[2024-01-24 10:57:50,265] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:50,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:50,266] [INFO] DQC Reference Directory: /var/lib/cwl/stg522527a9-3885-46ec-9992-e913ccc2abcb/dqc_reference
[2024-01-24 10:57:52,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:52,641] [INFO] Task started: Prodigal
[2024-01-24 10:57:52,641] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5bed869-ba90-4152-af16-8e32b8b3ec44/GCF_900183975.1_PD885.1_genomic.fna.gz | prodigal -d GCF_900183975.1_PD885.1_genomic.fna/cds.fna -a GCF_900183975.1_PD885.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:08,627] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:08,628] [INFO] Task started: HMMsearch
[2024-01-24 10:58:08,628] [INFO] Running command: hmmsearch --tblout GCF_900183975.1_PD885.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg522527a9-3885-46ec-9992-e913ccc2abcb/dqc_reference/reference_markers.hmm GCF_900183975.1_PD885.1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:08,895] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:08,896] [INFO] Found 6/6 markers.
[2024-01-24 10:58:08,934] [INFO] Query marker FASTA was written to GCF_900183975.1_PD885.1_genomic.fna/markers.fasta
[2024-01-24 10:58:08,934] [INFO] Task started: Blastn
[2024-01-24 10:58:08,935] [INFO] Running command: blastn -query GCF_900183975.1_PD885.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg522527a9-3885-46ec-9992-e913ccc2abcb/dqc_reference/reference_markers.fasta -out GCF_900183975.1_PD885.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:09,815] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:09,819] [INFO] Selected 13 target genomes.
[2024-01-24 10:58:09,820] [INFO] Target genome list was writen to GCF_900183975.1_PD885.1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:09,826] [INFO] Task started: fastANI
[2024-01-24 10:58:09,826] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5bed869-ba90-4152-af16-8e32b8b3ec44/GCF_900183975.1_PD885.1_genomic.fna.gz --refList GCF_900183975.1_PD885.1_genomic.fna/target_genomes.txt --output GCF_900183975.1_PD885.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:31,782] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:31,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg522527a9-3885-46ec-9992-e913ccc2abcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:31,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg522527a9-3885-46ec-9992-e913ccc2abcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:31,798] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:31,798] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:31,798] [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
Xanthomonas fragariae	strain=PD885	GCA_900183975.1	48664	48664	type	True	100.0	1440	1442	95	conclusive
Xanthomonas fragariae	strain=PD 885	GCA_900380235.1	48664	48664	type	True	99.7893	1166	1442	95	conclusive
Xanthomonas hortorum	strain=WHRI 7744	GCA_003064105.1	56454	56454	suspected-type	True	87.2014	1037	1442	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	87.0986	1086	1442	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	86.987	1050	1442	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	86.9484	1068	1442	95	below_threshold
Xanthomonas arboricola	strain=CFBP 2528	GCA_001013475.1	56448	56448	type	True	86.8572	1060	1442	95	below_threshold
Xanthomonas euroxanthea	strain=CPBF 424	GCA_900476395.1	2259622	2259622	type	True	86.6455	1069	1442	95	below_threshold
Xanthomonas nasturtii	strain=WHRI 8853	GCA_001660815.1	1843581	1843581	type	True	86.3507	1047	1442	95	below_threshold
Xanthomonas vasicola	strain=CFBP2543	GCA_002939925.1	56459	56459	type	True	85.6649	1013	1442	95	below_threshold
Xanthomonas bromi	strain=CFBP1976	GCA_002939755.1	56449	56449	type	True	85.6396	1019	1442	95	below_threshold
Xanthomonas oryzae	strain=WHRI 5234	GCA_003064145.1	347	347	pathovar	True	85.6148	992	1442	95	below_threshold
Xanthomonas bromi		GCA_900092025.1	56449	56449	type	True	85.5765	1036	1442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:31,800] [INFO] DFAST Taxonomy check result was written to GCF_900183975.1_PD885.1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:31,801] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:31,801] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:31,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg522527a9-3885-46ec-9992-e913ccc2abcb/dqc_reference/checkm_data
[2024-01-24 10:58:31,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:31,845] [INFO] Task started: CheckM
[2024-01-24 10:58:31,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900183975.1_PD885.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900183975.1_PD885.1_genomic.fna/checkm_input GCF_900183975.1_PD885.1_genomic.fna/checkm_result
[2024-01-24 10:59:20,383] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:20,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:20,405] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:20,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:20,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900183975.1_PD885.1_genomic.fna/markers.fasta)
[2024-01-24 10:59:20,406] [INFO] Task started: Blastn
[2024-01-24 10:59:20,406] [INFO] Running command: blastn -query GCF_900183975.1_PD885.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg522527a9-3885-46ec-9992-e913ccc2abcb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900183975.1_PD885.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:22,032] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:22,036] [INFO] Selected 13 target genomes.
[2024-01-24 10:59:22,037] [INFO] Target genome list was writen to GCF_900183975.1_PD885.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:22,047] [INFO] Task started: fastANI
[2024-01-24 10:59:22,048] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5bed869-ba90-4152-af16-8e32b8b3ec44/GCF_900183975.1_PD885.1_genomic.fna.gz --refList GCF_900183975.1_PD885.1_genomic.fna/target_genomes_gtdb.txt --output GCF_900183975.1_PD885.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:44,448] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:44,470] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:44,471] [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_900183975.1	s__Xanthomonas fragariae	100.0	1440	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.74	99.53	0.99	0.96	62	conclusive
GCF_017603965.1	s__Xanthomonas fragariae_A	94.8206	1142	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003064105.1	s__Xanthomonas hortorum	87.1789	1040	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	96.0883	96.84	96.16	0.86	0.83	8	-
GCF_002939985.1	s__Xanthomonas hortorum_A	86.9404	1067	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	96.0883	98.80	97.51	0.93	0.89	28	-
GCF_002939945.1	s__Xanthomonas arboricola_A	86.9211	1032	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	95.91	95.91	0.90	0.90	2	-
GCF_905142465.1	s__Xanthomonas sp905142465	86.9143	1079	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.1927	99.49	99.23	0.97	0.96	4	-
GCF_001423495.1	s__Xanthomonas sp001423495	86.8884	1020	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001013475.1	s__Xanthomonas arboricola	86.8635	1061	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.94	96.17	0.91	0.85	117	-
GCF_900476395.1	s__Xanthomonas euroxanthea	86.6342	1070	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.09	97.74	0.93	0.92	25	-
GCF_014197275.1	s__Xanthomonas campestris_B	86.4631	1010	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.71	98.71	0.92	0.92	2	-
GCF_001660815.1	s__Xanthomonas nasturtii	86.3574	1045	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.97	98.97	0.95	0.95	2	-
GCF_000772705.2	s__Xanthomonas vasicola	85.6747	1013	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.75	98.20	0.95	0.92	113	-
GCF_900092025.1	s__Xanthomonas bromi	85.6104	1031	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:44,473] [INFO] GTDB search result was written to GCF_900183975.1_PD885.1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:44,473] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:44,477] [INFO] DFAST_QC result json was written to GCF_900183975.1_PD885.1_genomic.fna/dqc_result.json
[2024-01-24 10:59:44,478] [INFO] DFAST_QC completed!
[2024-01-24 10:59:44,478] [INFO] Total running time: 0h1m54s