[2024-01-24 12:37:08,375] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:08,377] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:08,377] [INFO] DQC Reference Directory: /var/lib/cwl/stg47c527fc-6f46-4d2b-ae8f-86eecffa6cdf/dqc_reference
[2024-01-24 12:37:09,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:09,686] [INFO] Task started: Prodigal
[2024-01-24 12:37:09,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg83d41d88-f6e4-4e94-9bec-8ca1ec00343f/GCF_019614655.1_ASM1961465v1_genomic.fna.gz | prodigal -d GCF_019614655.1_ASM1961465v1_genomic.fna/cds.fna -a GCF_019614655.1_ASM1961465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:39,371] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:39,372] [INFO] Task started: HMMsearch
[2024-01-24 12:37:39,372] [INFO] Running command: hmmsearch --tblout GCF_019614655.1_ASM1961465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47c527fc-6f46-4d2b-ae8f-86eecffa6cdf/dqc_reference/reference_markers.hmm GCF_019614655.1_ASM1961465v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:39,737] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:39,739] [INFO] Found 6/6 markers.
[2024-01-24 12:37:39,797] [INFO] Query marker FASTA was written to GCF_019614655.1_ASM1961465v1_genomic.fna/markers.fasta
[2024-01-24 12:37:39,797] [INFO] Task started: Blastn
[2024-01-24 12:37:39,797] [INFO] Running command: blastn -query GCF_019614655.1_ASM1961465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47c527fc-6f46-4d2b-ae8f-86eecffa6cdf/dqc_reference/reference_markers.fasta -out GCF_019614655.1_ASM1961465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:40,809] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:40,814] [INFO] Selected 11 target genomes.
[2024-01-24 12:37:40,815] [INFO] Target genome list was writen to GCF_019614655.1_ASM1961465v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:40,828] [INFO] Task started: fastANI
[2024-01-24 12:37:40,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg83d41d88-f6e4-4e94-9bec-8ca1ec00343f/GCF_019614655.1_ASM1961465v1_genomic.fna.gz --refList GCF_019614655.1_ASM1961465v1_genomic.fna/target_genomes.txt --output GCF_019614655.1_ASM1961465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:03,211] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:03,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47c527fc-6f46-4d2b-ae8f-86eecffa6cdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:03,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47c527fc-6f46-4d2b-ae8f-86eecffa6cdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:03,227] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:38:03,227] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:38:03,227] [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 germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	100.0	2235	2237	95	inconclusive
Pseudomonas zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	96.1986	1946	2237	95	inconclusive
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	95.5287	1919	2237	95	inconclusive
Pseudomonas tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	92.7733	1906	2237	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	92.4911	1865	2237	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	89.4021	1745	2237	95	below_threshold
Pseudomonas baetica	strain=a390	GCA_003031005.1	674054	674054	type	True	89.3909	1722	2237	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.001	1712	2237	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	87.901	1662	2237	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	82.9709	1315	2237	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.3515	852	2237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:03,229] [INFO] DFAST Taxonomy check result was written to GCF_019614655.1_ASM1961465v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:03,230] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:03,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:03,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47c527fc-6f46-4d2b-ae8f-86eecffa6cdf/dqc_reference/checkm_data
[2024-01-24 12:38:03,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:03,295] [INFO] Task started: CheckM
[2024-01-24 12:38:03,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019614655.1_ASM1961465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019614655.1_ASM1961465v1_genomic.fna/checkm_input GCF_019614655.1_ASM1961465v1_genomic.fna/checkm_result
[2024-01-24 12:39:27,919] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:27,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:27,945] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:27,946] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:27,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019614655.1_ASM1961465v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:27,946] [INFO] Task started: Blastn
[2024-01-24 12:39:27,946] [INFO] Running command: blastn -query GCF_019614655.1_ASM1961465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47c527fc-6f46-4d2b-ae8f-86eecffa6cdf/dqc_reference/reference_markers_gtdb.fasta -out GCF_019614655.1_ASM1961465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:29,651] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:29,656] [INFO] Selected 19 target genomes.
[2024-01-24 12:39:29,656] [INFO] Target genome list was writen to GCF_019614655.1_ASM1961465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:29,675] [INFO] Task started: fastANI
[2024-01-24 12:39:29,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg83d41d88-f6e4-4e94-9bec-8ca1ec00343f/GCF_019614655.1_ASM1961465v1_genomic.fna.gz --refList GCF_019614655.1_ASM1961465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019614655.1_ASM1961465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:07,779] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:07,800] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:07,800] [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	95.5287	1919	2237	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	93.0192	1893	2237	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	93.0129	1845	2237	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_900187605.1	s__Pseudomonas_E sp900187605	92.9611	1890	2237	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_000783395.1	s__Pseudomonas_E helmanticensis	92.8712	1884	2237	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_004011755.1	s__Pseudomonas_E sp004011755	92.8143	1915	2237	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	92.8034	1915	2237	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_014268445.2	s__Pseudomonas_E sp900187515	92.7869	1902	2237	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_900580865.1	s__Pseudomonas_E sp900580865	92.7508	1891	2237	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_009834515.1	s__Pseudomonas_E sp009834515	92.6917	1915	2237	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	92.5548	1866	2237	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_013433315.1	s__Pseudomonas_E crudilactis	92.505	1863	2237	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_900582195.1	s__Pseudomonas_E sp900582195	92.4703	1820	2237	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_902497745.1	s__Pseudomonas_E fluorescens_BM	92.4537	1897	2237	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_001648775.1	s__Pseudomonas_E fluorescens_M	91.3637	1851	2237	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_009764645.1	s__Pseudomonas_E sp009764645	90.2727	1606	2237	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_016650635.1	s__Pseudomonas_E sp016650635	89.5905	1749	2237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.85	97.85	0.86	0.86	2	-
GCF_014472415.1	s__Pseudomonas_E sp014472415	89.186	1664	2237	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_003999415.1	s__Pseudomonas_E koreensis_E	89.0544	1703	2237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:07,805] [INFO] GTDB search result was written to GCF_019614655.1_ASM1961465v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:07,806] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:07,811] [INFO] DFAST_QC result json was written to GCF_019614655.1_ASM1961465v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:07,811] [INFO] DFAST_QC completed!
[2024-01-24 12:40:07,811] [INFO] Total running time: 0h2m59s