[2024-01-24 12:06:51,288] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:51,290] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:51,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a075954-0e2d-4bd7-a12c-07c2926d7128/dqc_reference
[2024-01-24 12:06:52,494] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:52,495] [INFO] Task started: Prodigal
[2024-01-24 12:06:52,495] [INFO] Running command: gunzip -c /var/lib/cwl/stg63dde86e-eb03-4081-957e-767e3c900b47/GCF_002095575.1_ASM209557v1_genomic.fna.gz | prodigal -d GCF_002095575.1_ASM209557v1_genomic.fna/cds.fna -a GCF_002095575.1_ASM209557v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:02,878] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:02,879] [INFO] Task started: HMMsearch
[2024-01-24 12:07:02,879] [INFO] Running command: hmmsearch --tblout GCF_002095575.1_ASM209557v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a075954-0e2d-4bd7-a12c-07c2926d7128/dqc_reference/reference_markers.hmm GCF_002095575.1_ASM209557v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:03,150] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:03,151] [INFO] Found 6/6 markers.
[2024-01-24 12:07:03,200] [INFO] Query marker FASTA was written to GCF_002095575.1_ASM209557v1_genomic.fna/markers.fasta
[2024-01-24 12:07:03,201] [INFO] Task started: Blastn
[2024-01-24 12:07:03,201] [INFO] Running command: blastn -query GCF_002095575.1_ASM209557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a075954-0e2d-4bd7-a12c-07c2926d7128/dqc_reference/reference_markers.fasta -out GCF_002095575.1_ASM209557v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:04,073] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:04,076] [INFO] Selected 19 target genomes.
[2024-01-24 12:07:04,076] [INFO] Target genome list was writen to GCF_002095575.1_ASM209557v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:04,104] [INFO] Task started: fastANI
[2024-01-24 12:07:04,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg63dde86e-eb03-4081-957e-767e3c900b47/GCF_002095575.1_ASM209557v1_genomic.fna.gz --refList GCF_002095575.1_ASM209557v1_genomic.fna/target_genomes.txt --output GCF_002095575.1_ASM209557v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:22,093] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:22,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a075954-0e2d-4bd7-a12c-07c2926d7128/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:22,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a075954-0e2d-4bd7-a12c-07c2926d7128/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:22,113] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:22,113] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:22,113] [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	100.0	1387	1390	95	conclusive
Pantoea latae	strain=AS1	GCA_002077695.1	1964541	1964541	type	True	90.8307	1166	1390	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	82.7695	958	1390	95	below_threshold
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	82.7656	957	1390	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	82.6125	866	1390	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_006494415.1	470932	470932	type	True	82.4762	943	1390	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	82.449	950	1390	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	82.0234	915	1390	95	below_threshold
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	81.9328	879	1390	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	81.7848	887	1390	95	below_threshold
Mixta calida	strain=DSM 22759	GCA_002953215.1	665913	665913	type	True	81.7258	847	1390	95	below_threshold
Mixta calida	strain=LMG 25383	GCA_002095355.1	665913	665913	type	True	81.7068	786	1390	95	below_threshold
Pantoea eucrina	strain=LMG 5346	GCA_002095385.1	472693	472693	type	True	81.6697	798	1390	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	81.6238	924	1390	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	80.2545	672	1390	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	80.0726	650	1390	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	79.1334	569	1390	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.9881	563	1390	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	77.8279	415	1390	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:22,115] [INFO] DFAST Taxonomy check result was written to GCF_002095575.1_ASM209557v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:22,115] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:22,115] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:22,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a075954-0e2d-4bd7-a12c-07c2926d7128/dqc_reference/checkm_data
[2024-01-24 12:07:22,117] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:22,159] [INFO] Task started: CheckM
[2024-01-24 12:07:22,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002095575.1_ASM209557v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002095575.1_ASM209557v1_genomic.fna/checkm_input GCF_002095575.1_ASM209557v1_genomic.fna/checkm_result
[2024-01-24 12:07:56,539] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:56,540] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:56,560] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:56,560] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:56,561] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002095575.1_ASM209557v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:56,561] [INFO] Task started: Blastn
[2024-01-24 12:07:56,561] [INFO] Running command: blastn -query GCF_002095575.1_ASM209557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a075954-0e2d-4bd7-a12c-07c2926d7128/dqc_reference/reference_markers_gtdb.fasta -out GCF_002095575.1_ASM209557v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:57,798] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:57,808] [INFO] Selected 11 target genomes.
[2024-01-24 12:07:57,809] [INFO] Target genome list was writen to GCF_002095575.1_ASM209557v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:57,818] [INFO] Task started: fastANI
[2024-01-24 12:07:57,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg63dde86e-eb03-4081-957e-767e3c900b47/GCF_002095575.1_ASM209557v1_genomic.fna.gz --refList GCF_002095575.1_ASM209557v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002095575.1_ASM209557v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:09,105] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:09,118] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:09,118] [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_002095575.1	s__Pantoea septica	100.0	1387	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.04	95.79	0.86	0.78	20	conclusive
GCF_002920175.1	s__Pantoea sp002920175	92.8415	1193	1390	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	90.839	1165	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003612015.1	s__Pantoea piersonii	90.6487	1151	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.15	96.25	0.97	0.92	11	-
GCF_003813865.1	s__Pantoea sp003813865	87.8713	1142	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013753875.1	s__Pantoea persica	87.0753	816	1390	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	86.4804	715	1390	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	81.7856	887	1390	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	81.5956	928	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.84	95.24	0.93	0.88	7	-
GCF_008801695.1	s__Pantoea stewartii	80.0888	673	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.82	98.55	0.82	0.77	34	-
GCF_002951615.1	s__Rahnella sp002951615	77.7045	399	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:09,120] [INFO] GTDB search result was written to GCF_002095575.1_ASM209557v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:09,120] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:09,124] [INFO] DFAST_QC result json was written to GCF_002095575.1_ASM209557v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:09,125] [INFO] DFAST_QC completed!
[2024-01-24 12:08:09,125] [INFO] Total running time: 0h1m18s