[2024-01-25 19:47:20,411] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:20,412] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:20,412] [INFO] DQC Reference Directory: /var/lib/cwl/stg96a48d19-1dad-496d-85e9-15a070b45a0f/dqc_reference
[2024-01-25 19:47:21,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:21,531] [INFO] Task started: Prodigal
[2024-01-25 19:47:21,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg39d02fcc-13d5-42db-afa8-df18113317b3/GCF_002811195.1_ASM281119v1_genomic.fna.gz | prodigal -d GCF_002811195.1_ASM281119v1_genomic.fna/cds.fna -a GCF_002811195.1_ASM281119v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:36,149] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:36,149] [INFO] Task started: HMMsearch
[2024-01-25 19:47:36,149] [INFO] Running command: hmmsearch --tblout GCF_002811195.1_ASM281119v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96a48d19-1dad-496d-85e9-15a070b45a0f/dqc_reference/reference_markers.hmm GCF_002811195.1_ASM281119v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:36,484] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:36,485] [INFO] Found 6/6 markers.
[2024-01-25 19:47:36,529] [INFO] Query marker FASTA was written to GCF_002811195.1_ASM281119v1_genomic.fna/markers.fasta
[2024-01-25 19:47:36,529] [INFO] Task started: Blastn
[2024-01-25 19:47:36,529] [INFO] Running command: blastn -query GCF_002811195.1_ASM281119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96a48d19-1dad-496d-85e9-15a070b45a0f/dqc_reference/reference_markers.fasta -out GCF_002811195.1_ASM281119v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:37,341] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:37,343] [INFO] Selected 17 target genomes.
[2024-01-25 19:47:37,344] [INFO] Target genome list was writen to GCF_002811195.1_ASM281119v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:37,357] [INFO] Task started: fastANI
[2024-01-25 19:47:37,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg39d02fcc-13d5-42db-afa8-df18113317b3/GCF_002811195.1_ASM281119v1_genomic.fna.gz --refList GCF_002811195.1_ASM281119v1_genomic.fna/target_genomes.txt --output GCF_002811195.1_ASM281119v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:54,384] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:54,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96a48d19-1dad-496d-85e9-15a070b45a0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:54,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96a48d19-1dad-496d-85e9-15a070b45a0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:54,395] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:47:54,395] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:54,396] [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 rodasii	strain=DSM 26611	GCA_002811195.1	1076549	1076549	type	True	100.0	1896	1900	95	conclusive
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	99.96	1869	1900	95	conclusive
Pantoea rwandensis	strain=LMG 26275	GCA_002095475.1	1076550	1076550	type	True	86.3695	1368	1900	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	84.9015	1281	1900	95	below_threshold
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	84.1042	1153	1900	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	84.0496	1176	1900	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	83.5784	1081	1900	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	80.6939	869	1900	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.7185	703	1900	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	79.7064	696	1900	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	78.9289	577	1900	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.7677	487	1900	95	below_threshold
Yersinia frederiksenii	strain=NCTC11470	GCA_900460425.1	29484	29484	suspected-type	True	78.0792	241	1900	95	below_threshold
Yersinia aldovae	strain=ATCC 35236	GCA_000173735.1	29483	29483	type	True	78.0498	245	1900	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	78.0055	248	1900	95	below_threshold
Yersinia frederiksenii	strain=ATCC 33641	GCA_000168015.1	29484	29484	suspected-type	True	77.9938	235	1900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:54,397] [INFO] DFAST Taxonomy check result was written to GCF_002811195.1_ASM281119v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:54,397] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:54,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:54,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96a48d19-1dad-496d-85e9-15a070b45a0f/dqc_reference/checkm_data
[2024-01-25 19:47:54,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:54,453] [INFO] Task started: CheckM
[2024-01-25 19:47:54,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002811195.1_ASM281119v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002811195.1_ASM281119v1_genomic.fna/checkm_input GCF_002811195.1_ASM281119v1_genomic.fna/checkm_result
[2024-01-25 19:48:38,867] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:38,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:38,891] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:38,892] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:38,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002811195.1_ASM281119v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:38,893] [INFO] Task started: Blastn
[2024-01-25 19:48:38,893] [INFO] Running command: blastn -query GCF_002811195.1_ASM281119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96a48d19-1dad-496d-85e9-15a070b45a0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002811195.1_ASM281119v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:40,050] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:40,053] [INFO] Selected 12 target genomes.
[2024-01-25 19:48:40,054] [INFO] Target genome list was writen to GCF_002811195.1_ASM281119v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:40,065] [INFO] Task started: fastANI
[2024-01-25 19:48:40,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg39d02fcc-13d5-42db-afa8-df18113317b3/GCF_002811195.1_ASM281119v1_genomic.fna.gz --refList GCF_002811195.1_ASM281119v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002811195.1_ASM281119v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:53,758] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:53,765] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:53,765] [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_002095465.1	s__Pantoea rodasii	99.96	1869	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	1.00	1.00	2	conclusive
GCF_016625195.1	s__Pantoea sp016625195	89.9197	1545	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759475.1	s__Pantoea rwandensis_B	89.7868	1242	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.54	98.22	0.92	0.90	5	-
GCF_000773965.1	s__Pantoea cancerogena_A	89.6257	1525	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	96.89	96.70	0.91	0.89	9	-
GCF_001506165.1	s__Pantoea vagans_C	86.9192	1254	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.95	97.99	0.91	0.89	3	-
GCF_011752625.1	s__Pantoea sp011752625	86.5317	1445	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095475.1	s__Pantoea rwandensis	86.368	1368	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002858935.1	s__Pantoea endophytica	84.9241	1278	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.84	95.24	0.93	0.88	7	-
GCF_001187905.1	s__Pantoea sp001187905	84.6921	1290	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
GCF_002895925.1	s__Mixta theicola	79.5362	599	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000173735.1	s__Yersinia aldovae	78.0236	246	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.00	96.65	0.94	0.91	11	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:53,767] [INFO] GTDB search result was written to GCF_002811195.1_ASM281119v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:53,767] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:53,770] [INFO] DFAST_QC result json was written to GCF_002811195.1_ASM281119v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:53,770] [INFO] DFAST_QC completed!
[2024-01-25 19:48:53,770] [INFO] Total running time: 0h1m33s