[2024-01-24 11:51:06,362] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,366] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,366] [INFO] DQC Reference Directory: /var/lib/cwl/stg58f8930e-ec55-406e-a972-78e055d1e147/dqc_reference
[2024-01-24 11:51:07,593] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:07,594] [INFO] Task started: Prodigal
[2024-01-24 11:51:07,594] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb76304f-aa4a-4351-a6cc-ca1ea535cfe0/GCF_002095535.1_ASM209553v1_genomic.fna.gz | prodigal -d GCF_002095535.1_ASM209553v1_genomic.fna/cds.fna -a GCF_002095535.1_ASM209553v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:26,951] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:26,952] [INFO] Task started: HMMsearch
[2024-01-24 11:51:26,952] [INFO] Running command: hmmsearch --tblout GCF_002095535.1_ASM209553v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58f8930e-ec55-406e-a972-78e055d1e147/dqc_reference/reference_markers.hmm GCF_002095535.1_ASM209553v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:27,353] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:27,356] [INFO] Found 6/6 markers.
[2024-01-24 11:51:27,414] [INFO] Query marker FASTA was written to GCF_002095535.1_ASM209553v1_genomic.fna/markers.fasta
[2024-01-24 11:51:27,414] [INFO] Task started: Blastn
[2024-01-24 11:51:27,414] [INFO] Running command: blastn -query GCF_002095535.1_ASM209553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58f8930e-ec55-406e-a972-78e055d1e147/dqc_reference/reference_markers.fasta -out GCF_002095535.1_ASM209553v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:28,275] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:28,282] [INFO] Selected 22 target genomes.
[2024-01-24 11:51:28,283] [INFO] Target genome list was writen to GCF_002095535.1_ASM209553v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:28,292] [INFO] Task started: fastANI
[2024-01-24 11:51:28,292] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb76304f-aa4a-4351-a6cc-ca1ea535cfe0/GCF_002095535.1_ASM209553v1_genomic.fna.gz --refList GCF_002095535.1_ASM209553v1_genomic.fna/target_genomes.txt --output GCF_002095535.1_ASM209553v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:49,404] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:49,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58f8930e-ec55-406e-a972-78e055d1e147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:49,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58f8930e-ec55-406e-a972-78e055d1e147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:49,425] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:49,425] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:49,426] [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 cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	100.0	2182	2183	95	conclusive
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	83.3169	1111	2183	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	83.2962	1130	2183	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	83.1342	1164	2183	95	below_threshold
Pantoea rodasii	strain=DSM 26611	GCA_002811195.1	1076549	1076549	type	True	82.9187	1195	2183	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	82.9155	1179	2183	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	82.8169	1012	2183	95	below_threshold
Pantoea rwandensis	strain=LMG 26275	GCA_002095475.1	1076550	1076550	type	True	82.2495	1138	2183	95	below_threshold
Pantoea eucrina	strain=LMG 5346	GCA_002095385.1	472693	472693	type	True	81.4546	780	2183	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	81.3408	891	2183	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_006494415.1	470932	470932	type	True	81.0034	904	2183	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	80.9564	917	2183	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	80.9402	849	2183	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	80.0768	757	2183	95	below_threshold
Mixta tenebrionis	strain=BIT-26	GCA_006517625.1	2562439	2562439	type	True	79.3785	672	2183	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	78.9752	610	2183	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	78.7564	474	2183	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	78.7079	479	2183	95	below_threshold
Serratia odorifera	strain=NCTC11214	GCA_900635445.1	618	618	type	True	78.4504	492	2183	95	below_threshold
Serratia odorifera	strain=DSM 4582	GCA_000163595.1	618	618	type	True	78.3797	492	2183	95	below_threshold
Edwardsiella piscicida	strain=ACC35.1	GCA_001896205.1	1263550	1263550	reftype	True	78.0807	276	2183	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	77.8507	441	2183	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:49,427] [INFO] DFAST Taxonomy check result was written to GCF_002095535.1_ASM209553v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:49,428] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:49,428] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:49,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58f8930e-ec55-406e-a972-78e055d1e147/dqc_reference/checkm_data
[2024-01-24 11:51:49,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:49,488] [INFO] Task started: CheckM
[2024-01-24 11:51:49,488] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002095535.1_ASM209553v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002095535.1_ASM209553v1_genomic.fna/checkm_input GCF_002095535.1_ASM209553v1_genomic.fna/checkm_result
[2024-01-24 11:52:47,894] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:47,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:47,921] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:47,921] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:47,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002095535.1_ASM209553v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:47,922] [INFO] Task started: Blastn
[2024-01-24 11:52:47,922] [INFO] Running command: blastn -query GCF_002095535.1_ASM209553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58f8930e-ec55-406e-a972-78e055d1e147/dqc_reference/reference_markers_gtdb.fasta -out GCF_002095535.1_ASM209553v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:49,065] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:49,068] [INFO] Selected 12 target genomes.
[2024-01-24 11:52:49,068] [INFO] Target genome list was writen to GCF_002095535.1_ASM209553v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:49,078] [INFO] Task started: fastANI
[2024-01-24 11:52:49,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb76304f-aa4a-4351-a6cc-ca1ea535cfe0/GCF_002095535.1_ASM209553v1_genomic.fna.gz --refList GCF_002095535.1_ASM209553v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002095535.1_ASM209553v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:04,164] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:04,178] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:04,178] [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_002095535.1	s__Pantoea cypripedii	100.0	2182	2183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	0.99	0.99	2	conclusive
GCF_011395035.1	s__Pantoea cypripedii_A	92.7165	1779	2183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000468095.1	s__Pantoea sp000468095	86.8624	1345	2183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.52	98.52	0.95	0.95	2	-
GCF_000175935.2	s__Pantoea sp000175935	86.5024	1573	2183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014155765.1	s__Pantoea dispersa	83.2962	1130	2183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.93	96.36	0.92	0.86	38	-
GCF_002858935.1	s__Pantoea endophytica	83.1376	1164	2183	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	82.9453	1143	2183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
GCF_002095485.1	s__Pantoea wallisii	82.8244	1012	2183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007833795.1	s__Pantoea dispersa_B	82.7307	1010	2183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014946725.1	s__Pantoea mediterraneensis_A	80.7693	783	2183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025565.1	s__Enterobacter cloacae	79.2192	561	2183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.05	95.14	0.91	0.80	129	-
GCA_018261615.1	s__Kosakonia sp018261615	78.9559	525	2183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:04,200] [INFO] GTDB search result was written to GCF_002095535.1_ASM209553v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:04,202] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:04,210] [INFO] DFAST_QC result json was written to GCF_002095535.1_ASM209553v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:04,210] [INFO] DFAST_QC completed!
[2024-01-24 11:53:04,210] [INFO] Total running time: 0h1m58s