[2024-01-25 18:15:05,493] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:05,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:05,494] [INFO] DQC Reference Directory: /var/lib/cwl/stg5363ae6d-9abd-46ad-9a1b-954ca1d3b665/dqc_reference
[2024-01-25 18:15:06,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:06,666] [INFO] Task started: Prodigal
[2024-01-25 18:15:06,666] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ff03fd2-1ebf-4107-974e-6466778e5a23/GCF_003612015.1_ASM361201v1_genomic.fna.gz | prodigal -d GCF_003612015.1_ASM361201v1_genomic.fna/cds.fna -a GCF_003612015.1_ASM361201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:17,572] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:17,572] [INFO] Task started: HMMsearch
[2024-01-25 18:15:17,572] [INFO] Running command: hmmsearch --tblout GCF_003612015.1_ASM361201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5363ae6d-9abd-46ad-9a1b-954ca1d3b665/dqc_reference/reference_markers.hmm GCF_003612015.1_ASM361201v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:17,801] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:17,802] [INFO] Found 6/6 markers.
[2024-01-25 18:15:17,840] [INFO] Query marker FASTA was written to GCF_003612015.1_ASM361201v1_genomic.fna/markers.fasta
[2024-01-25 18:15:17,840] [INFO] Task started: Blastn
[2024-01-25 18:15:17,840] [INFO] Running command: blastn -query GCF_003612015.1_ASM361201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5363ae6d-9abd-46ad-9a1b-954ca1d3b665/dqc_reference/reference_markers.fasta -out GCF_003612015.1_ASM361201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:18,671] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:18,674] [INFO] Selected 20 target genomes.
[2024-01-25 18:15:18,674] [INFO] Target genome list was writen to GCF_003612015.1_ASM361201v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:18,697] [INFO] Task started: fastANI
[2024-01-25 18:15:18,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ff03fd2-1ebf-4107-974e-6466778e5a23/GCF_003612015.1_ASM361201v1_genomic.fna.gz --refList GCF_003612015.1_ASM361201v1_genomic.fna/target_genomes.txt --output GCF_003612015.1_ASM361201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:15:37,956] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:37,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5363ae6d-9abd-46ad-9a1b-954ca1d3b665/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:15:37,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5363ae6d-9abd-46ad-9a1b-954ca1d3b665/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:15:37,968] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:15:37,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:15:37,969] [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 septica	strain=LMG 5345	GCA_002095575.1	472695	472695	type	True	90.6143	1168	1602	95	below_threshold
Pantoea latae	strain=AS1	GCA_002077695.1	1964541	1964541	type	True	89.4204	1292	1602	95	below_threshold
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	82.3056	976	1602	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	82.2367	989	1602	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	82.2364	890	1602	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_006494415.1	470932	470932	type	True	82.2051	961	1602	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	82.1194	977	1602	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	81.8784	949	1602	95	below_threshold
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	81.6568	882	1602	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	81.6269	923	1602	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	81.2723	964	1602	95	below_threshold
Pantoea eucrina	strain=LMG 5346	GCA_002095385.1	472693	472693	type	True	81.2377	827	1602	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	80.2359	740	1602	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	80.0846	761	1602	95	below_threshold
Siccibacter colletis	strain=1383	GCA_000696575.1	1505757	1505757	type	True	79.2414	602	1602	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	79.1442	560	1602	95	below_threshold
Klebsiella quasipneumoniae subsp. similipneumoniae	strain=07A044T	GCA_020525685.1	1463164	1463165	type	True	79.0538	603	1602	95	below_threshold
Klebsiella quasipneumoniae subsp. similipneumoniae	strain=07A044	GCA_000613225.1	1463164	1463165	type	True	78.9612	600	1602	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.8242	557	1602	95	below_threshold
Leminorella grimontii	strain=JCM 5902	GCA_024343555.1	82981	82981	type	True	77.5936	252	1602	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:15:37,970] [INFO] DFAST Taxonomy check result was written to GCF_003612015.1_ASM361201v1_genomic.fna/tc_result.tsv
[2024-01-25 18:15:37,971] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:15:37,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:15:37,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5363ae6d-9abd-46ad-9a1b-954ca1d3b665/dqc_reference/checkm_data
[2024-01-25 18:15:37,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:15:38,019] [INFO] Task started: CheckM
[2024-01-25 18:15:38,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003612015.1_ASM361201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003612015.1_ASM361201v1_genomic.fna/checkm_input GCF_003612015.1_ASM361201v1_genomic.fna/checkm_result
[2024-01-25 18:16:12,679] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:12,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:12,712] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:12,712] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:12,713] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003612015.1_ASM361201v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:12,713] [INFO] Task started: Blastn
[2024-01-25 18:16:12,713] [INFO] Running command: blastn -query GCF_003612015.1_ASM361201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5363ae6d-9abd-46ad-9a1b-954ca1d3b665/dqc_reference/reference_markers_gtdb.fasta -out GCF_003612015.1_ASM361201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:13,999] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:14,002] [INFO] Selected 9 target genomes.
[2024-01-25 18:16:14,002] [INFO] Target genome list was writen to GCF_003612015.1_ASM361201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:14,018] [INFO] Task started: fastANI
[2024-01-25 18:16:14,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ff03fd2-1ebf-4107-974e-6466778e5a23/GCF_003612015.1_ASM361201v1_genomic.fna.gz --refList GCF_003612015.1_ASM361201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003612015.1_ASM361201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:23,688] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:23,695] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:16:23,695] [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_003612015.1	s__Pantoea piersonii	100.0	1601	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.15	96.25	0.97	0.92	11	conclusive
GCF_002095575.1	s__Pantoea septica	90.6053	1169	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.04	95.79	0.86	0.78	20	-
GCF_002920175.1	s__Pantoea sp002920175	89.824	1288	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.09	99.09	0.94	0.94	2	-
GCF_002077695.1	s__Pantoea latae	89.4089	1293	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003813865.1	s__Pantoea sp003813865	87.1482	1250	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001485295.1	s__Pantoea sp001485295	86.0708	727	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095315.1	s__Pantoea conspicua	81.8691	951	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001922585.1	s__1-19 sp001922585	79.4721	597	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__1-19	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000439085.1	s__Leminorella grimontii	77.5938	259	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leminorella	95.0	99.99	99.98	1.00	0.99	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:23,697] [INFO] GTDB search result was written to GCF_003612015.1_ASM361201v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:23,698] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:23,701] [INFO] DFAST_QC result json was written to GCF_003612015.1_ASM361201v1_genomic.fna/dqc_result.json
[2024-01-25 18:16:23,701] [INFO] DFAST_QC completed!
[2024-01-25 18:16:23,701] [INFO] Total running time: 0h1m18s