49,298] [INFO] Task started: Prodigal
[2024-01-24 14:37:49,298] [INFO] Running command: gunzip -c /var/lib/cwl/stga2d668d8-40d7-41ea-9ed9-c3559e665d82/GCF_002291445.1_ASM229144v1_genomic.fna.gz | prodigal -d GCF_002291445.1_ASM229144v1_genomic.fna/cds.fna -a GCF_002291445.1_ASM229144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:05,735] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:05,735] [INFO] Task started: HMMsearch
[2024-01-24 14:38:05,736] [INFO] Running command: hmmsearch --tblout GCF_002291445.1_ASM229144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf886c92f-40f8-44c2-b650-0d8d7f9830eb/dqc_reference/reference_markers.hmm GCF_002291445.1_ASM229144v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:06,062] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:06,063] [INFO] Found 6/6 markers.
[2024-01-24 14:38:06,111] [INFO] Query marker FASTA was written to GCF_002291445.1_ASM229144v1_genomic.fna/markers.fasta
[2024-01-24 14:38:06,111] [INFO] Task started: Blastn
[2024-01-24 14:38:06,111] [INFO] Running command: blastn -query GCF_002291445.1_ASM229144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf886c92f-40f8-44c2-b650-0d8d7f9830eb/dqc_reference/reference_markers.fasta -out GCF_002291445.1_ASM229144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:07,077] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:07,080] [INFO] Selected 13 target genomes.
[2024-01-24 14:38:07,081] [INFO] Target genome list was writen to GCF_002291445.1_ASM229144v1_genomic.fna/target_genomes.txt
[2024-01-24 14:38:07,112] [INFO] Task started: fastANI
[2024-01-24 14:38:07,113] [INFO] Running command: fastANI --query /var/lib/cwl/stga2d668d8-40d7-41ea-9ed9-c3559e665d82/GCF_002291445.1_ASM229144v1_genomic.fna.gz --refList GCF_002291445.1_ASM229144v1_genomic.fna/target_genomes.txt --output GCF_002291445.1_ASM229144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:38:22,086] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:22,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf886c92f-40f8-44c2-b650-0d8d7f9830eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:38:22,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf886c92f-40f8-44c2-b650-0d8d7f9830eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:38:22,104] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:38:22,105] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:38:22,105] [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
Brenneria goodwinii	strain=FRB141	GCA_002291445.1	1109412	1109412	type	True	100.0	1786	1786	95	conclusive
Brenneria goodwinii	strain=FRB141	GCA_003666235.1	1109412	1109412	type	True	99.9275	1665	1786	95	conclusive
Brenneria izadpanahii	strain=Iran 50	GCA_017569925.1	2722756	2722756	type	True	90.789	1438	1786	95	below_threshold
Brenneria alni	strain=NCPPB 3934	GCA_003666245.1	71656	71656	type	True	83.9224	917	1786	95	below_threshold
Brenneria nigrifluens	strain=ATCC 13028	GCA_005484965.1	55210	55210	type	True	83.8572	1068	1786	95	below_threshold
Brenneria nigrifluens	strain=LMG 2694	GCA_003115835.1	55210	55210	type	True	83.8323	1031	1786	95	below_threshold
Brenneria roseae subsp. americana	strain=LMG 27715	GCA_003115815.1	1508507	1509241	type	True	82.5653	921	1786	95	below_threshold
Brenneria roseae subsp. roseae	strain=LMG 27714	GCA_003115845.1	1508506	1509241	type	True	82.5342	935	1786	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	80.4503	731	1786	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	80.3387	697	1786	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.1252	463	1786	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.7507	451	1786	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.6874	439	1786	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:38:22,109] [INFO] DFAST Taxonomy check result was written to GCF_002291445.1_ASM229144v1_genomic.fna/tc_result.tsv
[2024-01-24 14:38:22,110] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:38:22,110] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:38:22,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf886c92f-40f8-44c2-b650-0d8d7f9830eb/dqc_reference/checkm_data
[2024-01-24 14:38:22,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:38:22,169] [INFO] Task started: CheckM
[2024-01-24 14:38:22,169] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002291445.1_ASM229144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002291445.1_ASM229144v1_genomic.fna/checkm_input GCF_002291445.1_ASM229144v1_genomic.fna/checkm_result
[2024-01-24 14:39:10,338] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:10,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:10,362] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:10,362] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:10,363] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002291445.1_ASM229144v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:10,363] [INFO] Task started: Blastn
[2024-01-24 14:39:10,364] [INFO] Running command: blastn -query GCF_002291445.1_ASM229144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf886c92f-40f8-44c2-b650-0d8d7f9830eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002291445.1_ASM229144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:11,811] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:11,817] [INFO] Selected 6 target genomes.
[2024-01-24 14:39:11,818] [INFO] Target genome list was writen to GCF_002291445.1_ASM229144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:11,824] [INFO] Task started: fastANI
[2024-01-24 14:39:11,825] [INFO] Running command: fastANI --query /var/lib/cwl/stga2d668d8-40d7-41ea-9ed9-c3559e665d82/GCF_002291445.1_ASM229144v1_genomic.fna.gz --refList GCF_002291445.1_ASM229144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002291445.1_ASM229144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:20,881] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:20,889] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:20,889] [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_002291445.1	s__Brenneria goodwinii	100.0	1786	1786	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.30	98.94	0.94	0.91	4	conclusive
GCF_017569925.1	s__Brenneria izadpanahii	90.7911	1439	1786	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003666245.1	s__Brenneria alni	83.9269	917	1786	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005484965.1	s__Brenneria nigrifluens	83.8537	1071	1786	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	98.35	95.07	0.92	0.76	4	-
GCF_013155275.1	s__Brenneria sp013155275	83.6425	1012	1786	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.39	99.39	0.93	0.93	2	-
GCF_003115845.1	s__Brenneria roseae	82.5516	933	1786	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	96.57	96.57	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:39:20,891] [INFO] GTDB search result was written to GCF_002291445.1_ASM229144v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:20,891] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:20,894] [INFO] DFAST_QC result json was written to GCF_002291445.1_ASM229144v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:20,895] [INFO] DFAST_QC completed!
[2024-01-24 14:39:20,895] [INFO] Total running time: 0h1m35s