[2024-01-24 14:38:49,867] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:49,869] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:49,869] [INFO] DQC Reference Directory: /var/lib/cwl/stg48834bb2-10ad-40b7-b4c7-b8515aaad617/dqc_reference
[2024-01-24 14:38:52,374] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:52,376] [INFO] Task started: Prodigal
[2024-01-24 14:38:52,376] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f9ea572-85bb-4770-b628-2193b2bf7067/GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna.gz | prodigal -d GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/cds.fna -a GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:06,072] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:06,073] [INFO] Task started: HMMsearch
[2024-01-24 14:39:06,073] [INFO] Running command: hmmsearch --tblout GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48834bb2-10ad-40b7-b4c7-b8515aaad617/dqc_reference/reference_markers.hmm GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:06,444] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:06,449] [INFO] Found 6/6 markers.
[2024-01-24 14:39:06,510] [INFO] Query marker FASTA was written to GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/markers.fasta
[2024-01-24 14:39:06,511] [INFO] Task started: Blastn
[2024-01-24 14:39:06,511] [INFO] Running command: blastn -query GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48834bb2-10ad-40b7-b4c7-b8515aaad617/dqc_reference/reference_markers.fasta -out GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:07,426] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:07,431] [INFO] Selected 16 target genomes.
[2024-01-24 14:39:07,431] [INFO] Target genome list was writen to GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:07,446] [INFO] Task started: fastANI
[2024-01-24 14:39:07,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f9ea572-85bb-4770-b628-2193b2bf7067/GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna.gz --refList GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/target_genomes.txt --output GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:22,179] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:22,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48834bb2-10ad-40b7-b4c7-b8515aaad617/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:22,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48834bb2-10ad-40b7-b4c7-b8515aaad617/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:22,190] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:39:22,190] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:22,190] [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
Obesumbacterium proteus	strain=ATCC 12841	GCA_001655035.1	82983	82983	type	True	100.0	1647	1656	95	conclusive
Obesumbacterium proteus	strain=DSM 2777	GCA_001586165.1	82983	82983	type	True	99.9824	1599	1656	95	conclusive
Hafnia alvei	strain=ATCC 13337	GCA_003668715.1	569	569	type	True	94.2564	1327	1656	95	below_threshold
Hafnia alvei	strain=ATCC 13337	GCA_000735375.1	569	569	type	True	94.2035	1299	1656	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	84.2769	1082	1656	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_001655005.1	546367	546367	type	True	84.171	1071	1656	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.598	344	1656	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.5707	359	1656	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	78.5665	364	1656	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	78.4778	360	1656	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.458	369	1656	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:22,191] [INFO] DFAST Taxonomy check result was written to GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:22,192] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:22,192] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:22,192] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48834bb2-10ad-40b7-b4c7-b8515aaad617/dqc_reference/checkm_data
[2024-01-24 14:39:22,193] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:22,243] [INFO] Task started: CheckM
[2024-01-24 14:39:22,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/checkm_input GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/checkm_result
[2024-01-24 14:40:05,786] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:05,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:05,808] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:05,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:05,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/markers.fasta)
[2024-01-24 14:40:05,809] [INFO] Task started: Blastn
[2024-01-24 14:40:05,810] [INFO] Running command: blastn -query GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48834bb2-10ad-40b7-b4c7-b8515aaad617/dqc_reference/reference_markers_gtdb.fasta -out GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:06,891] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:06,895] [INFO] Selected 19 target genomes.
[2024-01-24 14:40:06,896] [INFO] Target genome list was writen to GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:06,913] [INFO] Task started: fastANI
[2024-01-24 14:40:06,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f9ea572-85bb-4770-b628-2193b2bf7067/GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna.gz --refList GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/target_genomes_gtdb.txt --output GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:24,201] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:24,224] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:24,226] [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_001586165.1	s__Hafnia proteus	99.9824	1599	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	98.09	96.49	0.93	0.89	5	conclusive
GCF_000735375.1	s__Hafnia alvei	94.2035	1299	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	97.59	95.60	0.91	0.87	31	-
GCF_900095695.1	s__Hafnia alvei_B	92.8839	1327	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001655005.1	s__Hafnia paralvei	84.171	1071	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	98.49	95.65	0.88	0.84	34	-
GCF_014639435.1	s__Ewingella psychrotolerans	79.1208	288	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002291425.1	s__Gibbsiella quercinecans	78.7534	316	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gibbsiella	95.0	99.45	98.17	0.96	0.87	5	-
GCF_002951615.1	s__Rahnella sp002951615	78.6458	349	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834385.1	s__Rahnella sp002834385	78.6069	351	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363015.1	s__Enterobacillus tribolii	78.4382	442	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001976145.1	s__Chania oryzae	78.4112	370	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	98.90	98.79	0.94	0.94	3	-
GCF_014189855.1	s__Buttiauxella sp014189855	78.2633	345	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013337685.1	s__Citrobacter gillenii	78.2522	322	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.72	97.36	0.89	0.84	39	-
GCF_001152565.1	s__Yersinia pekkanenii	78.1881	309	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.90	99.90	0.98	0.98	2	-
GCF_001267535.1	s__Erwinia iniecta	78.0477	287	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.95	99.95	0.99	0.99	2	-
GCF_001922585.1	s__1-19 sp001922585	77.5987	199	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__1-19	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112475.1	s__Pragia fontium	77.5342	171	1656	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pragia	95.0	99.20	98.63	0.97	0.95	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:24,227] [INFO] GTDB search result was written to GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:24,228] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:24,233] [INFO] DFAST_QC result json was written to GCF_001655035.1_Opr12841_DRAFTv1_genomic.fna/dqc_result.json
[2024-01-24 14:40:24,233] [INFO] DFAST_QC completed!
[2024-01-24 14:40:24,233] [INFO] Total running time: 0h1m34s