[2024-01-24 12:45:10,338] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,340] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg1eb022da-0ca9-45a4-b607-8d9a3194a0a8/dqc_reference
[2024-01-24 12:45:13,087] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,088] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,088] [INFO] Running command: gunzip -c /var/lib/cwl/stg24bfcc45-1b63-4584-adf5-2c6785d203c4/GCF_002095385.1_ASM209538v1_genomic.fna.gz | prodigal -d GCF_002095385.1_ASM209538v1_genomic.fna/cds.fna -a GCF_002095385.1_ASM209538v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:22,750] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:22,750] [INFO] Task started: HMMsearch
[2024-01-24 12:45:22,750] [INFO] Running command: hmmsearch --tblout GCF_002095385.1_ASM209538v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1eb022da-0ca9-45a4-b607-8d9a3194a0a8/dqc_reference/reference_markers.hmm GCF_002095385.1_ASM209538v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:23,042] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:23,048] [INFO] Found 6/6 markers.
[2024-01-24 12:45:23,087] [INFO] Query marker FASTA was written to GCF_002095385.1_ASM209538v1_genomic.fna/markers.fasta
[2024-01-24 12:45:23,088] [INFO] Task started: Blastn
[2024-01-24 12:45:23,088] [INFO] Running command: blastn -query GCF_002095385.1_ASM209538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eb022da-0ca9-45a4-b607-8d9a3194a0a8/dqc_reference/reference_markers.fasta -out GCF_002095385.1_ASM209538v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:24,066] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:24,070] [INFO] Selected 14 target genomes.
[2024-01-24 12:45:24,070] [INFO] Target genome list was writen to GCF_002095385.1_ASM209538v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:24,076] [INFO] Task started: fastANI
[2024-01-24 12:45:24,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg24bfcc45-1b63-4584-adf5-2c6785d203c4/GCF_002095385.1_ASM209538v1_genomic.fna.gz --refList GCF_002095385.1_ASM209538v1_genomic.fna/target_genomes.txt --output GCF_002095385.1_ASM209538v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:37,396] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:37,397] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1eb022da-0ca9-45a4-b607-8d9a3194a0a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:37,398] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1eb022da-0ca9-45a4-b607-8d9a3194a0a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:37,410] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:37,410] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:37,410] [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
Pantoea eucrina	strain=LMG 5346	GCA_002095385.1	472693	472693	type	True	100.0	1247	1251	95	conclusive
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	83.261	920	1251	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	83.2584	944	1251	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	82.8996	902	1251	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	81.9176	856	1251	95	below_threshold
Pantoea septica	strain=LMG 5345	GCA_002095575.1	472695	472695	type	True	81.6858	807	1251	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	81.6454	813	1251	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	81.3149	782	1251	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	81.0932	764	1251	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	81.041	830	1251	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	79.9435	619	1251	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.4015	624	1251	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.3255	563	1251	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.5655	424	1251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:37,412] [INFO] DFAST Taxonomy check result was written to GCF_002095385.1_ASM209538v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:37,413] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:37,413] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:37,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1eb022da-0ca9-45a4-b607-8d9a3194a0a8/dqc_reference/checkm_data
[2024-01-24 12:45:37,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:37,521] [INFO] Task started: CheckM
[2024-01-24 12:45:37,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002095385.1_ASM209538v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002095385.1_ASM209538v1_genomic.fna/checkm_input GCF_002095385.1_ASM209538v1_genomic.fna/checkm_result
[2024-01-24 12:46:11,183] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:11,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:11,205] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:11,205] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:11,206] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002095385.1_ASM209538v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:11,206] [INFO] Task started: Blastn
[2024-01-24 12:46:11,206] [INFO] Running command: blastn -query GCF_002095385.1_ASM209538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eb022da-0ca9-45a4-b607-8d9a3194a0a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002095385.1_ASM209538v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:12,742] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:12,746] [INFO] Selected 8 target genomes.
[2024-01-24 12:46:12,746] [INFO] Target genome list was writen to GCF_002095385.1_ASM209538v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:12,761] [INFO] Task started: fastANI
[2024-01-24 12:46:12,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg24bfcc45-1b63-4584-adf5-2c6785d203c4/GCF_002095385.1_ASM209538v1_genomic.fna.gz --refList GCF_002095385.1_ASM209538v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002095385.1_ASM209538v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:21,904] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:21,921] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:21,922] [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_002095385.1	s__Pantoea eucrina	100.0	1247	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.84	96.54	0.93	0.90	17	conclusive
GCF_001691555.1	s__Pantoea eucrina_A	93.3935	1145	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.39	99.35	0.94	0.93	4	-
GCF_014155765.1	s__Pantoea dispersa	83.249	945	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.93	96.36	0.92	0.86	38	-
GCF_007833795.1	s__Pantoea dispersa_B	83.1781	946	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095485.1	s__Pantoea wallisii	82.8921	903	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900068835.1	s__Pantoea ludwigii_B	81.9558	857	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.17	96.60	0.91	0.89	10	-
GCF_002858935.1	s__Pantoea endophytica	81.913	856	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.84	95.24	0.93	0.88	7	-
GCF_000468095.1	s__Pantoea sp000468095	81.2393	714	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.52	98.52	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:21,924] [INFO] GTDB search result was written to GCF_002095385.1_ASM209538v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:21,925] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:21,930] [INFO] DFAST_QC result json was written to GCF_002095385.1_ASM209538v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:21,930] [INFO] DFAST_QC completed!
[2024-01-24 12:46:21,931] [INFO] Total running time: 0h1m12s