[2024-01-25 19:52:05,464] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:52:05,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:52:05,465] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa5334df-807a-4a3e-9151-281d28efcd21/dqc_reference
[2024-01-25 19:52:06,603] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:52:06,603] [INFO] Task started: Prodigal
[2024-01-25 19:52:06,604] [INFO] Running command: gunzip -c /var/lib/cwl/stg30601007-bd1a-4120-a714-0f3bea83395e/GCF_018406645.1_ASM1840664v1_genomic.fna.gz | prodigal -d GCF_018406645.1_ASM1840664v1_genomic.fna/cds.fna -a GCF_018406645.1_ASM1840664v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:16,622] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:16,622] [INFO] Task started: HMMsearch
[2024-01-25 19:52:16,622] [INFO] Running command: hmmsearch --tblout GCF_018406645.1_ASM1840664v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa5334df-807a-4a3e-9151-281d28efcd21/dqc_reference/reference_markers.hmm GCF_018406645.1_ASM1840664v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:16,889] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:16,891] [INFO] Found 6/6 markers.
[2024-01-25 19:52:16,920] [INFO] Query marker FASTA was written to GCF_018406645.1_ASM1840664v1_genomic.fna/markers.fasta
[2024-01-25 19:52:16,921] [INFO] Task started: Blastn
[2024-01-25 19:52:16,921] [INFO] Running command: blastn -query GCF_018406645.1_ASM1840664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa5334df-807a-4a3e-9151-281d28efcd21/dqc_reference/reference_markers.fasta -out GCF_018406645.1_ASM1840664v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:17,800] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:17,803] [INFO] Selected 24 target genomes.
[2024-01-25 19:52:17,804] [INFO] Target genome list was writen to GCF_018406645.1_ASM1840664v1_genomic.fna/target_genomes.txt
[2024-01-25 19:52:17,823] [INFO] Task started: fastANI
[2024-01-25 19:52:17,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg30601007-bd1a-4120-a714-0f3bea83395e/GCF_018406645.1_ASM1840664v1_genomic.fna.gz --refList GCF_018406645.1_ASM1840664v1_genomic.fna/target_genomes.txt --output GCF_018406645.1_ASM1840664v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:35,617] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:35,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa5334df-807a-4a3e-9151-281d28efcd21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:35,618] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa5334df-807a-4a3e-9151-281d28efcd21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:35,632] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:52:35,632] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:52:35,632] [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
Lysobacter gilvus	strain=HX-5-24	GCA_009740395.1	2682097	2682097	type	True	84.9427	782	1090	95	below_threshold
Lysobacter dokdonensis	strain=DS-58	GCA_000770795.1	414050	414050	type	True	84.8325	778	1090	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	81.5869	609	1090	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	81.505	545	1090	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	81.2853	545	1090	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	81.251	537	1090	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	81.0101	591	1090	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	81.0059	556	1090	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.9755	559	1090	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	80.9037	552	1090	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.8968	511	1090	95	below_threshold
Lysobacter prati	strain=SYSU H10001	GCA_009765215.1	2596704	2596704	type	True	80.8755	566	1090	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	80.7123	506	1090	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	80.5971	501	1090	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	80.5833	511	1090	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	80.5568	493	1090	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	80.5382	511	1090	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	80.5266	542	1090	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	80.5143	591	1090	95	below_threshold
Lysobacter daejeonensis	strain=GH1-9	GCA_000768355.1	346181	346181	type	True	80.4843	482	1090	95	below_threshold
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	80.4135	495	1090	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	80.3344	451	1090	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	80.2205	533	1090	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	80.1316	543	1090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:52:35,635] [INFO] DFAST Taxonomy check result was written to GCF_018406645.1_ASM1840664v1_genomic.fna/tc_result.tsv
[2024-01-25 19:52:35,635] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:35,635] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:35,635] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa5334df-807a-4a3e-9151-281d28efcd21/dqc_reference/checkm_data
[2024-01-25 19:52:35,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:35,671] [INFO] Task started: CheckM
[2024-01-25 19:52:35,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018406645.1_ASM1840664v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018406645.1_ASM1840664v1_genomic.fna/checkm_input GCF_018406645.1_ASM1840664v1_genomic.fna/checkm_result
[2024-01-25 19:53:56,200] [INFO] Task succeeded: CheckM
[2024-01-25 19:53:56,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:53:56,219] [INFO] ===== Completeness check finished =====
[2024-01-25 19:53:56,219] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:53:56,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018406645.1_ASM1840664v1_genomic.fna/markers.fasta)
[2024-01-25 19:53:56,220] [INFO] Task started: Blastn
[2024-01-25 19:53:56,221] [INFO] Running command: blastn -query GCF_018406645.1_ASM1840664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa5334df-807a-4a3e-9151-281d28efcd21/dqc_reference/reference_markers_gtdb.fasta -out GCF_018406645.1_ASM1840664v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:57,835] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:57,838] [INFO] Selected 18 target genomes.
[2024-01-25 19:53:57,839] [INFO] Target genome list was writen to GCF_018406645.1_ASM1840664v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:53:57,853] [INFO] Task started: fastANI
[2024-01-25 19:53:57,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg30601007-bd1a-4120-a714-0f3bea83395e/GCF_018406645.1_ASM1840664v1_genomic.fna.gz --refList GCF_018406645.1_ASM1840664v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018406645.1_ASM1840664v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:54:12,406] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:12,417] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:54:12,417] [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_018406645.1	s__Lysobacter_A helvus	100.0	1089	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009740395.1	s__Lysobacter_A gilvus	84.9383	780	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000770795.1	s__Lysobacter_A dokdonensis	84.7945	779	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	81.7835	448	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382285.1	s__Lysobacter soli	81.5897	609	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.84	96.81	0.94	0.93	3	-
GCF_016735495.2	s__Lysobacter sp016735495	81.4978	607	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337105.1	s__Thermomonas sp006337105	81.2613	547	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320095.1	s__Luteimonas_B telluris	81.1883	522	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428685.1	s__Lysobacter sp001428685	80.9843	581	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.42	98.61	0.98	0.96	4	-
GCF_010211755.1	s__Pseudoxanthomonas_A sangjuensis	80.7123	506	1090	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_018612875.1	s__Lysobacter sp018612875	80.7057	552	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.97	0.96	0.96	4	-
GCF_900114355.1	s__Lysobacter sp900114355	80.6881	592	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652935.1	s__Luteimonas padinae	80.605	488	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836665.1	s__Luteimonas sp014836665	80.5773	503	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719825.1	s__Lysobacter psychrotolerans	80.5378	541	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104255.1	s__Pseudoxanthomonas_A sp900104255	80.5112	526	1090	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_016774335.1	s__Luteimonas sp016774335	80.2045	535	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008244685.1	s__Luteimonas sp008244685	80.1124	545	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:54:12,419] [INFO] GTDB search result was written to GCF_018406645.1_ASM1840664v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:54:12,419] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:54:12,423] [INFO] DFAST_QC result json was written to GCF_018406645.1_ASM1840664v1_genomic.fna/dqc_result.json
[2024-01-25 19:54:12,423] [INFO] DFAST_QC completed!
[2024-01-25 19:54:12,424] [INFO] Total running time: 0h2m7s