[2024-01-24 14:07:31,029] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:31,031] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:31,031] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f1d2cd8-f7b9-4136-bc66-61701b4ed7ec/dqc_reference
[2024-01-24 14:07:32,313] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:32,314] [INFO] Task started: Prodigal
[2024-01-24 14:07:32,314] [INFO] Running command: gunzip -c /var/lib/cwl/stg924e982d-c0ed-43b3-8533-3a5325f7f83a/GCF_009192945.1_ASM919294v1_genomic.fna.gz | prodigal -d GCF_009192945.1_ASM919294v1_genomic.fna/cds.fna -a GCF_009192945.1_ASM919294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:52,738] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:52,739] [INFO] Task started: HMMsearch
[2024-01-24 14:07:52,739] [INFO] Running command: hmmsearch --tblout GCF_009192945.1_ASM919294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f1d2cd8-f7b9-4136-bc66-61701b4ed7ec/dqc_reference/reference_markers.hmm GCF_009192945.1_ASM919294v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:53,042] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:53,043] [INFO] Found 6/6 markers.
[2024-01-24 14:07:53,086] [INFO] Query marker FASTA was written to GCF_009192945.1_ASM919294v1_genomic.fna/markers.fasta
[2024-01-24 14:07:53,086] [INFO] Task started: Blastn
[2024-01-24 14:07:53,086] [INFO] Running command: blastn -query GCF_009192945.1_ASM919294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f1d2cd8-f7b9-4136-bc66-61701b4ed7ec/dqc_reference/reference_markers.fasta -out GCF_009192945.1_ASM919294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:54,044] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:54,047] [INFO] Selected 23 target genomes.
[2024-01-24 14:07:54,047] [INFO] Target genome list was writen to GCF_009192945.1_ASM919294v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:54,108] [INFO] Task started: fastANI
[2024-01-24 14:07:54,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg924e982d-c0ed-43b3-8533-3a5325f7f83a/GCF_009192945.1_ASM919294v1_genomic.fna.gz --refList GCF_009192945.1_ASM919294v1_genomic.fna/target_genomes.txt --output GCF_009192945.1_ASM919294v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:08:19,181] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:19,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f1d2cd8-f7b9-4136-bc66-61701b4ed7ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:08:19,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f1d2cd8-f7b9-4136-bc66-61701b4ed7ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:08:19,200] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:08:19,200] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:08:19,200] [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=LMG 27592	GCA_009192945.1	1321368	1321368	type	True	100.0	1664	1667	95	conclusive
Xanthomonas maliensis	strain=M97	GCA_000401255.1	1321368	1321368	type	True	99.5187	1098	1667	95	conclusive
Xanthomonas euroxanthea	strain=CPBF 424	GCA_900476395.1	2259622	2259622	type	True	84.3251	1137	1667	95	below_threshold
Xanthomonas euvesicatoria pv. alfalfae	strain=CFBP 3836	GCA_000488955.1	359387	456327	pathovar	True	83.9727	1195	1667	95	below_threshold
Xanthomonas euvesicatoria pv. alfalfae	strain=CFBP3836	GCA_017724035.1	359387	456327	pathovar	True	83.9659	1202	1667	95	below_threshold
Xanthomonas euvesicatoria	strain=LMG 27970	GCA_001401555.1	456327	456327	type	True	83.8841	888	1667	95	below_threshold
Xanthomonas floridensis	strain=WHRI 8848	GCA_001642575.1	1843580	1843580	type	True	83.8777	1187	1667	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	83.8754	1166	1667	95	below_threshold
Xanthomonas phaseoli	strain=NCPPB 1833	GCA_017746675.1	1985254	1985254	pathovar	True	83.8628	1192	1667	95	below_threshold
Xanthomonas phaseoli	strain=LMG 695	GCA_001402235.1	1985254	1985254	pathovar	True	83.8292	1105	1667	95	below_threshold
Xanthomonas phaseoli	strain=LMG 695	GCA_001564415.1	1985254	1985254	pathovar	True	83.819	1198	1667	95	below_threshold
Xanthomonas citri	strain=LMG872	GCA_020011215.1	346	346	pathovar	True	83.7404	1097	1667	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	83.7403	1136	1667	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	83.709	1178	1667	95	below_threshold
Xanthomonas campestris	strain=NCPPB 528	GCA_020813135.1	339	339	type	True	83.6344	1122	1667	95	below_threshold
Xanthomonas nasturtii	strain=WHRI 8853	GCA_001660815.1	1843581	1843581	type	True	83.6281	1094	1667	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	83.5565	1122	1667	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	83.4964	1125	1667	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.3082	969	1667	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	82.2446	997	1667	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	81.9318	810	1667	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	81.2933	678	1667	95	below_threshold
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	81.2435	666	1667	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:08:19,202] [INFO] DFAST Taxonomy check result was written to GCF_009192945.1_ASM919294v1_genomic.fna/tc_result.tsv
[2024-01-24 14:08:19,203] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:08:19,203] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:08:19,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f1d2cd8-f7b9-4136-bc66-61701b4ed7ec/dqc_reference/checkm_data
[2024-01-24 14:08:19,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:08:19,255] [INFO] Task started: CheckM
[2024-01-24 14:08:19,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009192945.1_ASM919294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009192945.1_ASM919294v1_genomic.fna/checkm_input GCF_009192945.1_ASM919294v1_genomic.fna/checkm_result
[2024-01-24 14:09:26,316] [INFO] Task succeeded: CheckM
[2024-01-24 14:09:26,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:09:26,342] [INFO] ===== Completeness check finished =====
[2024-01-24 14:09:26,342] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:09:26,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009192945.1_ASM919294v1_genomic.fna/markers.fasta)
[2024-01-24 14:09:26,343] [INFO] Task started: Blastn
[2024-01-24 14:09:26,343] [INFO] Running command: blastn -query GCF_009192945.1_ASM919294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f1d2cd8-f7b9-4136-bc66-61701b4ed7ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_009192945.1_ASM919294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:09:28,047] [INFO] Task succeeded: Blastn
[2024-01-24 14:09:28,050] [INFO] Selected 22 target genomes.
[2024-01-24 14:09:28,051] [INFO] Target genome list was writen to GCF_009192945.1_ASM919294v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:09:28,072] [INFO] Task started: fastANI
[2024-01-24 14:09:28,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg924e982d-c0ed-43b3-8533-3a5325f7f83a/GCF_009192945.1_ASM919294v1_genomic.fna.gz --refList GCF_009192945.1_ASM919294v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009192945.1_ASM919294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:51,724] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:51,748] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:51,748] [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	100.0	1664	1667	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_900476395.1	s__Xanthomonas euroxanthea	84.3368	1135	1667	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	84.2436	1152	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012848175.1	s__Xanthomonas campestris_C	84.208	1159	1667	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	84.2025	1132	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002940015.1	s__Xanthomonas melonis	84.0616	1122	1667	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	83.9958	1150	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.94	96.17	0.91	0.85	117	-
GCF_013112235.1	s__Xanthomonas perforans	83.9537	1196	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.28	96.72	0.95	0.89	246	-
GCF_003999565.1	s__Xanthomonas phaseoli	83.9275	1172	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.19	96.38	0.95	0.90	158	-
GCF_001642575.1	s__Xanthomonas floridensis	83.8614	1190	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905142465.1	s__Xanthomonas sp905142465	83.738	1141	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.1927	99.49	99.23	0.97	0.96	4	-
GCF_001304695.1	s__Xanthomonas axonopodis	83.7012	1005	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.43	97.90	0.94	0.92	5	-
GCF_002939885.1	s__Xanthomonas cucurbitae	83.6613	1058	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	99.30	0.96	0.96	2	-
GCF_001660815.1	s__Xanthomonas nasturtii	83.6219	1095	1667	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	83.5808	1097	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	96.0883	98.80	97.51	0.93	0.89	28	-
GCF_014197275.1	s__Xanthomonas campestris_B	83.5739	1144	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.71	98.71	0.92	0.92	2	-
GCF_000007145.1	s__Xanthomonas campestris	83.5574	1134	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.22	96.56	0.94	0.87	68	-
GCA_003505795.1	s__UBA8801 sp003505795	83.0468	529	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__UBA8801	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008119715.1	s__Xanthomonas_A sontii	82.2092	890	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	97.63	96.72	0.89	0.85	12	-
GCA_002429615.1	s__Stenotrophomonas_A sp002429615	81.9675	672	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216795.1	s__Stenotrophomonas_A sp004216795	81.9216	782	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431645.1	s__Stenotrophomonas_A panacihumi	81.8784	762	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:51,750] [INFO] GTDB search result was written to GCF_009192945.1_ASM919294v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:51,750] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:51,755] [INFO] DFAST_QC result json was written to GCF_009192945.1_ASM919294v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:51,755] [INFO] DFAST_QC completed!
[2024-01-24 14:09:51,756] [INFO] Total running time: 0h2m21s