[2024-01-24 15:02:46,671] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:46,673] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:46,673] [INFO] DQC Reference Directory: /var/lib/cwl/stge9a768c4-7f3b-4a53-a291-4f7e5de686b8/dqc_reference
[2024-01-24 15:02:48,065] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:48,066] [INFO] Task started: Prodigal
[2024-01-24 15:02:48,066] [INFO] Running command: gunzip -c /var/lib/cwl/stg26557305-3634-4764-829b-30686ee10d91/GCF_002095485.1_ASM209548v1_genomic.fna.gz | prodigal -d GCF_002095485.1_ASM209548v1_genomic.fna/cds.fna -a GCF_002095485.1_ASM209548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:00,764] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:00,765] [INFO] Task started: HMMsearch
[2024-01-24 15:03:00,765] [INFO] Running command: hmmsearch --tblout GCF_002095485.1_ASM209548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9a768c4-7f3b-4a53-a291-4f7e5de686b8/dqc_reference/reference_markers.hmm GCF_002095485.1_ASM209548v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:01,139] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:01,140] [INFO] Found 6/6 markers.
[2024-01-24 15:03:01,187] [INFO] Query marker FASTA was written to GCF_002095485.1_ASM209548v1_genomic.fna/markers.fasta
[2024-01-24 15:03:01,187] [INFO] Task started: Blastn
[2024-01-24 15:03:01,187] [INFO] Running command: blastn -query GCF_002095485.1_ASM209548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9a768c4-7f3b-4a53-a291-4f7e5de686b8/dqc_reference/reference_markers.fasta -out GCF_002095485.1_ASM209548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:02,095] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:02,099] [INFO] Selected 13 target genomes.
[2024-01-24 15:03:02,100] [INFO] Target genome list was writen to GCF_002095485.1_ASM209548v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:02,106] [INFO] Task started: fastANI
[2024-01-24 15:03:02,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg26557305-3634-4764-829b-30686ee10d91/GCF_002095485.1_ASM209548v1_genomic.fna.gz --refList GCF_002095485.1_ASM209548v1_genomic.fna/target_genomes.txt --output GCF_002095485.1_ASM209548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:16,286] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:16,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9a768c4-7f3b-4a53-a291-4f7e5de686b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:16,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9a768c4-7f3b-4a53-a291-4f7e5de686b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:16,302] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:16,302] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:16,302] [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 wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	100.0	1484	1485	95	conclusive
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	85.6877	1145	1485	95	below_threshold
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	85.6532	1142	1485	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	83.9308	1121	1485	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	83.628	1078	1485	95	below_threshold
Pantoea rodasii	strain=DSM 26611	GCA_002811195.1	1076549	1076549	type	True	83.5887	1072	1485	95	below_threshold
Pantoea eucrina	strain=LMG 5346	GCA_002095385.1	472693	472693	type	True	82.7843	922	1485	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	82.7075	1026	1485	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	81.3406	894	1485	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	79.9725	683	1485	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.9385	700	1485	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.2962	578	1485	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.8813	490	1485	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:16,304] [INFO] DFAST Taxonomy check result was written to GCF_002095485.1_ASM209548v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:16,305] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:16,305] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:16,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9a768c4-7f3b-4a53-a291-4f7e5de686b8/dqc_reference/checkm_data
[2024-01-24 15:03:16,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:16,356] [INFO] Task started: CheckM
[2024-01-24 15:03:16,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002095485.1_ASM209548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002095485.1_ASM209548v1_genomic.fna/checkm_input GCF_002095485.1_ASM209548v1_genomic.fna/checkm_result
[2024-01-24 15:03:58,920] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:58,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:58,935] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:58,935] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:58,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002095485.1_ASM209548v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:58,936] [INFO] Task started: Blastn
[2024-01-24 15:03:58,937] [INFO] Running command: blastn -query GCF_002095485.1_ASM209548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9a768c4-7f3b-4a53-a291-4f7e5de686b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002095485.1_ASM209548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:00,192] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:00,197] [INFO] Selected 16 target genomes.
[2024-01-24 15:04:00,197] [INFO] Target genome list was writen to GCF_002095485.1_ASM209548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:00,226] [INFO] Task started: fastANI
[2024-01-24 15:04:00,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg26557305-3634-4764-829b-30686ee10d91/GCF_002095485.1_ASM209548v1_genomic.fna.gz --refList GCF_002095485.1_ASM209548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002095485.1_ASM209548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:19,806] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:19,824] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:19,824] [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_002095485.1	s__Pantoea wallisii	100.0	1484	1485	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_014155765.1	s__Pantoea dispersa	85.6955	1144	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.93	96.36	0.92	0.86	38	-
GCF_007833795.1	s__Pantoea dispersa_B	85.2127	1131	1485	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	83.952	1003	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.54	98.22	0.92	0.90	5	-
GCF_002858935.1	s__Pantoea endophytica	83.9227	1122	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.84	95.24	0.93	0.88	7	-
GCF_000773965.1	s__Pantoea cancerogena_A	83.785	1051	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	96.89	96.70	0.91	0.89	9	-
GCF_016625195.1	s__Pantoea sp016625195	83.7604	1072	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095465.1	s__Pantoea rodasii	83.6194	1079	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	1.00	1.00	2	-
GCF_900068845.1	s__Pantoea ludwigii_A	83.3907	1067	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752625.1	s__Pantoea sp011752625	83.102	1057	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095385.1	s__Pantoea eucrina	82.7843	922	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.84	96.54	0.93	0.90	17	-
GCF_002095535.1	s__Pantoea cypripedii	82.7075	1026	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	0.99	0.99	2	-
GCF_011395035.1	s__Pantoea cypripedii_A	82.6294	1013	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001691555.1	s__Pantoea eucrina_A	82.589	893	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.39	99.35	0.94	0.93	4	-
GCF_002095575.1	s__Pantoea septica	81.8784	864	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.04	95.79	0.86	0.78	20	-
GCF_008801695.1	s__Pantoea stewartii	80.0452	637	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.82	98.55	0.82	0.77	34	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:19,828] [INFO] GTDB search result was written to GCF_002095485.1_ASM209548v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:19,829] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:19,833] [INFO] DFAST_QC result json was written to GCF_002095485.1_ASM209548v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:19,833] [INFO] DFAST_QC completed!
[2024-01-24 15:04:19,833] [INFO] Total running time: 0h1m33s