[2024-01-24 15:09:55,546] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:09:55,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:09:55,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg25fb07c5-67b9-4e85-98d5-4c479796e96b/dqc_reference
[2024-01-24 15:09:58,160] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:09:58,161] [INFO] Task started: Prodigal
[2024-01-24 15:09:58,161] [INFO] Running command: gunzip -c /var/lib/cwl/stg19ef1c6e-7e9c-42ef-b643-5c9c40e9cb8f/GCF_004522155.1_ASM452215v1_genomic.fna.gz | prodigal -d GCF_004522155.1_ASM452215v1_genomic.fna/cds.fna -a GCF_004522155.1_ASM452215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:07,982] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:07,983] [INFO] Task started: HMMsearch
[2024-01-24 15:10:07,983] [INFO] Running command: hmmsearch --tblout GCF_004522155.1_ASM452215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25fb07c5-67b9-4e85-98d5-4c479796e96b/dqc_reference/reference_markers.hmm GCF_004522155.1_ASM452215v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:08,272] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:08,274] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg19ef1c6e-7e9c-42ef-b643-5c9c40e9cb8f/GCF_004522155.1_ASM452215v1_genomic.fna.gz]
[2024-01-24 15:10:08,305] [INFO] Query marker FASTA was written to GCF_004522155.1_ASM452215v1_genomic.fna/markers.fasta
[2024-01-24 15:10:08,305] [INFO] Task started: Blastn
[2024-01-24 15:10:08,305] [INFO] Running command: blastn -query GCF_004522155.1_ASM452215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25fb07c5-67b9-4e85-98d5-4c479796e96b/dqc_reference/reference_markers.fasta -out GCF_004522155.1_ASM452215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:09,349] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:09,362] [INFO] Selected 13 target genomes.
[2024-01-24 15:10:09,363] [INFO] Target genome list was writen to GCF_004522155.1_ASM452215v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:09,372] [INFO] Task started: fastANI
[2024-01-24 15:10:09,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ef1c6e-7e9c-42ef-b643-5c9c40e9cb8f/GCF_004522155.1_ASM452215v1_genomic.fna.gz --refList GCF_004522155.1_ASM452215v1_genomic.fna/target_genomes.txt --output GCF_004522155.1_ASM452215v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:20,935] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:20,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25fb07c5-67b9-4e85-98d5-4c479796e96b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:20,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25fb07c5-67b9-4e85-98d5-4c479796e96b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:20,954] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:20,955] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:20,955] [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
Paracoccus luteus	strain=CFH 10530	GCA_004522155.1	2508543	2508543	type	True	100.0	1090	1090	95	conclusive
Paracoccus endophyticus	strain=SYSUP0003	GCA_003286075.1	2233774	2233774	type	True	87.892	810	1090	95	below_threshold
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	83.8189	711	1090	95	below_threshold
Paracoccus solventivorans	strain=DSM 6637	GCA_900142875.1	53463	53463	type	True	83.3923	659	1090	95	below_threshold
Paracoccus salipaludis	strain=WN007	GCA_002287065.1	2032623	2032623	type	True	83.139	704	1090	95	below_threshold
Paracoccus chinensis	strain=CGMCC 1.7655	GCA_900102885.1	525640	525640	type	True	83.0933	692	1090	95	below_threshold
Paracoccus sanguinis	strain=DSM 29303	GCA_900106665.1	1545044	1545044	type	True	83.0011	748	1090	95	below_threshold
Paracoccus contaminans	strain=RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T	GCA_002105555.1	1945662	1945662	type	True	82.8419	685	1090	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.2932	628	1090	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	80.9749	620	1090	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.1625	521	1090	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.769	562	1090	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	79.4095	522	1090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:20,957] [INFO] DFAST Taxonomy check result was written to GCF_004522155.1_ASM452215v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:20,958] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:20,958] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:20,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25fb07c5-67b9-4e85-98d5-4c479796e96b/dqc_reference/checkm_data
[2024-01-24 15:10:20,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:20,995] [INFO] Task started: CheckM
[2024-01-24 15:10:20,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004522155.1_ASM452215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004522155.1_ASM452215v1_genomic.fna/checkm_input GCF_004522155.1_ASM452215v1_genomic.fna/checkm_result
[2024-01-24 15:10:56,773] [INFO] Task succeeded: CheckM
[2024-01-24 15:10:56,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:10:56,795] [INFO] ===== Completeness check finished =====
[2024-01-24 15:10:56,796] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:10:56,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004522155.1_ASM452215v1_genomic.fna/markers.fasta)
[2024-01-24 15:10:56,796] [INFO] Task started: Blastn
[2024-01-24 15:10:56,797] [INFO] Running command: blastn -query GCF_004522155.1_ASM452215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25fb07c5-67b9-4e85-98d5-4c479796e96b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004522155.1_ASM452215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:58,507] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:58,510] [INFO] Selected 11 target genomes.
[2024-01-24 15:10:58,510] [INFO] Target genome list was writen to GCF_004522155.1_ASM452215v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:10:58,518] [INFO] Task started: fastANI
[2024-01-24 15:10:58,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ef1c6e-7e9c-42ef-b643-5c9c40e9cb8f/GCF_004522155.1_ASM452215v1_genomic.fna.gz --refList GCF_004522155.1_ASM452215v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004522155.1_ASM452215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:08,067] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:08,077] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:08,077] [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_004522155.1	s__Paracoccus luteus	100.0	1090	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003286075.1	s__Paracoccus endophyticus	87.8588	812	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763805.1	s__Paracoccus sphaerophysae	83.8732	706	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142875.1	s__Paracoccus solventivorans	83.4132	657	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.61	95.99	0.87	0.87	3	-
GCF_002287065.1	s__Paracoccus salipaludis	83.1377	704	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102885.1	s__Paracoccus chinensis	83.0621	695	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106665.1	s__Paracoccus sanguinis	82.9713	751	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.10	96.00	0.89	0.81	6	-
GCF_900108405.1	s__Paracoccus alkenifer	82.9643	655	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016617715.1	s__Paracoccus sp014164625	82.9187	698	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.50	99.01	0.95	0.90	3	-
GCF_002105555.1	s__Paracoccus contaminans	82.802	690	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007018965.1	s__Paracoccus marinus	82.4101	661	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:08,079] [INFO] GTDB search result was written to GCF_004522155.1_ASM452215v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:08,080] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:08,084] [INFO] DFAST_QC result json was written to GCF_004522155.1_ASM452215v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:08,084] [INFO] DFAST_QC completed!
[2024-01-24 15:11:08,084] [INFO] Total running time: 0h1m13s