[2024-01-24 14:19:16,084] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:16,086] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:16,086] [INFO] DQC Reference Directory: /var/lib/cwl/stg08d2fa58-6867-4118-911e-bb86421393fc/dqc_reference
[2024-01-24 14:19:17,346] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:17,347] [INFO] Task started: Prodigal
[2024-01-24 14:19:17,347] [INFO] Running command: gunzip -c /var/lib/cwl/stgb28ed804-1a96-466c-a1c0-095b38f7eea7/GCF_000769985.1_ASM76998v1_genomic.fna.gz | prodigal -d GCF_000769985.1_ASM76998v1_genomic.fna/cds.fna -a GCF_000769985.1_ASM76998v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:24,321] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:24,322] [INFO] Task started: HMMsearch
[2024-01-24 14:19:24,322] [INFO] Running command: hmmsearch --tblout GCF_000769985.1_ASM76998v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08d2fa58-6867-4118-911e-bb86421393fc/dqc_reference/reference_markers.hmm GCF_000769985.1_ASM76998v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:24,601] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:24,602] [INFO] Found 6/6 markers.
[2024-01-24 14:19:24,633] [INFO] Query marker FASTA was written to GCF_000769985.1_ASM76998v1_genomic.fna/markers.fasta
[2024-01-24 14:19:24,634] [INFO] Task started: Blastn
[2024-01-24 14:19:24,634] [INFO] Running command: blastn -query GCF_000769985.1_ASM76998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08d2fa58-6867-4118-911e-bb86421393fc/dqc_reference/reference_markers.fasta -out GCF_000769985.1_ASM76998v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:25,636] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:25,641] [INFO] Selected 15 target genomes.
[2024-01-24 14:19:25,641] [INFO] Target genome list was writen to GCF_000769985.1_ASM76998v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:25,647] [INFO] Task started: fastANI
[2024-01-24 14:19:25,647] [INFO] Running command: fastANI --query /var/lib/cwl/stgb28ed804-1a96-466c-a1c0-095b38f7eea7/GCF_000769985.1_ASM76998v1_genomic.fna.gz --refList GCF_000769985.1_ASM76998v1_genomic.fna/target_genomes.txt --output GCF_000769985.1_ASM76998v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:36,153] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:36,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08d2fa58-6867-4118-911e-bb86421393fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:36,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08d2fa58-6867-4118-911e-bb86421393fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:36,173] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:36,173] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:36,174] [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 defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	100.0	702	707	95	conclusive
Lysobacter defluvii	strain=DSM 18482	GCA_000423325.1	391738	391738	type	True	99.9859	706	707	95	conclusive
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	83.7264	488	707	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	82.4067	490	707	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	82.3556	466	707	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.7681	436	707	95	below_threshold
Lysobacter spongiicola	strain=DSM 21749	GCA_900167055.1	435289	435289	type	True	81.7093	482	707	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	81.5127	438	707	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	81.2893	409	707	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.2105	443	707	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	81.1863	440	707	95	below_threshold
Lysobacter antarcticus	strain=GW1-59	GCA_019802285.1	2862543	2862543	type	True	80.7458	387	707	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	80.6099	436	707	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	80.4398	427	707	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	80.3892	350	707	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:36,175] [INFO] DFAST Taxonomy check result was written to GCF_000769985.1_ASM76998v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:36,176] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:36,176] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:36,176] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08d2fa58-6867-4118-911e-bb86421393fc/dqc_reference/checkm_data
[2024-01-24 14:19:36,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:36,206] [INFO] Task started: CheckM
[2024-01-24 14:19:36,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000769985.1_ASM76998v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000769985.1_ASM76998v1_genomic.fna/checkm_input GCF_000769985.1_ASM76998v1_genomic.fna/checkm_result
[2024-01-24 14:20:08,386] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:08,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:08,492] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:08,493] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:08,493] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000769985.1_ASM76998v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:08,493] [INFO] Task started: Blastn
[2024-01-24 14:20:08,493] [INFO] Running command: blastn -query GCF_000769985.1_ASM76998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08d2fa58-6867-4118-911e-bb86421393fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000769985.1_ASM76998v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:11,077] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:11,081] [INFO] Selected 18 target genomes.
[2024-01-24 14:20:11,081] [INFO] Target genome list was writen to GCF_000769985.1_ASM76998v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:11,096] [INFO] Task started: fastANI
[2024-01-24 14:20:11,096] [INFO] Running command: fastANI --query /var/lib/cwl/stgb28ed804-1a96-466c-a1c0-095b38f7eea7/GCF_000769985.1_ASM76998v1_genomic.fna.gz --refList GCF_000769985.1_ASM76998v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000769985.1_ASM76998v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:27,013] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:27,028] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:27,028] [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_000423325.1	s__Lysobacter defluvii	99.9859	706	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000768335.1	s__Lysobacter arseniciresistens	83.7456	487	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907164845.1	s__Lysobacter sp907164845	82.3839	492	707	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	82.3648	466	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_001830245.1	s__Lysobacter sp001830245	81.8838	443	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.71	99.71	0.92	0.92	2	-
GCF_006546735.2	s__Lysobacter maris	81.8804	436	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.39	98.39	0.88	0.88	2	-
GCF_003586305.1	s__Lysobacter tabacisoli	81.701	443	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167055.1	s__Lysobacter spongiicola	81.6741	485	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	81.5296	444	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382365.1	s__Lysobacter silvisoli	81.5288	437	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	81.475	455	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_014145325.1	s__Lysobacter spongiae	81.2172	438	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	81.1114	466	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_004346265.1	s__Thermomonas haemolytica	81.0639	385	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_018847975.1	s__Lysobacter sp018847975	80.8903	434	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829315.1	s__Xanthomonas_A translucens_A	80.8501	436	707	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_017939625.1	s__Pseudoxanthomonas_A helianthi	80.3564	352	707	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_001043115.1	s__Xanthomonas_A sp001043115	80.345	421	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	96.72	96.71	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:27,030] [INFO] GTDB search result was written to GCF_000769985.1_ASM76998v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:27,031] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:27,035] [INFO] DFAST_QC result json was written to GCF_000769985.1_ASM76998v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:27,035] [INFO] DFAST_QC completed!
[2024-01-24 14:20:27,035] [INFO] Total running time: 0h1m11s