[2024-01-25 20:27:05,573] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:05,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:05,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f6348ba-2fef-405a-8384-fbf0c884d3b8/dqc_reference
[2024-01-25 20:27:06,771] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:06,772] [INFO] Task started: Prodigal
[2024-01-25 20:27:06,772] [INFO] Running command: gunzip -c /var/lib/cwl/stg508c0792-d534-4319-8615-f1c43061ae0c/GCF_022419205.1_ASM2241920v1_genomic.fna.gz | prodigal -d GCF_022419205.1_ASM2241920v1_genomic.fna/cds.fna -a GCF_022419205.1_ASM2241920v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:13,495] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:13,496] [INFO] Task started: HMMsearch
[2024-01-25 20:27:13,496] [INFO] Running command: hmmsearch --tblout GCF_022419205.1_ASM2241920v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f6348ba-2fef-405a-8384-fbf0c884d3b8/dqc_reference/reference_markers.hmm GCF_022419205.1_ASM2241920v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:13,674] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:13,675] [INFO] Found 6/6 markers.
[2024-01-25 20:27:13,698] [INFO] Query marker FASTA was written to GCF_022419205.1_ASM2241920v1_genomic.fna/markers.fasta
[2024-01-25 20:27:13,698] [INFO] Task started: Blastn
[2024-01-25 20:27:13,698] [INFO] Running command: blastn -query GCF_022419205.1_ASM2241920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f6348ba-2fef-405a-8384-fbf0c884d3b8/dqc_reference/reference_markers.fasta -out GCF_022419205.1_ASM2241920v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:14,596] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:14,599] [INFO] Selected 12 target genomes.
[2024-01-25 20:27:14,599] [INFO] Target genome list was writen to GCF_022419205.1_ASM2241920v1_genomic.fna/target_genomes.txt
[2024-01-25 20:27:14,608] [INFO] Task started: fastANI
[2024-01-25 20:27:14,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg508c0792-d534-4319-8615-f1c43061ae0c/GCF_022419205.1_ASM2241920v1_genomic.fna.gz --refList GCF_022419205.1_ASM2241920v1_genomic.fna/target_genomes.txt --output GCF_022419205.1_ASM2241920v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:27:22,511] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:22,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f6348ba-2fef-405a-8384-fbf0c884d3b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:27:22,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f6348ba-2fef-405a-8384-fbf0c884d3b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:27:22,520] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:27:22,521] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:27:22,521] [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
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	89.9863	685	797	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	89.9401	656	797	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	83.9357	634	797	95	below_threshold
Thermomonas hydrothermalis	strain=DSM 14834	GCA_900129205.1	213588	213588	type	True	83.3822	594	797	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	82.766	564	797	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014652775.1	1463158	1463158	type	True	81.2494	531	797	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	81.1451	450	797	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	80.571	497	797	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	80.5551	463	797	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	80.4015	458	797	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	80.2902	489	797	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	79.767	436	797	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:27:22,522] [INFO] DFAST Taxonomy check result was written to GCF_022419205.1_ASM2241920v1_genomic.fna/tc_result.tsv
[2024-01-25 20:27:22,522] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:27:22,523] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:27:22,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f6348ba-2fef-405a-8384-fbf0c884d3b8/dqc_reference/checkm_data
[2024-01-25 20:27:22,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:27:22,553] [INFO] Task started: CheckM
[2024-01-25 20:27:22,553] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022419205.1_ASM2241920v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022419205.1_ASM2241920v1_genomic.fna/checkm_input GCF_022419205.1_ASM2241920v1_genomic.fna/checkm_result
[2024-01-25 20:27:48,663] [INFO] Task succeeded: CheckM
[2024-01-25 20:27:48,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:27:48,718] [INFO] ===== Completeness check finished =====
[2024-01-25 20:27:48,718] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:27:48,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022419205.1_ASM2241920v1_genomic.fna/markers.fasta)
[2024-01-25 20:27:48,719] [INFO] Task started: Blastn
[2024-01-25 20:27:48,719] [INFO] Running command: blastn -query GCF_022419205.1_ASM2241920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f6348ba-2fef-405a-8384-fbf0c884d3b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_022419205.1_ASM2241920v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:50,567] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:50,577] [INFO] Selected 9 target genomes.
[2024-01-25 20:27:50,577] [INFO] Target genome list was writen to GCF_022419205.1_ASM2241920v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:27:50,592] [INFO] Task started: fastANI
[2024-01-25 20:27:50,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg508c0792-d534-4319-8615-f1c43061ae0c/GCF_022419205.1_ASM2241920v1_genomic.fna.gz --refList GCF_022419205.1_ASM2241920v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022419205.1_ASM2241920v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:27:56,338] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:56,345] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:27:56,345] [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_017305095.1	s__Thermomonas sp017305095	90.472	706	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346265.1	s__Thermomonas haemolytica	89.9892	685	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_014395425.1	s__Thermomonas brevis	84.529	647	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014678725.1	s__Thermomonas sp014678725	84.0644	643	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423885.1	s__Thermomonas fusca	83.9392	634	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	96.57	96.57	0.92	0.92	2	-
GCF_900129205.1	s__Thermomonas hydrothermalis	83.3712	595	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720345.1	s__Thermomonas sp016720345	82.7547	530	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.48	99.08	0.97	0.93	11	-
GCA_017302075.1	s__Thermomonas sp017302075	82.6467	470	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302095.1	s__Thermomonas sp017302095	82.2967	368	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:27:56,346] [INFO] GTDB search result was written to GCF_022419205.1_ASM2241920v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:27:56,347] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:27:56,349] [INFO] DFAST_QC result json was written to GCF_022419205.1_ASM2241920v1_genomic.fna/dqc_result.json
[2024-01-25 20:27:56,350] [INFO] DFAST_QC completed!
[2024-01-25 20:27:56,350] [INFO] Total running time: 0h0m51s