[2024-01-24 12:23:03,980] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,981] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,982] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f026726-1cb1-438d-8fa5-ec8ddd5b6adb/dqc_reference
[2024-01-24 12:23:05,392] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,393] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,393] [INFO] Running command: gunzip -c /var/lib/cwl/stg03153997-5926-450b-adc1-dc93b910047c/GCF_002095475.1_ASM209547v1_genomic.fna.gz | prodigal -d GCF_002095475.1_ASM209547v1_genomic.fna/cds.fna -a GCF_002095475.1_ASM209547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:22,059] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:22,059] [INFO] Task started: HMMsearch
[2024-01-24 12:23:22,060] [INFO] Running command: hmmsearch --tblout GCF_002095475.1_ASM209547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f026726-1cb1-438d-8fa5-ec8ddd5b6adb/dqc_reference/reference_markers.hmm GCF_002095475.1_ASM209547v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:22,353] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:22,354] [INFO] Found 6/6 markers.
[2024-01-24 12:23:22,406] [INFO] Query marker FASTA was written to GCF_002095475.1_ASM209547v1_genomic.fna/markers.fasta
[2024-01-24 12:23:22,406] [INFO] Task started: Blastn
[2024-01-24 12:23:22,406] [INFO] Running command: blastn -query GCF_002095475.1_ASM209547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f026726-1cb1-438d-8fa5-ec8ddd5b6adb/dqc_reference/reference_markers.fasta -out GCF_002095475.1_ASM209547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:23,313] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:23,317] [INFO] Selected 13 target genomes.
[2024-01-24 12:23:23,317] [INFO] Target genome list was writen to GCF_002095475.1_ASM209547v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:23,322] [INFO] Task started: fastANI
[2024-01-24 12:23:23,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg03153997-5926-450b-adc1-dc93b910047c/GCF_002095475.1_ASM209547v1_genomic.fna.gz --refList GCF_002095475.1_ASM209547v1_genomic.fna/target_genomes.txt --output GCF_002095475.1_ASM209547v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:37,150] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:37,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f026726-1cb1-438d-8fa5-ec8ddd5b6adb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:37,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f026726-1cb1-438d-8fa5-ec8ddd5b6adb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:37,167] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:37,167] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:37,167] [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 rwandensis	strain=LMG 26275	GCA_002095475.1	1076550	1076550	type	True	100.0	1893	1894	95	conclusive
Pantoea rodasii	strain=DSM 26611	GCA_002811195.1	1076549	1076549	type	True	86.3264	1365	1894	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	86.325	1377	1894	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	83.7411	1231	1894	95	below_threshold
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	83.2676	1085	1894	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	83.2033	1107	1894	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	82.9314	1034	1894	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	82.2364	1132	1894	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	80.2367	797	1894	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	79.7351	655	1894	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.1781	598	1894	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	78.715	505	1894	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.6847	416	1894	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:37,169] [INFO] DFAST Taxonomy check result was written to GCF_002095475.1_ASM209547v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:37,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:37,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:37,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f026726-1cb1-438d-8fa5-ec8ddd5b6adb/dqc_reference/checkm_data
[2024-01-24 12:23:37,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:37,232] [INFO] Task started: CheckM
[2024-01-24 12:23:37,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002095475.1_ASM209547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002095475.1_ASM209547v1_genomic.fna/checkm_input GCF_002095475.1_ASM209547v1_genomic.fna/checkm_result
[2024-01-24 12:24:27,328] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:27,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:27,355] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:27,356] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:27,356] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002095475.1_ASM209547v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:27,357] [INFO] Task started: Blastn
[2024-01-24 12:24:27,357] [INFO] Running command: blastn -query GCF_002095475.1_ASM209547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f026726-1cb1-438d-8fa5-ec8ddd5b6adb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002095475.1_ASM209547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:28,798] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:28,802] [INFO] Selected 7 target genomes.
[2024-01-24 12:24:28,802] [INFO] Target genome list was writen to GCF_002095475.1_ASM209547v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:28,808] [INFO] Task started: fastANI
[2024-01-24 12:24:28,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg03153997-5926-450b-adc1-dc93b910047c/GCF_002095475.1_ASM209547v1_genomic.fna.gz --refList GCF_002095475.1_ASM209547v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002095475.1_ASM209547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:38,422] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:38,431] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:38,431] [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_002095475.1	s__Pantoea rwandensis	100.0	1893	1894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011752625.1	s__Pantoea sp011752625	92.9562	1636	1894	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	87.793	1186	1894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.54	98.22	0.92	0.90	5	-
GCF_001506165.1	s__Pantoea vagans_C	86.8031	1199	1894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.95	97.99	0.91	0.89	3	-
GCF_016625195.1	s__Pantoea sp016625195	86.7735	1408	1894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000773965.1	s__Pantoea cancerogena_A	86.7495	1377	1894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	96.89	96.70	0.91	0.89	9	-
GCF_002095465.1	s__Pantoea rodasii	86.3297	1376	1894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:38,432] [INFO] GTDB search result was written to GCF_002095475.1_ASM209547v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:38,433] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:38,436] [INFO] DFAST_QC result json was written to GCF_002095475.1_ASM209547v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:38,436] [INFO] DFAST_QC completed!
[2024-01-24 12:24:38,436] [INFO] Total running time: 0h1m34s