[2024-01-24 12:30:52,427] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:52,431] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:52,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg9cea7e21-1554-413e-b2f3-fe114652b173/dqc_reference
[2024-01-24 12:30:53,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:53,744] [INFO] Task started: Prodigal
[2024-01-24 12:30:53,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg478ad544-8c2d-403c-a9b8-ea5107c224c2/GCF_024169245.1_ASM2416924v1_genomic.fna.gz | prodigal -d GCF_024169245.1_ASM2416924v1_genomic.fna/cds.fna -a GCF_024169245.1_ASM2416924v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:18,187] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:18,188] [INFO] Task started: HMMsearch
[2024-01-24 12:31:18,188] [INFO] Running command: hmmsearch --tblout GCF_024169245.1_ASM2416924v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9cea7e21-1554-413e-b2f3-fe114652b173/dqc_reference/reference_markers.hmm GCF_024169245.1_ASM2416924v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:18,553] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:18,555] [INFO] Found 6/6 markers.
[2024-01-24 12:31:18,610] [INFO] Query marker FASTA was written to GCF_024169245.1_ASM2416924v1_genomic.fna/markers.fasta
[2024-01-24 12:31:18,610] [INFO] Task started: Blastn
[2024-01-24 12:31:18,610] [INFO] Running command: blastn -query GCF_024169245.1_ASM2416924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cea7e21-1554-413e-b2f3-fe114652b173/dqc_reference/reference_markers.fasta -out GCF_024169245.1_ASM2416924v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:19,626] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:19,629] [INFO] Selected 14 target genomes.
[2024-01-24 12:31:19,630] [INFO] Target genome list was writen to GCF_024169245.1_ASM2416924v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:19,637] [INFO] Task started: fastANI
[2024-01-24 12:31:19,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg478ad544-8c2d-403c-a9b8-ea5107c224c2/GCF_024169245.1_ASM2416924v1_genomic.fna.gz --refList GCF_024169245.1_ASM2416924v1_genomic.fna/target_genomes.txt --output GCF_024169245.1_ASM2416924v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:44,540] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:44,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9cea7e21-1554-413e-b2f3-fe114652b173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:44,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9cea7e21-1554-413e-b2f3-fe114652b173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:44,556] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:31:44,556] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:31:44,557] [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 siliginis	strain=SWRI31	GCA_019145195.1	2842346	2842346	type	True	93.0225	1638	1991	95	below_threshold
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	93.0067	1762	1991	95	below_threshold
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	92.9954	1717	1991	95	below_threshold
Pseudomonas atacamensis	strain=M7D1	GCA_004801935.1	2565368	2565368	type	True	92.9435	1745	1991	95	below_threshold
Pseudomonas khorasanensis	strain=SWRI153	GCA_014268505.2	2745508	2745508	type	True	89.5094	1643	1991	95	below_threshold
Pseudomonas hamedanensis	strain=SWRI65	GCA_014268595.2	2745504	2745504	type	True	89.4116	1707	1991	95	below_threshold
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	88.6391	1662	1991	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	88.3629	1679	1991	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	88.0434	1616	1991	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	87.9955	1592	1991	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	87.431	1609	1991	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	87.3895	1537	1991	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	83.5362	1245	1991	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	82.0212	804	1991	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:44,558] [INFO] DFAST Taxonomy check result was written to GCF_024169245.1_ASM2416924v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:44,560] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:44,560] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:44,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9cea7e21-1554-413e-b2f3-fe114652b173/dqc_reference/checkm_data
[2024-01-24 12:31:44,562] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:44,618] [INFO] Task started: CheckM
[2024-01-24 12:31:44,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024169245.1_ASM2416924v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024169245.1_ASM2416924v1_genomic.fna/checkm_input GCF_024169245.1_ASM2416924v1_genomic.fna/checkm_result
[2024-01-24 12:32:57,583] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:57,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:57,605] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:57,605] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:57,606] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024169245.1_ASM2416924v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:57,606] [INFO] Task started: Blastn
[2024-01-24 12:32:57,606] [INFO] Running command: blastn -query GCF_024169245.1_ASM2416924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cea7e21-1554-413e-b2f3-fe114652b173/dqc_reference/reference_markers_gtdb.fasta -out GCF_024169245.1_ASM2416924v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:59,331] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:59,335] [INFO] Selected 11 target genomes.
[2024-01-24 12:32:59,335] [INFO] Target genome list was writen to GCF_024169245.1_ASM2416924v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:59,344] [INFO] Task started: fastANI
[2024-01-24 12:32:59,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg478ad544-8c2d-403c-a9b8-ea5107c224c2/GCF_024169245.1_ASM2416924v1_genomic.fna.gz --refList GCF_024169245.1_ASM2416924v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024169245.1_ASM2416924v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:22,165] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:22,182] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:33:22,182] [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_900105805.1	s__Pseudomonas_E moraviensis_A	94.2632	1793	1991	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.30	0.96	0.94	7	-
GCF_001605965.1	s__Pseudomonas_E koreensis_C	93.0294	1728	1991	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.5366	98.03	96.36	0.95	0.90	10	-
GCF_004801935.1	s__Pseudomonas_E atacamensis	92.9435	1745	1991	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.5366	97.08	95.72	0.92	0.89	59	-
GCF_000817895.1	s__Pseudomonas_E fluorescens_AO	92.8444	1740	1991	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.16	98.16	0.95	0.95	2	-
GCF_002836515.1	s__Pseudomonas_E sp002836515	92.022	1652	1991	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_900105485.1	s__Pseudomonas_E granadensis	88.6332	1658	1991	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.04	95.81	0.93	0.92	8	-
GCF_009834515.1	s__Pseudomonas_E sp009834515	88.4215	1668	1991	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_016651305.1	s__Pseudomonas_E sp016651305	87.9468	1624	1991	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_011369485.1	s__Pseudomonas_E sp011369485	87.8748	1545	1991	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_017976235.1	s__Pseudomonas_E anatoliensis	87.6768	1587	1991	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.18	97.58	0.93	0.90	4	-
GCF_017980685.1	s__Pseudomonas_E iridis	87.4861	1526	1991	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 12:33:22,184] [INFO] GTDB search result was written to GCF_024169245.1_ASM2416924v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:22,184] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:22,187] [INFO] DFAST_QC result json was written to GCF_024169245.1_ASM2416924v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:22,188] [INFO] DFAST_QC completed!
[2024-01-24 12:33:22,188] [INFO] Total running time: 0h2m30s