[2024-01-24 12:37:25,235] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:25,238] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:25,239] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f7138ff-55c6-46ea-b5fd-73f94ea2198f/dqc_reference
[2024-01-24 12:37:26,526] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:26,527] [INFO] Task started: Prodigal
[2024-01-24 12:37:26,527] [INFO] Running command: gunzip -c /var/lib/cwl/stg366c461c-8cbe-4758-a4db-ae5c6c249fb8/GCF_002287065.1_ASM228706v1_genomic.fna.gz | prodigal -d GCF_002287065.1_ASM228706v1_genomic.fna/cds.fna -a GCF_002287065.1_ASM228706v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:36,660] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:36,661] [INFO] Task started: HMMsearch
[2024-01-24 12:37:36,661] [INFO] Running command: hmmsearch --tblout GCF_002287065.1_ASM228706v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f7138ff-55c6-46ea-b5fd-73f94ea2198f/dqc_reference/reference_markers.hmm GCF_002287065.1_ASM228706v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:36,930] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:36,931] [INFO] Found 6/6 markers.
[2024-01-24 12:37:36,965] [INFO] Query marker FASTA was written to GCF_002287065.1_ASM228706v1_genomic.fna/markers.fasta
[2024-01-24 12:37:36,965] [INFO] Task started: Blastn
[2024-01-24 12:37:36,966] [INFO] Running command: blastn -query GCF_002287065.1_ASM228706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f7138ff-55c6-46ea-b5fd-73f94ea2198f/dqc_reference/reference_markers.fasta -out GCF_002287065.1_ASM228706v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:37,979] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:37,983] [INFO] Selected 14 target genomes.
[2024-01-24 12:37:37,983] [INFO] Target genome list was writen to GCF_002287065.1_ASM228706v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:37,992] [INFO] Task started: fastANI
[2024-01-24 12:37:37,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg366c461c-8cbe-4758-a4db-ae5c6c249fb8/GCF_002287065.1_ASM228706v1_genomic.fna.gz --refList GCF_002287065.1_ASM228706v1_genomic.fna/target_genomes.txt --output GCF_002287065.1_ASM228706v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:48,745] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:48,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f7138ff-55c6-46ea-b5fd-73f94ea2198f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:48,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f7138ff-55c6-46ea-b5fd-73f94ea2198f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:48,757] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:48,757] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:48,758] [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 salipaludis	strain=WN007	GCA_002287065.1	2032623	2032623	type	True	100.0	1159	1163	95	conclusive
Paracoccus chinensis	strain=CGMCC 1.7655	GCA_900102885.1	525640	525640	type	True	90.9163	923	1163	95	below_threshold
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	83.6507	699	1163	95	below_threshold
Paracoccus solventivorans	strain=DSM 6637	GCA_900142875.1	53463	53463	type	True	83.639	691	1163	95	below_threshold
Paracoccus sanguinis	strain=DSM 29303	GCA_900106665.1	1545044	1545044	type	True	83.3886	736	1163	95	below_threshold
Paracoccus endophyticus	strain=SYSUP0003	GCA_003286075.1	2233774	2233774	type	True	83.3283	698	1163	95	below_threshold
Paracoccus luteus	strain=CFH 10530	GCA_004522155.1	2508543	2508543	type	True	83.3013	703	1163	95	below_threshold
Paracoccus alkenifer	strain=DSM 11593	GCA_900108405.1	65735	65735	type	True	82.6025	648	1163	95	below_threshold
Paracoccus aeridis	strain=JC501	GCA_004923205.2	1966466	1966466	type	True	82.439	652	1163	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.5847	619	1163	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	81.0308	588	1163	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	79.956	508	1163	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	79.0877	458	1163	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.2957	383	1163	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:48,760] [INFO] DFAST Taxonomy check result was written to GCF_002287065.1_ASM228706v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:48,760] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:48,761] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:48,761] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f7138ff-55c6-46ea-b5fd-73f94ea2198f/dqc_reference/checkm_data
[2024-01-24 12:37:48,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:48,805] [INFO] Task started: CheckM
[2024-01-24 12:37:48,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002287065.1_ASM228706v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002287065.1_ASM228706v1_genomic.fna/checkm_input GCF_002287065.1_ASM228706v1_genomic.fna/checkm_result
[2024-01-24 12:38:40,261] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:40,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:40,279] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:40,279] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:40,280] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002287065.1_ASM228706v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:40,280] [INFO] Task started: Blastn
[2024-01-24 12:38:40,280] [INFO] Running command: blastn -query GCF_002287065.1_ASM228706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f7138ff-55c6-46ea-b5fd-73f94ea2198f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002287065.1_ASM228706v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:42,308] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:42,312] [INFO] Selected 9 target genomes.
[2024-01-24 12:38:42,313] [INFO] Target genome list was writen to GCF_002287065.1_ASM228706v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:42,322] [INFO] Task started: fastANI
[2024-01-24 12:38:42,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg366c461c-8cbe-4758-a4db-ae5c6c249fb8/GCF_002287065.1_ASM228706v1_genomic.fna.gz --refList GCF_002287065.1_ASM228706v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002287065.1_ASM228706v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:49,779] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:49,791] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:49,791] [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_002287065.1	s__Paracoccus salipaludis	100.0	1159	1163	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_900102885.1	s__Paracoccus chinensis	90.8984	924	1163	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	87.0729	827	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.50	99.01	0.95	0.90	3	-
GCF_900142875.1	s__Paracoccus solventivorans	83.6655	689	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.61	95.99	0.87	0.87	3	-
GCF_000763805.1	s__Paracoccus sphaerophysae	83.6089	703	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003286075.1	s__Paracoccus endophyticus	83.3155	699	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522155.1	s__Paracoccus luteus	83.2677	706	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108405.1	s__Paracoccus alkenifer	82.6229	646	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923205.2	s__Paracoccus aeridis	82.4721	650	1163	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 12:38:49,793] [INFO] GTDB search result was written to GCF_002287065.1_ASM228706v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:49,794] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:49,798] [INFO] DFAST_QC result json was written to GCF_002287065.1_ASM228706v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:49,798] [INFO] DFAST_QC completed!
[2024-01-24 12:38:49,798] [INFO] Total running time: 0h1m25s