[2024-01-25 17:51:05,530] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:05,531] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:05,531] [INFO] DQC Reference Directory: /var/lib/cwl/stg806d3263-87dd-4829-8f95-fa091721e74a/dqc_reference
[2024-01-25 17:51:06,651] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:06,651] [INFO] Task started: Prodigal
[2024-01-25 17:51:06,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg2408a9ec-9a8b-45e8-ac8c-520d53e4984e/GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna.gz | prodigal -d GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/cds.fna -a GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:20,395] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:20,395] [INFO] Task started: HMMsearch
[2024-01-25 17:51:20,395] [INFO] Running command: hmmsearch --tblout GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg806d3263-87dd-4829-8f95-fa091721e74a/dqc_reference/reference_markers.hmm GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:20,698] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:20,699] [INFO] Found 6/6 markers.
[2024-01-25 17:51:20,744] [INFO] Query marker FASTA was written to GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/markers.fasta
[2024-01-25 17:51:20,745] [INFO] Task started: Blastn
[2024-01-25 17:51:20,745] [INFO] Running command: blastn -query GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/markers.fasta -db /var/lib/cwl/stg806d3263-87dd-4829-8f95-fa091721e74a/dqc_reference/reference_markers.fasta -out GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:21,582] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:21,584] [INFO] Selected 21 target genomes.
[2024-01-25 17:51:21,585] [INFO] Target genome list was writen to GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/target_genomes.txt
[2024-01-25 17:51:21,594] [INFO] Task started: fastANI
[2024-01-25 17:51:21,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg2408a9ec-9a8b-45e8-ac8c-520d53e4984e/GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna.gz --refList GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/target_genomes.txt --output GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:41,748] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:41,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg806d3263-87dd-4829-8f95-fa091721e74a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:41,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg806d3263-87dd-4829-8f95-fa091721e74a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:41,760] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:51:41,760] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:41,761] [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 maliensis	strain=M97	GCA_000401255.1	1321368	1321368	type	True	100.0	1123	1147	95	conclusive
Xanthomonas maliensis	strain=LMG 27592	GCA_009192945.1	1321368	1321368	type	True	99.9054	1123	1147	95	conclusive
Xanthomonas euroxanthea	strain=CPBF 424	GCA_900476395.1	2259622	2259622	type	True	83.893	859	1147	95	below_threshold
Xanthomonas euvesicatoria pv. alfalfae	strain=CFBP3836	GCA_017724035.1	359387	456327	pathovar	True	83.4957	882	1147	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	83.4872	871	1147	95	below_threshold
Xanthomonas euvesicatoria pv. alfalfae	strain=CFBP 3836	GCA_000488955.1	359387	456327	pathovar	True	83.4766	892	1147	95	below_threshold
Xanthomonas phaseoli	strain=LMG784	GCA_001482665.1	1985254	1985254	pathovar	True	83.4326	860	1147	95	below_threshold
Xanthomonas floridensis	strain=WHRI 8848	GCA_001642575.1	1843580	1843580	type	True	83.423	878	1147	95	below_threshold
Xanthomonas phaseoli	strain=LMG 695	GCA_001564415.1	1985254	1985254	pathovar	True	83.3944	892	1147	95	below_threshold
Xanthomonas phaseoli	strain=LMG 695	GCA_001402235.1	1985254	1985254	pathovar	True	83.2958	840	1147	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	83.2762	852	1147	95	below_threshold
Xanthomonas pisi	strain=DSM 18956	GCA_001010415.1	56457	56457	type	True	83.2383	687	1147	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	83.2092	891	1147	95	below_threshold
Xanthomonas citri	strain=LMG872	GCA_020011215.1	346	346	pathovar	True	83.2063	838	1147	95	below_threshold
Xanthomonas euvesicatoria	strain=LMG 27970	GCA_001401555.1	456327	456327	type	True	83.1607	688	1147	95	below_threshold
Xanthomonas campestris	strain=NCPPB 347	GCA_020731405.1	339	339	pathovar	True	83.0949	844	1147	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	83.0862	836	1147	95	below_threshold
Xanthomonas nasturtii	strain=WHRI 8853	GCA_001660815.1	1843581	1843581	type	True	83.073	828	1147	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	83.0455	842	1147	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	81.7557	758	1147	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	81.3748	617	1147	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:41,762] [INFO] DFAST Taxonomy check result was written to GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/tc_result.tsv
[2024-01-25 17:51:41,762] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:41,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:41,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg806d3263-87dd-4829-8f95-fa091721e74a/dqc_reference/checkm_data
[2024-01-25 17:51:41,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:41,812] [INFO] Task started: CheckM
[2024-01-25 17:51:41,812] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/checkm_input GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/checkm_result
[2024-01-25 17:52:31,476] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:31,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.71%
Contamintation: 3.01%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:31,497] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:31,497] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:31,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/markers.fasta)
[2024-01-25 17:52:31,498] [INFO] Task started: Blastn
[2024-01-25 17:52:31,498] [INFO] Running command: blastn -query GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/markers.fasta -db /var/lib/cwl/stg806d3263-87dd-4829-8f95-fa091721e74a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:33,170] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:33,173] [INFO] Selected 22 target genomes.
[2024-01-25 17:52:33,173] [INFO] Target genome list was writen to GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:33,196] [INFO] Task started: fastANI
[2024-01-25 17:52:33,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg2408a9ec-9a8b-45e8-ac8c-520d53e4984e/GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna.gz --refList GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/target_genomes_gtdb.txt --output GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:55,991] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:56,005] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:56,005] [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_009192945.1	s__Xanthomonas maliensis	99.9054	1123	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.91	99.91	0.98	0.98	2	conclusive
GCF_003353015.1	s__Xanthomonas arboricola_E	83.9662	856	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900476395.1	s__Xanthomonas euroxanthea	83.8819	860	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.09	97.74	0.93	0.92	25	-
GCF_002939785.1	s__Xanthomonas codiaei	83.7181	883	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002940205.1	s__Xanthomonas arboricola_C	83.7076	851	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001013475.1	s__Xanthomonas arboricola	83.6923	863	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.94	96.17	0.91	0.85	117	-
GCF_012848175.1	s__Xanthomonas campestris_C	83.6415	870	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013112235.1	s__Xanthomonas perforans	83.5668	890	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.28	96.72	0.95	0.89	246	-
GCF_002940015.1	s__Xanthomonas melonis	83.5201	847	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642575.1	s__Xanthomonas floridensis	83.423	878	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999565.1	s__Xanthomonas phaseoli	83.3844	887	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.19	96.38	0.95	0.90	158	-
GCF_002939885.1	s__Xanthomonas cucurbitae	83.2735	799	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	99.30	0.96	0.96	2	-
GCF_905142465.1	s__Xanthomonas sp905142465	83.2703	855	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.1927	99.49	99.23	0.97	0.96	4	-
GCF_008801575.1	s__Xanthomonas cissicola	83.2562	861	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	97.71	95.83	0.91	0.86	247	-
GCF_001010415.1	s__Xanthomonas pisi	83.2428	686	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000007145.1	s__Xanthomonas campestris	83.1354	864	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.22	96.56	0.94	0.87	68	-
GCF_014197275.1	s__Xanthomonas campestris_B	83.1043	865	1147	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	83.0729	828	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.97	98.97	0.95	0.95	2	-
GCF_002939985.1	s__Xanthomonas hortorum_A	82.9704	844	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	96.0883	98.80	97.51	0.93	0.89	28	-
GCA_003505795.1	s__UBA8801 sp003505795	82.1548	422	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__UBA8801	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829315.1	s__Xanthomonas_A translucens_A	81.8569	779	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199795.1	s__Xanthomonas_A sp014199795	81.7918	753	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	98.20	98.15	0.95	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:56,007] [INFO] GTDB search result was written to GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:56,008] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:56,012] [INFO] DFAST_QC result json was written to GCF_000401255.1_Xanthomonas_sp._97M_genomic.fna/dqc_result.json
[2024-01-25 17:52:56,012] [INFO] DFAST_QC completed!
[2024-01-25 17:52:56,012] [INFO] Total running time: 0h1m50s