[2023-06-18 19:16:57,905] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:16:57,908] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:16:57,909] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb88ddea-7423-4d2d-add0-e5b1995ec740/dqc_reference
[2023-06-18 19:17:01,105] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:17:01,106] [INFO] Task started: Prodigal
[2023-06-18 19:17:01,107] [INFO] Running command: gunzip -c /var/lib/cwl/stg27fca10d-27f9-4d95-bbf9-f494cd2b58e0/GCA_018677755.1_ASM1867775v1_genomic.fna.gz | prodigal -d GCA_018677755.1_ASM1867775v1_genomic.fna/cds.fna -a GCA_018677755.1_ASM1867775v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:17:09,354] [INFO] Task succeeded: Prodigal
[2023-06-18 19:17:09,355] [INFO] Task started: HMMsearch
[2023-06-18 19:17:09,355] [INFO] Running command: hmmsearch --tblout GCA_018677755.1_ASM1867775v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb88ddea-7423-4d2d-add0-e5b1995ec740/dqc_reference/reference_markers.hmm GCA_018677755.1_ASM1867775v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:17:09,672] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:17:09,673] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg27fca10d-27f9-4d95-bbf9-f494cd2b58e0/GCA_018677755.1_ASM1867775v1_genomic.fna.gz]
[2023-06-18 19:17:09,717] [INFO] Query marker FASTA was written to GCA_018677755.1_ASM1867775v1_genomic.fna/markers.fasta
[2023-06-18 19:17:09,718] [INFO] Task started: Blastn
[2023-06-18 19:17:09,718] [INFO] Running command: blastn -query GCA_018677755.1_ASM1867775v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb88ddea-7423-4d2d-add0-e5b1995ec740/dqc_reference/reference_markers.fasta -out GCA_018677755.1_ASM1867775v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:17:10,823] [INFO] Task succeeded: Blastn
[2023-06-18 19:17:10,827] [INFO] Selected 30 target genomes.
[2023-06-18 19:17:10,828] [INFO] Target genome list was writen to GCA_018677755.1_ASM1867775v1_genomic.fna/target_genomes.txt
[2023-06-18 19:17:10,830] [INFO] Task started: fastANI
[2023-06-18 19:17:10,831] [INFO] Running command: fastANI --query /var/lib/cwl/stg27fca10d-27f9-4d95-bbf9-f494cd2b58e0/GCA_018677755.1_ASM1867775v1_genomic.fna.gz --refList GCA_018677755.1_ASM1867775v1_genomic.fna/target_genomes.txt --output GCA_018677755.1_ASM1867775v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:17:32,141] [INFO] Task succeeded: fastANI
[2023-06-18 19:17:32,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb88ddea-7423-4d2d-add0-e5b1995ec740/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:17:32,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb88ddea-7423-4d2d-add0-e5b1995ec740/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:17:32,169] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 19:17:32,169] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 19:17:32,170] [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
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	76.3028	64	854	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	76.2954	81	854	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.2241	85	854	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	76.2171	54	854	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.1964	82	854	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.1439	79	854	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	76.122	75	854	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	76.1144	77	854	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	76.0962	75	854	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	76.0759	69	854	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	76.0517	70	854	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	76.0288	71	854	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	75.9939	65	854	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	75.9227	62	854	95	below_threshold
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	75.9138	53	854	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.8787	86	854	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	75.8138	70	854	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	75.756	73	854	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.7031	54	854	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	75.6143	53	854	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.5147	63	854	95	below_threshold
Pseudomonas entomophila	strain=L48	GCA_000026105.1	312306	312306	suspected-type	True	75.1439	51	854	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 19:17:32,172] [INFO] DFAST Taxonomy check result was written to GCA_018677755.1_ASM1867775v1_genomic.fna/tc_result.tsv
[2023-06-18 19:17:32,172] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:17:32,172] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:17:32,173] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb88ddea-7423-4d2d-add0-e5b1995ec740/dqc_reference/checkm_data
[2023-06-18 19:17:32,174] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:17:32,212] [INFO] Task started: CheckM
[2023-06-18 19:17:32,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018677755.1_ASM1867775v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018677755.1_ASM1867775v1_genomic.fna/checkm_input GCA_018677755.1_ASM1867775v1_genomic.fna/checkm_result
[2023-06-18 19:18:00,671] [INFO] Task succeeded: CheckM
[2023-06-18 19:18:00,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 19:18:00,693] [INFO] ===== Completeness check finished =====
[2023-06-18 19:18:00,693] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:18:00,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018677755.1_ASM1867775v1_genomic.fna/markers.fasta)
[2023-06-18 19:18:00,694] [INFO] Task started: Blastn
[2023-06-18 19:18:00,694] [INFO] Running command: blastn -query GCA_018677755.1_ASM1867775v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb88ddea-7423-4d2d-add0-e5b1995ec740/dqc_reference/reference_markers_gtdb.fasta -out GCA_018677755.1_ASM1867775v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:18:02,329] [INFO] Task succeeded: Blastn
[2023-06-18 19:18:02,334] [INFO] Selected 23 target genomes.
[2023-06-18 19:18:02,335] [INFO] Target genome list was writen to GCA_018677755.1_ASM1867775v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:18:02,342] [INFO] Task started: fastANI
[2023-06-18 19:18:02,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg27fca10d-27f9-4d95-bbf9-f494cd2b58e0/GCA_018677755.1_ASM1867775v1_genomic.fna.gz --refList GCA_018677755.1_ASM1867775v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018677755.1_ASM1867775v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:18:15,541] [INFO] Task succeeded: fastANI
[2023-06-18 19:18:15,559] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 19:18:15,560] [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
GCA_013042915.1	s__JABDPF01 sp013042915	99.5265	714	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__JABDPF01	95.0	99.63	99.57	0.88	0.85	4	conclusive
GCF_008725655.1	s__W260 sp008725655	77.1612	145	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__W260	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001885.1	s__JABDPF01 sp013001885	76.7128	168	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__JABDPF01	95.0	99.83	99.83	0.95	0.93	4	-
GCA_011773845.1	s__WVWV01 sp011773845	76.6774	122	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__WVWV01	95.0	100.00	100.00	0.99	0.98	6	-
GCF_000953855.2	s__Mizugakiibacter sediminis	76.3639	87	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761445.1	s__Oleiagrimonas soli	76.122	75	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018122625.2	s__Coralloluteibacterium stylophorae	76.0818	73	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Coralloluteibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009912395.1	s__Luteibacter sp009912395	75.8958	56	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	75.8787	86	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007135935.1	s__Wenzhouxiangella sp007135935	75.8642	53	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103845.1	s__Pseudomonas jinjuensis	75.7531	70	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900104805.1	s__Pseudomonas_K oryzae	75.671	65	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240295.1	s__Plasticicumulans sp003962905	75.6567	62	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCF_018417595.1	s__Pseudomonas_E entomophila_C	75.4316	55	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 19:18:15,562] [INFO] GTDB search result was written to GCA_018677755.1_ASM1867775v1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:18:15,563] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:18:15,571] [INFO] DFAST_QC result json was written to GCA_018677755.1_ASM1867775v1_genomic.fna/dqc_result.json
[2023-06-18 19:18:15,571] [INFO] DFAST_QC completed!
[2023-06-18 19:18:15,571] [INFO] Total running time: 0h1m18s