[2024-01-24 13:32:18,336] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:18,338] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:18,338] [INFO] DQC Reference Directory: /var/lib/cwl/stg5056d3b3-13a9-4db5-b9d9-b38624c453ef/dqc_reference
[2024-01-24 13:32:19,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:19,684] [INFO] Task started: Prodigal
[2024-01-24 13:32:19,684] [INFO] Running command: gunzip -c /var/lib/cwl/stge9f57d0b-61e7-48a3-bb9d-93d11343c14e/GCF_004358165.1_ASM435816v1_genomic.fna.gz | prodigal -d GCF_004358165.1_ASM435816v1_genomic.fna/cds.fna -a GCF_004358165.1_ASM435816v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:30,713] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:30,713] [INFO] Task started: HMMsearch
[2024-01-24 13:32:30,713] [INFO] Running command: hmmsearch --tblout GCF_004358165.1_ASM435816v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5056d3b3-13a9-4db5-b9d9-b38624c453ef/dqc_reference/reference_markers.hmm GCF_004358165.1_ASM435816v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:30,974] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:30,975] [INFO] Found 6/6 markers.
[2024-01-24 13:32:31,005] [INFO] Query marker FASTA was written to GCF_004358165.1_ASM435816v1_genomic.fna/markers.fasta
[2024-01-24 13:32:31,006] [INFO] Task started: Blastn
[2024-01-24 13:32:31,006] [INFO] Running command: blastn -query GCF_004358165.1_ASM435816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5056d3b3-13a9-4db5-b9d9-b38624c453ef/dqc_reference/reference_markers.fasta -out GCF_004358165.1_ASM435816v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:32,033] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:32,036] [INFO] Selected 14 target genomes.
[2024-01-24 13:32:32,037] [INFO] Target genome list was writen to GCF_004358165.1_ASM435816v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:32,042] [INFO] Task started: fastANI
[2024-01-24 13:32:32,042] [INFO] Running command: fastANI --query /var/lib/cwl/stge9f57d0b-61e7-48a3-bb9d-93d11343c14e/GCF_004358165.1_ASM435816v1_genomic.fna.gz --refList GCF_004358165.1_ASM435816v1_genomic.fna/target_genomes.txt --output GCF_004358165.1_ASM435816v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:44,105] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:44,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5056d3b3-13a9-4db5-b9d9-b38624c453ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:44,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5056d3b3-13a9-4db5-b9d9-b38624c453ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:44,118] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:44,118] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:44,119] [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
Luteimonas terrae	strain=THG-MD21	GCA_004358165.1	1530191	1530191	type	True	100.0	1183	1183	95	conclusive
Luteimonas fraxinea	strain=D4P002	GCA_021233355.1	2901869	2901869	type	True	87.1968	1013	1183	95	below_threshold
Luteimonas chenhongjianii	strain=100111	GCA_002327105.1	2006110	2006110	type	True	84.8705	854	1183	95	below_threshold
Luteimonas deserti	strain=SJ-16	GCA_013425765.1	2752306	2752306	type	True	84.0557	846	1183	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	82.3121	731	1183	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	81.4861	605	1183	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	81.3614	639	1183	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.0891	655	1183	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	80.8251	552	1183	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.7557	551	1183	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	80.6629	650	1183	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	80.5187	598	1183	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	80.4802	533	1183	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	80.0825	675	1183	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:44,120] [INFO] DFAST Taxonomy check result was written to GCF_004358165.1_ASM435816v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:44,123] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:44,123] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:44,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5056d3b3-13a9-4db5-b9d9-b38624c453ef/dqc_reference/checkm_data
[2024-01-24 13:32:44,124] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:44,164] [INFO] Task started: CheckM
[2024-01-24 13:32:44,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004358165.1_ASM435816v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004358165.1_ASM435816v1_genomic.fna/checkm_input GCF_004358165.1_ASM435816v1_genomic.fna/checkm_result
[2024-01-24 13:33:44,100] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:44,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:44,127] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:44,128] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:44,128] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004358165.1_ASM435816v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:44,129] [INFO] Task started: Blastn
[2024-01-24 13:33:44,129] [INFO] Running command: blastn -query GCF_004358165.1_ASM435816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5056d3b3-13a9-4db5-b9d9-b38624c453ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_004358165.1_ASM435816v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:46,221] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:46,234] [INFO] Selected 10 target genomes.
[2024-01-24 13:33:46,235] [INFO] Target genome list was writen to GCF_004358165.1_ASM435816v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:46,257] [INFO] Task started: fastANI
[2024-01-24 13:33:46,258] [INFO] Running command: fastANI --query /var/lib/cwl/stge9f57d0b-61e7-48a3-bb9d-93d11343c14e/GCF_004358165.1_ASM435816v1_genomic.fna.gz --refList GCF_004358165.1_ASM435816v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004358165.1_ASM435816v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:55,473] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:55,490] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:55,491] [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_004358165.1	s__Luteimonas terrae	100.0	1183	1183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	96.65	96.65	0.95	0.95	2	conclusive
GCA_002307375.1	s__Luteimonas sp002307375	87.1573	929	1183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506295.1	s__Luteimonas sp902506295	87.0348	946	1183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002324875.1	s__Luteimonas sp002324875	85.4317	856	1183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_001014645.1	s__Luteimonas sp001014645	84.942	867	1183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002327105.1	s__Luteimonas chenhongjianii	84.8959	851	1183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	98.75	98.75	0.95	0.95	2	-
GCF_002849595.1	s__Luteimonas sp002849595	84.5463	870	1183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.97	99.97	0.99	0.99	2	-
GCF_013425765.1	s__Luteimonas sp013425765	84.0675	845	1183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192745.1	s__Luteimonas sp014192745	83.9042	860	1183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002240395.1	s__Luteimonas citri_A	83.7759	846	1183	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 13:33:55,493] [INFO] GTDB search result was written to GCF_004358165.1_ASM435816v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:55,493] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:55,498] [INFO] DFAST_QC result json was written to GCF_004358165.1_ASM435816v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:55,498] [INFO] DFAST_QC completed!
[2024-01-24 13:33:55,498] [INFO] Total running time: 0h1m37s