[2024-01-25 17:42:20,380] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:20,381] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:20,382] [INFO] DQC Reference Directory: /var/lib/cwl/stga6618c48-3d9c-4497-b5b8-87da1baea97e/dqc_reference
[2024-01-25 17:42:21,568] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:21,569] [INFO] Task started: Prodigal
[2024-01-25 17:42:21,570] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c0a5276-5cd3-4131-a5a4-5ce71ecd9809/GCF_017161565.1_ASM1716156v1_genomic.fna.gz | prodigal -d GCF_017161565.1_ASM1716156v1_genomic.fna/cds.fna -a GCF_017161565.1_ASM1716156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:30,733] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:30,733] [INFO] Task started: HMMsearch
[2024-01-25 17:42:30,733] [INFO] Running command: hmmsearch --tblout GCF_017161565.1_ASM1716156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6618c48-3d9c-4497-b5b8-87da1baea97e/dqc_reference/reference_markers.hmm GCF_017161565.1_ASM1716156v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:30,952] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:30,953] [INFO] Found 6/6 markers.
[2024-01-25 17:42:30,983] [INFO] Query marker FASTA was written to GCF_017161565.1_ASM1716156v1_genomic.fna/markers.fasta
[2024-01-25 17:42:30,984] [INFO] Task started: Blastn
[2024-01-25 17:42:30,984] [INFO] Running command: blastn -query GCF_017161565.1_ASM1716156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6618c48-3d9c-4497-b5b8-87da1baea97e/dqc_reference/reference_markers.fasta -out GCF_017161565.1_ASM1716156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:31,839] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:31,842] [INFO] Selected 12 target genomes.
[2024-01-25 17:42:31,842] [INFO] Target genome list was writen to GCF_017161565.1_ASM1716156v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:31,853] [INFO] Task started: fastANI
[2024-01-25 17:42:31,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c0a5276-5cd3-4131-a5a4-5ce71ecd9809/GCF_017161565.1_ASM1716156v1_genomic.fna.gz --refList GCF_017161565.1_ASM1716156v1_genomic.fna/target_genomes.txt --output GCF_017161565.1_ASM1716156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:43,333] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:43,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6618c48-3d9c-4497-b5b8-87da1baea97e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:43,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6618c48-3d9c-4497-b5b8-87da1baea97e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:43,342] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:42:43,342] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:43,342] [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
Erwinia amylovora	strain=ATCC 15580	GCA_017161565.1	552	552	type	True	100.0	1278	1278	95	conclusive
Erwinia amylovora	strain=NBRC 12687	GCA_000696075.1	552	552	type	True	99.9893	1229	1278	95	conclusive
Erwinia amylovora	strain=type strain: CFBP 1232	GCA_000367625.2	552	552	type	True	99.9769	1242	1278	95	conclusive
Erwinia pyrifoliae	strain=DSM 12163	GCA_000026985.1	79967	79967	type	True	90.7684	1108	1278	95	below_threshold
Erwinia piriflorinigrans	strain=CFBP 5888	GCA_001050515.1	665097	665097	type	True	85.6008	983	1278	95	below_threshold
Erwinia tasmaniensis	strain=Et1/99	GCA_000026185.1	338565	338565	type	True	85.3495	983	1278	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	82.079	831	1278	95	below_threshold
Erwinia aphidicola	strain=JCM 21238	GCA_014773485.1	68334	68334	type	True	81.86	834	1278	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.725	565	1278	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.0918	406	1278	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	79.0041	379	1278	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.588	344	1278	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:43,344] [INFO] DFAST Taxonomy check result was written to GCF_017161565.1_ASM1716156v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:43,344] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:43,344] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:43,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6618c48-3d9c-4497-b5b8-87da1baea97e/dqc_reference/checkm_data
[2024-01-25 17:42:43,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:43,384] [INFO] Task started: CheckM
[2024-01-25 17:42:43,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017161565.1_ASM1716156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017161565.1_ASM1716156v1_genomic.fna/checkm_input GCF_017161565.1_ASM1716156v1_genomic.fna/checkm_result
[2024-01-25 17:43:13,552] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:13,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:13,572] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:13,572] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:13,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017161565.1_ASM1716156v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:13,573] [INFO] Task started: Blastn
[2024-01-25 17:43:13,573] [INFO] Running command: blastn -query GCF_017161565.1_ASM1716156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6618c48-3d9c-4497-b5b8-87da1baea97e/dqc_reference/reference_markers_gtdb.fasta -out GCF_017161565.1_ASM1716156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:15,014] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:15,017] [INFO] Selected 9 target genomes.
[2024-01-25 17:43:15,017] [INFO] Target genome list was writen to GCF_017161565.1_ASM1716156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:15,034] [INFO] Task started: fastANI
[2024-01-25 17:43:15,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c0a5276-5cd3-4131-a5a4-5ce71ecd9809/GCF_017161565.1_ASM1716156v1_genomic.fna.gz --refList GCF_017161565.1_ASM1716156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017161565.1_ASM1716156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:24,806] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:24,812] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:24,813] [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_017161565.1	s__Erwinia amylovora	100.0	1277	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.73	98.13	0.99	0.95	141	conclusive
GCF_000026985.1	s__Erwinia pyrifoliae	90.7518	1110	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.33	98.13	0.97	0.93	4	-
GCF_001050515.1	s__Erwinia piriflorinigrans	85.6096	982	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000026185.1	s__Erwinia tasmaniensis	85.3409	981	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001756855.1	s__Erwinia dacicola	82.1026	309	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.47	98.24	0.66	0.61	4	-
GCF_014773485.1	s__Erwinia aphidicola	81.864	833	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.08	98.09	0.88	0.85	7	-
GCF_012271765.1	s__Erwinia rhapontici	81.3887	765	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.76	96.56	0.93	0.92	9	-
GCF_018141005.1	s__Erwinia sp001422605	81.0235	698	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.39	98.36	0.92	0.92	3	-
GCF_003751505.1	s__Erwinia sp003751505	80.9151	683	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:24,814] [INFO] GTDB search result was written to GCF_017161565.1_ASM1716156v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:24,815] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:24,817] [INFO] DFAST_QC result json was written to GCF_017161565.1_ASM1716156v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:24,817] [INFO] DFAST_QC completed!
[2024-01-25 17:43:24,817] [INFO] Total running time: 0h1m4s