[2024-01-24 10:47:24,494] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,496] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,496] [INFO] DQC Reference Directory: /var/lib/cwl/stge600a245-813f-4f68-a2d4-c7ba7b1e7463/dqc_reference
[2024-01-24 10:47:26,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,533] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,533] [INFO] Running command: gunzip -c /var/lib/cwl/stgffc5baf9-ae33-4110-93e0-2135a63c7318/GCF_014268445.2_ASM1426844v2_genomic.fna.gz | prodigal -d GCF_014268445.2_ASM1426844v2_genomic.fna/cds.fna -a GCF_014268445.2_ASM1426844v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:56,047] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:56,047] [INFO] Task started: HMMsearch
[2024-01-24 10:47:56,047] [INFO] Running command: hmmsearch --tblout GCF_014268445.2_ASM1426844v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge600a245-813f-4f68-a2d4-c7ba7b1e7463/dqc_reference/reference_markers.hmm GCF_014268445.2_ASM1426844v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:56,399] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:56,403] [INFO] Found 6/6 markers.
[2024-01-24 10:47:56,458] [INFO] Query marker FASTA was written to GCF_014268445.2_ASM1426844v2_genomic.fna/markers.fasta
[2024-01-24 10:47:56,459] [INFO] Task started: Blastn
[2024-01-24 10:47:56,459] [INFO] Running command: blastn -query GCF_014268445.2_ASM1426844v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge600a245-813f-4f68-a2d4-c7ba7b1e7463/dqc_reference/reference_markers.fasta -out GCF_014268445.2_ASM1426844v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:57,445] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:57,449] [INFO] Selected 11 target genomes.
[2024-01-24 10:47:57,449] [INFO] Target genome list was writen to GCF_014268445.2_ASM1426844v2_genomic.fna/target_genomes.txt
[2024-01-24 10:47:57,455] [INFO] Task started: fastANI
[2024-01-24 10:47:57,455] [INFO] Running command: fastANI --query /var/lib/cwl/stgffc5baf9-ae33-4110-93e0-2135a63c7318/GCF_014268445.2_ASM1426844v2_genomic.fna.gz --refList GCF_014268445.2_ASM1426844v2_genomic.fna/target_genomes.txt --output GCF_014268445.2_ASM1426844v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:19,039] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:19,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge600a245-813f-4f68-a2d4-c7ba7b1e7463/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:19,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge600a245-813f-4f68-a2d4-c7ba7b1e7463/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:19,049] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:19,050] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:19,050] [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
Pseudomonas tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	100.0	2206	2207	95	conclusive
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	94.2287	1978	2207	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	92.8028	1889	2207	95	below_threshold
Pseudomonas zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	92.7396	1858	2207	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	92.4974	1846	2207	95	below_threshold
Pseudomonas baetica	strain=a390	GCA_003031005.1	674054	674054	type	True	89.5269	1713	2207	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	89.5248	1718	2207	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	88.1355	1635	2207	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.0675	1723	2207	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.1503	1302	2207	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.4808	838	2207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:19,052] [INFO] DFAST Taxonomy check result was written to GCF_014268445.2_ASM1426844v2_genomic.fna/tc_result.tsv
[2024-01-24 10:48:19,052] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:19,052] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:19,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge600a245-813f-4f68-a2d4-c7ba7b1e7463/dqc_reference/checkm_data
[2024-01-24 10:48:19,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:19,117] [INFO] Task started: CheckM
[2024-01-24 10:48:19,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014268445.2_ASM1426844v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014268445.2_ASM1426844v2_genomic.fna/checkm_input GCF_014268445.2_ASM1426844v2_genomic.fna/checkm_result
[2024-01-24 10:49:41,612] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:41,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:41,635] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:41,635] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:41,636] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014268445.2_ASM1426844v2_genomic.fna/markers.fasta)
[2024-01-24 10:49:41,636] [INFO] Task started: Blastn
[2024-01-24 10:49:41,636] [INFO] Running command: blastn -query GCF_014268445.2_ASM1426844v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge600a245-813f-4f68-a2d4-c7ba7b1e7463/dqc_reference/reference_markers_gtdb.fasta -out GCF_014268445.2_ASM1426844v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:43,310] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:43,314] [INFO] Selected 14 target genomes.
[2024-01-24 10:49:43,314] [INFO] Target genome list was writen to GCF_014268445.2_ASM1426844v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:43,324] [INFO] Task started: fastANI
[2024-01-24 10:49:43,324] [INFO] Running command: fastANI --query /var/lib/cwl/stgffc5baf9-ae33-4110-93e0-2135a63c7318/GCF_014268445.2_ASM1426844v2_genomic.fna.gz --refList GCF_014268445.2_ASM1426844v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014268445.2_ASM1426844v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:13,176] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:13,191] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:13,191] [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_014268445.2	s__Pseudomonas_E sp900187515	100.0	2206	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.92	96.07	0.93	0.91	8	conclusive
GCF_013433315.1	s__Pseudomonas_E crudilactis	94.2304	1977	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	98.37	0.96	0.95	4	-
GCF_004011755.1	s__Pseudomonas_E sp004011755	93.6682	1941	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.20	98.13	0.94	0.93	4	-
GCF_018138145.1	s__Pseudomonas_E koreensis_A	93.6062	1934	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	97.00	0.95	0.94	5	-
GCF_000783395.1	s__Pseudomonas_E helmanticensis	93.5775	1852	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.23	95.21	0.89	0.89	3	-
GCF_900580865.1	s__Pseudomonas_E sp900580865	93.5025	1883	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053805.1	s__Pseudomonas_E sp003053805	93.2439	1902	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.38	98.38	0.96	0.96	2	-
GCF_900187605.1	s__Pseudomonas_E sp900187605	93.0992	1885	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.55	98.53	0.93	0.93	4	-
GCF_902497745.1	s__Pseudomonas_E fluorescens_BM	93.0351	1914	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938625.1	s__Pseudomonas_E fluorescens_BD	92.7764	1843	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015461835.1	s__Pseudomonas_E neuropathica	92.4974	1846	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.00	95.48	0.91	0.90	7	-
GCF_001648775.1	s__Pseudomonas_E fluorescens_M	91.5584	1865	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001297015.1	s__Pseudomonas_E sp001297015	91.4567	1801	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	98.77	0.95	0.94	9	-
GCF_000282515.1	s__Pseudomonas_E sp000282515	90.4786	1675	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.31	97.31	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:13,193] [INFO] GTDB search result was written to GCF_014268445.2_ASM1426844v2_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:13,193] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:13,197] [INFO] DFAST_QC result json was written to GCF_014268445.2_ASM1426844v2_genomic.fna/dqc_result.json
[2024-01-24 10:50:13,197] [INFO] DFAST_QC completed!
[2024-01-24 10:50:13,197] [INFO] Total running time: 0h2m49s