[2024-01-25 20:08:05,751] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:08:05,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:08:05,753] [INFO] DQC Reference Directory: /var/lib/cwl/stga67c90e0-e35e-4a22-91dc-824c5a5b82f1/dqc_reference
[2024-01-25 20:08:06,892] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:08:06,893] [INFO] Task started: Prodigal
[2024-01-25 20:08:06,893] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f4a9a7f-89fd-4f92-bff1-7634b65c8944/GCF_000757425.2_Tmorbiroseiassem5_genomic.fna.gz | prodigal -d GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/cds.fna -a GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:08:16,593] [INFO] Task succeeded: Prodigal
[2024-01-25 20:08:16,593] [INFO] Task started: HMMsearch
[2024-01-25 20:08:16,593] [INFO] Running command: hmmsearch --tblout GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga67c90e0-e35e-4a22-91dc-824c5a5b82f1/dqc_reference/reference_markers.hmm GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:08:16,857] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:08:16,858] [INFO] Found 6/6 markers.
[2024-01-25 20:08:16,896] [INFO] Query marker FASTA was written to GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/markers.fasta
[2024-01-25 20:08:16,896] [INFO] Task started: Blastn
[2024-01-25 20:08:16,896] [INFO] Running command: blastn -query GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/markers.fasta -db /var/lib/cwl/stga67c90e0-e35e-4a22-91dc-824c5a5b82f1/dqc_reference/reference_markers.fasta -out GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:17,672] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:17,679] [INFO] Selected 15 target genomes.
[2024-01-25 20:08:17,679] [INFO] Target genome list was writen to GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/target_genomes.txt
[2024-01-25 20:08:17,689] [INFO] Task started: fastANI
[2024-01-25 20:08:17,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f4a9a7f-89fd-4f92-bff1-7634b65c8944/GCF_000757425.2_Tmorbiroseiassem5_genomic.fna.gz --refList GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/target_genomes.txt --output GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:08:29,526] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:29,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga67c90e0-e35e-4a22-91dc-824c5a5b82f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:08:29,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga67c90e0-e35e-4a22-91dc-824c5a5b82f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:08:29,537] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:08:29,537] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:08:29,537] [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
Tatumella morbirosei	strain=LMG 23360	GCA_000757425.2	642227	642227	type	True	100.0	1468	1468	95	conclusive
Tatumella citrea	strain=DSM 13699	GCA_002163585.1	53336	53336	type	True	87.4862	1228	1468	95	below_threshold
Tatumella ptyseos	strain=NCTC11468	GCA_900478715.1	82987	82987	type	True	80.5618	554	1468	95	below_threshold
Tatumella ptyseos	strain=ATCC 33301	GCA_000439895.1	82987	82987	type	True	80.2692	532	1468	95	below_threshold
Tatumella ptyseos	strain=ATCC 33301	GCA_000735525.1	82987	82987	type	True	80.1991	535	1468	95	below_threshold
Tatumella saanichensis	strain=NML 06-3099	GCA_000439375.1	480813	480813	type	True	79.8213	455	1468	95	below_threshold
[Pantoea] beijingensis	strain=JZB2120001	GCA_022647505.1	1324864	1324864	type	True	79.1777	232	1468	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	78.5883	271	1468	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	78.5349	287	1468	95	below_threshold
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	78.4576	283	1468	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	78.3882	284	1468	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	78.3607	220	1468	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	78.2615	232	1468	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	77.7748	219	1468	95	below_threshold
Rahnella contaminans	strain=Lac-M11	GCA_011065485.1	2703882	2703882	type	True	77.6358	184	1468	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:08:29,538] [INFO] DFAST Taxonomy check result was written to GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/tc_result.tsv
[2024-01-25 20:08:29,539] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:08:29,539] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:08:29,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga67c90e0-e35e-4a22-91dc-824c5a5b82f1/dqc_reference/checkm_data
[2024-01-25 20:08:29,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:08:29,584] [INFO] Task started: CheckM
[2024-01-25 20:08:29,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/checkm_input GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/checkm_result
[2024-01-25 20:09:01,072] [INFO] Task succeeded: CheckM
[2024-01-25 20:09:01,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:09:01,119] [INFO] ===== Completeness check finished =====
[2024-01-25 20:09:01,119] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:09:01,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/markers.fasta)
[2024-01-25 20:09:01,120] [INFO] Task started: Blastn
[2024-01-25 20:09:01,120] [INFO] Running command: blastn -query GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/markers.fasta -db /var/lib/cwl/stga67c90e0-e35e-4a22-91dc-824c5a5b82f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:09:02,265] [INFO] Task succeeded: Blastn
[2024-01-25 20:09:02,268] [INFO] Selected 8 target genomes.
[2024-01-25 20:09:02,268] [INFO] Target genome list was writen to GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:09:02,286] [INFO] Task started: fastANI
[2024-01-25 20:09:02,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f4a9a7f-89fd-4f92-bff1-7634b65c8944/GCF_000757425.2_Tmorbiroseiassem5_genomic.fna.gz --refList GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/target_genomes_gtdb.txt --output GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:09:09,152] [INFO] Task succeeded: fastANI
[2024-01-25 20:09:09,158] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:09:09,159] [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_000757425.2	s__Tatumella morbirosei	100.0	1467	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	95.37	95.37	0.92	0.92	2	conclusive
GCF_002163585.1	s__Tatumella citrea	87.4973	1228	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018257575.1	s__Tatumella sp018257575	81.3954	677	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	99.64	99.52	0.95	0.93	6	-
GCF_018257515.1	s__Tatumella sp018257515	80.2126	575	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735525.1	s__Tatumella ptyseos	80.1964	536	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	99.71	99.17	0.96	0.91	4	-
GCF_000439375.1	s__Tatumella saanichensis	79.8092	455	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001267535.1	s__Erwinia iniecta	78.5462	279	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.95	99.95	0.99	0.99	2	-
GCF_002095315.1	s__Pantoea conspicua	78.5146	289	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:09:09,160] [INFO] GTDB search result was written to GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/result_gtdb.tsv
[2024-01-25 20:09:09,160] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:09:09,163] [INFO] DFAST_QC result json was written to GCF_000757425.2_Tmorbiroseiassem5_genomic.fna/dqc_result.json
[2024-01-25 20:09:09,163] [INFO] DFAST_QC completed!
[2024-01-25 20:09:09,163] [INFO] Total running time: 0h1m3s