[2024-01-24 14:19:01,240] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:01,243] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:01,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg79e820bf-03a6-4796-af7c-8a63aec137b2/dqc_reference
[2024-01-24 14:19:02,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:02,661] [INFO] Task started: Prodigal
[2024-01-24 14:19:02,662] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2347efd-961d-4ecc-b1c2-2007f89058e2/GCF_004361065.1_ASM436106v1_genomic.fna.gz | prodigal -d GCF_004361065.1_ASM436106v1_genomic.fna/cds.fna -a GCF_004361065.1_ASM436106v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:12,780] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:12,780] [INFO] Task started: HMMsearch
[2024-01-24 14:19:12,780] [INFO] Running command: hmmsearch --tblout GCF_004361065.1_ASM436106v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79e820bf-03a6-4796-af7c-8a63aec137b2/dqc_reference/reference_markers.hmm GCF_004361065.1_ASM436106v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:13,070] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:13,071] [INFO] Found 6/6 markers.
[2024-01-24 14:19:13,107] [INFO] Query marker FASTA was written to GCF_004361065.1_ASM436106v1_genomic.fna/markers.fasta
[2024-01-24 14:19:13,107] [INFO] Task started: Blastn
[2024-01-24 14:19:13,108] [INFO] Running command: blastn -query GCF_004361065.1_ASM436106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79e820bf-03a6-4796-af7c-8a63aec137b2/dqc_reference/reference_markers.fasta -out GCF_004361065.1_ASM436106v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:14,207] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:14,210] [INFO] Selected 16 target genomes.
[2024-01-24 14:19:14,211] [INFO] Target genome list was writen to GCF_004361065.1_ASM436106v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:14,217] [INFO] Task started: fastANI
[2024-01-24 14:19:14,217] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2347efd-961d-4ecc-b1c2-2007f89058e2/GCF_004361065.1_ASM436106v1_genomic.fna.gz --refList GCF_004361065.1_ASM436106v1_genomic.fna/target_genomes.txt --output GCF_004361065.1_ASM436106v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:26,831] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:26,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79e820bf-03a6-4796-af7c-8a63aec137b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:26,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79e820bf-03a6-4796-af7c-8a63aec137b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:26,845] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:26,846] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:26,846] [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 terrigena	strain=17J7-1	GCA_004361065.1	2488749	2488749	type	True	100.0	1026	1031	95	conclusive
Lysobacter segetis	strain=17J68-2	GCA_004359965.1	2492394	2492394	type	True	85.1549	757	1031	95	below_threshold
Lysobacter xinjiangensis	strain=KCTC 22558	GCA_014651995.1	546892	546892	type	True	85.0041	760	1031	95	below_threshold
Lysobacter lacus	strain=UKS-15	GCA_008274655.1	1643323	1643323	type	True	83.36	621	1031	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	81.0561	601	1031	95	below_threshold
Lysobacter bugurensis	strain=KCTC 23077	GCA_014652095.1	543356	543356	type	True	80.8688	583	1031	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	80.8186	621	1031	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	80.7554	506	1031	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	80.7148	576	1031	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	80.5477	549	1031	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	80.2723	585	1031	95	below_threshold
Lysobacter solisilvae	strain=R19	GCA_016613535.2	2763317	2763317	type	True	80.1061	532	1031	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	80.0789	571	1031	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.0015	491	1031	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	79.8511	514	1031	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	79.8099	501	1031	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:26,850] [INFO] DFAST Taxonomy check result was written to GCF_004361065.1_ASM436106v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:26,851] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:26,851] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:26,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79e820bf-03a6-4796-af7c-8a63aec137b2/dqc_reference/checkm_data
[2024-01-24 14:19:26,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:26,889] [INFO] Task started: CheckM
[2024-01-24 14:19:26,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004361065.1_ASM436106v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004361065.1_ASM436106v1_genomic.fna/checkm_input GCF_004361065.1_ASM436106v1_genomic.fna/checkm_result
[2024-01-24 14:20:02,155] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:02,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.14%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:02,180] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:02,180] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:02,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004361065.1_ASM436106v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:02,181] [INFO] Task started: Blastn
[2024-01-24 14:20:02,181] [INFO] Running command: blastn -query GCF_004361065.1_ASM436106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79e820bf-03a6-4796-af7c-8a63aec137b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_004361065.1_ASM436106v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:04,279] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:04,282] [INFO] Selected 7 target genomes.
[2024-01-24 14:20:04,282] [INFO] Target genome list was writen to GCF_004361065.1_ASM436106v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:04,303] [INFO] Task started: fastANI
[2024-01-24 14:20:04,304] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2347efd-961d-4ecc-b1c2-2007f89058e2/GCF_004361065.1_ASM436106v1_genomic.fna.gz --refList GCF_004361065.1_ASM436106v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004361065.1_ASM436106v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:10,302] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:10,309] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:10,310] [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_004361065.1	s__Lysobacter terrigena	100.0	1026	1031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003367355.1	s__Lysobacter sp003367355	88.3796	869	1031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426005.1	s__Lysobacter sp000426005	86.695	859	1031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359965.1	s__Lysobacter segetis	85.1411	758	1031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651995.1	s__Lysobacter xinjiangensis	85.0176	759	1031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382285.1	s__Lysobacter soli	80.8533	619	1031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.84	96.81	0.94	0.93	3	-
GCF_015453285.1	s__Lysobacter niastensis	80.7111	576	1031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:10,311] [INFO] GTDB search result was written to GCF_004361065.1_ASM436106v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:10,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:10,315] [INFO] DFAST_QC result json was written to GCF_004361065.1_ASM436106v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:10,316] [INFO] DFAST_QC completed!
[2024-01-24 14:20:10,316] [INFO] Total running time: 0h1m9s