[2024-01-24 12:22:38,044] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:38,045] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:38,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg31e6acb0-430a-4324-8666-b8d6f5da644e/dqc_reference
[2024-01-24 12:22:39,350] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:39,351] [INFO] Task started: Prodigal
[2024-01-24 12:22:39,352] [INFO] Running command: gunzip -c /var/lib/cwl/stg46615c45-3b27-4f06-a956-78f6e95b387b/GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/cds.fna -a GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:53,121] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:53,121] [INFO] Task started: HMMsearch
[2024-01-24 12:22:53,121] [INFO] Running command: hmmsearch --tblout GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31e6acb0-430a-4324-8666-b8d6f5da644e/dqc_reference/reference_markers.hmm GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:53,389] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:53,390] [INFO] Found 6/6 markers.
[2024-01-24 12:22:53,426] [INFO] Query marker FASTA was written to GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:22:53,427] [INFO] Task started: Blastn
[2024-01-24 12:22:53,427] [INFO] Running command: blastn -query GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg31e6acb0-430a-4324-8666-b8d6f5da644e/dqc_reference/reference_markers.fasta -out GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:54,356] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:54,360] [INFO] Selected 24 target genomes.
[2024-01-24 12:22:54,361] [INFO] Target genome list was writen to GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:22:54,370] [INFO] Task started: fastANI
[2024-01-24 12:22:54,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg46615c45-3b27-4f06-a956-78f6e95b387b/GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna.gz --refList GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:14,725] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:14,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31e6acb0-430a-4324-8666-b8d6f5da644e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:14,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31e6acb0-430a-4324-8666-b8d6f5da644e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:14,743] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:23:14,743] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:14,744] [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
Pseudoxanthomonas indica	strain=P15	GCA_900167565.1	428993	428993	type	True	100.0	1318	1318	95	conclusive
Pseudoxanthomonas indica	strain=CCM 7430	GCA_014635165.1	428993	428993	type	True	99.99	1312	1318	95	conclusive
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	83.8894	915	1318	95	below_threshold
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	82.1787	736	1318	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	82.133	774	1318	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	82.1297	781	1318	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	82.1263	779	1318	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	81.0877	689	1318	95	below_threshold
Pseudoxanthomonas dokdonensis	strain=DSM 21858	GCA_001431405.1	344882	344882	type	True	81.0219	705	1318	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	81.0136	668	1318	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	80.961	663	1318	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	80.9545	692	1318	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	80.9229	581	1318	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	80.7164	635	1318	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	80.6523	559	1318	95	below_threshold
Pseudoxanthomonas composti	strain=GSS15	GCA_004122095.1	2137479	2137479	type	True	80.6108	668	1318	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	80.1994	577	1318	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	80.1119	575	1318	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	80.0861	602	1318	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	80.0518	612	1318	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	79.9317	495	1318	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	79.771	487	1318	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	79.2585	482	1318	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	79.1903	446	1318	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:14,745] [INFO] DFAST Taxonomy check result was written to GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:23:14,746] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:14,746] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:14,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31e6acb0-430a-4324-8666-b8d6f5da644e/dqc_reference/checkm_data
[2024-01-24 12:23:14,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:14,787] [INFO] Task started: CheckM
[2024-01-24 12:23:14,787] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/checkm_input GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:24:10,595] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:10,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:10,620] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:10,620] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:10,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:24:10,621] [INFO] Task started: Blastn
[2024-01-24 12:24:10,621] [INFO] Running command: blastn -query GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg31e6acb0-430a-4324-8666-b8d6f5da644e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:12,227] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:12,230] [INFO] Selected 20 target genomes.
[2024-01-24 12:24:12,230] [INFO] Target genome list was writen to GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:12,248] [INFO] Task started: fastANI
[2024-01-24 12:24:12,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg46615c45-3b27-4f06-a956-78f6e95b387b/GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna.gz --refList GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:29,697] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:29,723] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:29,723] [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_900167565.1	s__Pseudoxanthomonas_A indica	100.0	1318	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_019218945.1	s__Pseudoxanthomonas_A sp019218945	83.9835	908	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.15	98.62	0.97	0.96	4	-
GCF_006542425.1	s__Pseudoxanthomonas_A sp006542425	83.6118	927	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427635.1	s__Pseudoxanthomonas_A sp001427635	82.1734	771	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093385.1	s__Pseudoxanthomonas_A mexicana	82.1727	735	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.97	96.88	0.87	0.86	4	-
GCF_010093445.1	s__Pseudoxanthomonas_A japonensis	82.1287	779	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.78	96.68	0.83	0.68	4	-
GCF_900215535.1	s__Pseudoxanthomonas_A wuyuanensis	82.1195	780	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001427585.1	s__Pseudoxanthomonas_A sp001427585	81.9849	776	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851805.1	s__Pseudoxanthomonas_A sp014851805	81.8949	783	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104255.1	s__Pseudoxanthomonas_A sp900104255	81.8534	800	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716465.1	s__Pseudoxanthomonas_A sp006716465	81.5688	776	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003505795.1	s__UBA8801 sp003505795	81.3822	417	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__UBA8801	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431405.1	s__Pseudoxanthomonas_A dokdonensis	81.0304	704	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002940085.1	s__Xanthomonas_A sacchari	80.9674	691	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	97.45	95.41	0.95	0.91	6	-
GCF_900109775.1	s__Pseudoxanthomonas_A sp900109775	80.9057	635	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002893095.1	s__Stenotrophomonas sp002893095	80.5862	626	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.47	97.41	0.90	0.90	3	-
GCF_900107375.1	s__Lysobacter sp900107375	80.3931	633	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814555.1	s__Lysobacter tengchongensis	80.0666	605	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004352825.1	s__Luteimonas arsenica	79.9382	494	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652935.1	s__Luteimonas padinae	79.7722	487	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:29,725] [INFO] GTDB search result was written to GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:29,725] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:29,731] [INFO] DFAST_QC result json was written to GCF_900167565.1_IMG-taxon_2708742389_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:24:29,731] [INFO] DFAST_QC completed!
[2024-01-24 12:24:29,731] [INFO] Total running time: 0h1m52s