[2024-01-24 13:57:43,774] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,777] [INFO] DQC Reference Directory: /var/lib/cwl/stgf49f2fc8-e871-4207-8d58-53c904fab2d5/dqc_reference
[2024-01-24 13:57:45,037] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,038] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,039] [INFO] Running command: gunzip -c /var/lib/cwl/stg667ee4b3-65ef-4317-a97d-ca25b5f78ec7/GCF_014268485.2_ASM1426848v2_genomic.fna.gz | prodigal -d GCF_014268485.2_ASM1426848v2_genomic.fna/cds.fna -a GCF_014268485.2_ASM1426848v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:11,326] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:11,327] [INFO] Task started: HMMsearch
[2024-01-24 13:58:11,327] [INFO] Running command: hmmsearch --tblout GCF_014268485.2_ASM1426848v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf49f2fc8-e871-4207-8d58-53c904fab2d5/dqc_reference/reference_markers.hmm GCF_014268485.2_ASM1426848v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:11,836] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:11,837] [INFO] Found 6/6 markers.
[2024-01-24 13:58:11,912] [INFO] Query marker FASTA was written to GCF_014268485.2_ASM1426848v2_genomic.fna/markers.fasta
[2024-01-24 13:58:11,912] [INFO] Task started: Blastn
[2024-01-24 13:58:11,913] [INFO] Running command: blastn -query GCF_014268485.2_ASM1426848v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf49f2fc8-e871-4207-8d58-53c904fab2d5/dqc_reference/reference_markers.fasta -out GCF_014268485.2_ASM1426848v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:12,988] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:12,991] [INFO] Selected 11 target genomes.
[2024-01-24 13:58:12,991] [INFO] Target genome list was writen to GCF_014268485.2_ASM1426848v2_genomic.fna/target_genomes.txt
[2024-01-24 13:58:13,008] [INFO] Task started: fastANI
[2024-01-24 13:58:13,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg667ee4b3-65ef-4317-a97d-ca25b5f78ec7/GCF_014268485.2_ASM1426848v2_genomic.fna.gz --refList GCF_014268485.2_ASM1426848v2_genomic.fna/target_genomes.txt --output GCF_014268485.2_ASM1426848v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:36,315] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:36,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf49f2fc8-e871-4207-8d58-53c904fab2d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:36,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf49f2fc8-e871-4207-8d58-53c904fab2d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:36,326] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:58:36,326] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:58:36,327] [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 zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	100.0	2209	2210	95	inconclusive
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	96.1898	1924	2210	95	inconclusive
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	96.167	1960	2210	95	inconclusive
Pseudomonas tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	92.6635	1871	2210	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	92.6156	1849	2210	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	89.4034	1718	2210	95	below_threshold
Pseudomonas baetica	strain=a390	GCA_003031005.1	674054	674054	type	True	89.3392	1690	2210	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.0249	1700	2210	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	87.9786	1632	2210	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	82.9937	1254	2210	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.3764	852	2210	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:36,328] [INFO] DFAST Taxonomy check result was written to GCF_014268485.2_ASM1426848v2_genomic.fna/tc_result.tsv
[2024-01-24 13:58:36,329] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:36,329] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:36,329] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf49f2fc8-e871-4207-8d58-53c904fab2d5/dqc_reference/checkm_data
[2024-01-24 13:58:36,330] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:36,394] [INFO] Task started: CheckM
[2024-01-24 13:58:36,395] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014268485.2_ASM1426848v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014268485.2_ASM1426848v2_genomic.fna/checkm_input GCF_014268485.2_ASM1426848v2_genomic.fna/checkm_result
[2024-01-24 13:59:52,731] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:52,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:52,786] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:52,786] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:52,786] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014268485.2_ASM1426848v2_genomic.fna/markers.fasta)
[2024-01-24 13:59:52,787] [INFO] Task started: Blastn
[2024-01-24 13:59:52,787] [INFO] Running command: blastn -query GCF_014268485.2_ASM1426848v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf49f2fc8-e871-4207-8d58-53c904fab2d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014268485.2_ASM1426848v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:54,810] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:54,814] [INFO] Selected 19 target genomes.
[2024-01-24 13:59:54,814] [INFO] Target genome list was writen to GCF_014268485.2_ASM1426848v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:55,056] [INFO] Task started: fastANI
[2024-01-24 13:59:55,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg667ee4b3-65ef-4317-a97d-ca25b5f78ec7/GCF_014268485.2_ASM1426848v2_genomic.fna.gz --refList GCF_014268485.2_ASM1426848v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014268485.2_ASM1426848v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:34,183] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:34,199] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:34,200] [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_015461835.1	s__Pseudomonas_E neuropathica	96.1898	1924	2210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.00	95.48	0.91	0.90	7	conclusive
GCF_003053805.1	s__Pseudomonas_E sp003053805	93.0486	1911	2210	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_003732425.1	s__Pseudomonas_E fluorescens_BE	92.9486	1844	2210	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_018138145.1	s__Pseudomonas_E koreensis_A	92.8353	1908	2210	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_900187605.1	s__Pseudomonas_E sp900187605	92.6951	1881	2210	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_014268445.2	s__Pseudomonas_E sp900187515	92.658	1873	2210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.92	96.07	0.93	0.91	8	-
GCF_013433315.1	s__Pseudomonas_E crudilactis	92.6308	1847	2210	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_000783395.1	s__Pseudomonas_E helmanticensis	92.5856	1856	2210	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_009834515.1	s__Pseudomonas_E sp009834515	92.5377	1892	2210	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_900580865.1	s__Pseudomonas_E sp900580865	92.507	1847	2210	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_004011755.1	s__Pseudomonas_E sp004011755	92.4838	1909	2210	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_005938625.1	s__Pseudomonas_E fluorescens_BD	92.4494	1841	2210	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_902497745.1	s__Pseudomonas_E fluorescens_BM	92.3966	1889	2210	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_900582195.1	s__Pseudomonas_E sp900582195	92.3273	1824	2210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	98.42	0.95	0.95	2	-
GCF_001648775.1	s__Pseudomonas_E fluorescens_M	91.51	1817	2210	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_000282515.1	s__Pseudomonas_E sp000282515	90.2495	1659	2210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.31	97.31	0.87	0.87	2	-
GCF_001269815.1	s__Pseudomonas_E sp001269815	89.9115	1685	2210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.38	97.36	0.89	0.88	4	-
GCF_003999415.1	s__Pseudomonas_E koreensis_E	89.115	1691	2210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.92	0.92	2	-
GCF_017980685.1	s__Pseudomonas_E iridis	88.8073	1595	2210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.83	96.38	0.88	0.86	9	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:34,201] [INFO] GTDB search result was written to GCF_014268485.2_ASM1426848v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:34,202] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:34,206] [INFO] DFAST_QC result json was written to GCF_014268485.2_ASM1426848v2_genomic.fna/dqc_result.json
[2024-01-24 14:00:34,206] [INFO] DFAST_QC completed!
[2024-01-24 14:00:34,207] [INFO] Total running time: 0h2m50s