[2024-01-24 11:48:21,282] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,285] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg22849880-a0f7-486a-8f13-987ae98650f3/dqc_reference
[2024-01-24 11:48:24,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,566] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,567] [INFO] Running command: gunzip -c /var/lib/cwl/stg256e2640-dd58-4fb0-89e9-25b535621fe6/GCF_002095465.1_ASM209546v1_genomic.fna.gz | prodigal -d GCF_002095465.1_ASM209546v1_genomic.fna/cds.fna -a GCF_002095465.1_ASM209546v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:40,950] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:40,951] [INFO] Task started: HMMsearch
[2024-01-24 11:48:40,951] [INFO] Running command: hmmsearch --tblout GCF_002095465.1_ASM209546v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22849880-a0f7-486a-8f13-987ae98650f3/dqc_reference/reference_markers.hmm GCF_002095465.1_ASM209546v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:41,279] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:41,280] [INFO] Found 6/6 markers.
[2024-01-24 11:48:41,331] [INFO] Query marker FASTA was written to GCF_002095465.1_ASM209546v1_genomic.fna/markers.fasta
[2024-01-24 11:48:41,331] [INFO] Task started: Blastn
[2024-01-24 11:48:41,331] [INFO] Running command: blastn -query GCF_002095465.1_ASM209546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22849880-a0f7-486a-8f13-987ae98650f3/dqc_reference/reference_markers.fasta -out GCF_002095465.1_ASM209546v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:42,172] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:42,175] [INFO] Selected 17 target genomes.
[2024-01-24 11:48:42,176] [INFO] Target genome list was writen to GCF_002095465.1_ASM209546v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:42,212] [INFO] Task started: fastANI
[2024-01-24 11:48:42,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg256e2640-dd58-4fb0-89e9-25b535621fe6/GCF_002095465.1_ASM209546v1_genomic.fna.gz --refList GCF_002095465.1_ASM209546v1_genomic.fna/target_genomes.txt --output GCF_002095465.1_ASM209546v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:48:58,996] [INFO] Task succeeded: fastANI
[2024-01-24 11:48:58,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22849880-a0f7-486a-8f13-987ae98650f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:48:58,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22849880-a0f7-486a-8f13-987ae98650f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:48:59,016] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:48:59,016] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:48:59,017] [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=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	100.0	1881	1882	95	conclusive
Pantoea rodasii	strain=DSM 26611	GCA_002811195.1	1076549	1076549	type	True	99.9731	1879	1882	95	conclusive
Pantoea rwandensis	strain=LMG 26275	GCA_002095475.1	1076550	1076550	type	True	86.3234	1363	1882	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	84.8807	1269	1882	95	below_threshold
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	83.9835	1174	1882	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	83.9654	1164	1882	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	83.4516	1078	1882	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	80.7152	858	1882	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	79.7933	689	1882	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.7492	688	1882	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.9004	473	1882	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	78.8728	479	1882	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	78.2101	239	1882	95	below_threshold
Yersinia aldovae	strain=ATCC 35236	GCA_000173735.1	29483	29483	type	True	78.2062	236	1882	95	below_threshold
Yersinia frederiksenii	strain=NCTC11470	GCA_900460425.1	29484	29484	suspected-type	True	77.9285	248	1882	95	below_threshold
Yersinia frederiksenii	strain=ATCC 33641	GCA_000168015.1	29484	29484	suspected-type	True	77.8858	245	1882	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:48:59,018] [INFO] DFAST Taxonomy check result was written to GCF_002095465.1_ASM209546v1_genomic.fna/tc_result.tsv
[2024-01-24 11:48:59,018] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:48:59,019] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:48:59,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22849880-a0f7-486a-8f13-987ae98650f3/dqc_reference/checkm_data
[2024-01-24 11:48:59,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:48:59,080] [INFO] Task started: CheckM
[2024-01-24 11:48:59,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002095465.1_ASM209546v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002095465.1_ASM209546v1_genomic.fna/checkm_input GCF_002095465.1_ASM209546v1_genomic.fna/checkm_result
[2024-01-24 11:49:48,805] [INFO] Task succeeded: CheckM
[2024-01-24 11:49:48,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:49:48,825] [INFO] ===== Completeness check finished =====
[2024-01-24 11:49:48,826] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:49:48,827] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002095465.1_ASM209546v1_genomic.fna/markers.fasta)
[2024-01-24 11:49:48,827] [INFO] Task started: Blastn
[2024-01-24 11:49:48,827] [INFO] Running command: blastn -query GCF_002095465.1_ASM209546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22849880-a0f7-486a-8f13-987ae98650f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002095465.1_ASM209546v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:49:49,951] [INFO] Task succeeded: Blastn
[2024-01-24 11:49:49,955] [INFO] Selected 13 target genomes.
[2024-01-24 11:49:49,955] [INFO] Target genome list was writen to GCF_002095465.1_ASM209546v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:49:49,964] [INFO] Task started: fastANI
[2024-01-24 11:49:49,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg256e2640-dd58-4fb0-89e9-25b535621fe6/GCF_002095465.1_ASM209546v1_genomic.fna.gz --refList GCF_002095465.1_ASM209546v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002095465.1_ASM209546v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:50:04,649] [INFO] Task succeeded: fastANI
[2024-01-24 11:50:04,666] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:50:04,667] [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	100.0	1881	1882	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	89.9249	1548	1882	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	89.7002	1251	1882	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	89.6523	1496	1882	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	86.977	1246	1882	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	86.5076	1439	1882	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	86.3147	1364	1882	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	84.8931	1267	1882	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	84.5965	1291	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
GCF_900068845.1	s__Pantoea ludwigii_A	84.3278	1254	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002895925.1	s__Mixta theicola	79.6239	590	1882	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	78.1781	237	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.00	96.65	0.94	0.91	11	-
--------------------------------------------------------------------------------
[2024-01-24 11:50:04,669] [INFO] GTDB search result was written to GCF_002095465.1_ASM209546v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:50:04,669] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:50:04,673] [INFO] DFAST_QC result json was written to GCF_002095465.1_ASM209546v1_genomic.fna/dqc_result.json
[2024-01-24 11:50:04,673] [INFO] DFAST_QC completed!
[2024-01-24 11:50:04,673] [INFO] Total running time: 0h1m43s