[2024-01-24 13:13:39,460] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:39,463] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:39,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg97b40874-f4fe-4549-bfac-342a7b265590/dqc_reference
[2024-01-24 13:13:40,801] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:40,803] [INFO] Task started: Prodigal
[2024-01-24 13:13:40,803] [INFO] Running command: gunzip -c /var/lib/cwl/stgd99ba149-773b-43ec-ab95-e14bca2b8b1d/GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/cds.fna -a GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:50,623] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:50,623] [INFO] Task started: HMMsearch
[2024-01-24 13:13:50,624] [INFO] Running command: hmmsearch --tblout GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97b40874-f4fe-4549-bfac-342a7b265590/dqc_reference/reference_markers.hmm GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:50,901] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:50,903] [INFO] Found 6/6 markers.
[2024-01-24 13:13:50,944] [INFO] Query marker FASTA was written to GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:13:50,944] [INFO] Task started: Blastn
[2024-01-24 13:13:50,944] [INFO] Running command: blastn -query GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg97b40874-f4fe-4549-bfac-342a7b265590/dqc_reference/reference_markers.fasta -out GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:51,989] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:51,992] [INFO] Selected 15 target genomes.
[2024-01-24 13:13:51,992] [INFO] Target genome list was writen to GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:13:51,998] [INFO] Task started: fastANI
[2024-01-24 13:13:51,998] [INFO] Running command: fastANI --query /var/lib/cwl/stgd99ba149-773b-43ec-ab95-e14bca2b8b1d/GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna.gz --refList GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:05,292] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:05,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97b40874-f4fe-4549-bfac-342a7b265590/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:05,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97b40874-f4fe-4549-bfac-342a7b265590/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:05,307] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:05,307] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:05,307] [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 sanguinis	strain=DSM 29303	GCA_900106665.1	1545044	1545044	type	True	100.0	1184	1185	95	conclusive
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	85.7434	808	1185	95	below_threshold
Paracoccus salipaludis	strain=WN007	GCA_002287065.1	2032623	2032623	type	True	83.2099	756	1185	95	below_threshold
Paracoccus solventivorans	strain=DSM 6637	GCA_900142875.1	53463	53463	type	True	83.0637	697	1185	95	below_threshold
Paracoccus chinensis	strain=CGMCC 1.7655	GCA_900102885.1	525640	525640	type	True	82.8735	719	1185	95	below_threshold
Paracoccus luteus	strain=CFH 10530	GCA_004522155.1	2508543	2508543	type	True	82.842	753	1185	95	below_threshold
Paracoccus contaminans	strain=RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T	GCA_002105555.1	1945662	1945662	type	True	82.5721	720	1185	95	below_threshold
Paracoccus endophyticus	strain=SYSUP0003	GCA_003286075.1	2233774	2233774	type	True	82.5721	726	1185	95	below_threshold
Paracoccus aeridis	strain=JC501	GCA_004923205.2	1966466	1966466	type	True	82.3765	656	1185	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	81.3776	644	1185	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	80.1666	579	1185	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	79.8381	560	1185	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	78.7418	447	1185	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	78.6668	468	1185	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	77.9104	399	1185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:05,309] [INFO] DFAST Taxonomy check result was written to GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:14:05,310] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:05,310] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:05,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97b40874-f4fe-4549-bfac-342a7b265590/dqc_reference/checkm_data
[2024-01-24 13:14:05,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:05,347] [INFO] Task started: CheckM
[2024-01-24 13:14:05,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/checkm_input GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:14:42,419] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:42,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:42,437] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:42,438] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:42,438] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:14:42,438] [INFO] Task started: Blastn
[2024-01-24 13:14:42,438] [INFO] Running command: blastn -query GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg97b40874-f4fe-4549-bfac-342a7b265590/dqc_reference/reference_markers_gtdb.fasta -out GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:44,388] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:44,391] [INFO] Selected 12 target genomes.
[2024-01-24 13:14:44,391] [INFO] Target genome list was writen to GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:44,402] [INFO] Task started: fastANI
[2024-01-24 13:14:44,402] [INFO] Running command: fastANI --query /var/lib/cwl/stgd99ba149-773b-43ec-ab95-e14bca2b8b1d/GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna.gz --refList GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:55,452] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:55,463] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:55,463] [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_900106665.1	s__Paracoccus sanguinis	100.0	1184	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.10	96.00	0.89	0.81	6	conclusive
GCF_000763805.1	s__Paracoccus sphaerophysae	85.7038	812	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002287065.1	s__Paracoccus salipaludis	83.2062	757	1185	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	83.0531	699	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.61	95.99	0.87	0.87	3	-
GCF_900102885.1	s__Paracoccus chinensis	82.8773	719	1185	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	82.8354	753	1185	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	82.5748	707	1185	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	82.5739	719	1185	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	82.5339	729	1185	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	82.3837	655	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019061185.1	s__Paracoccus sp019061185	82.1636	649	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016446475.1	s__Paracoccus binzhouensis	81.3431	647	1185	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 13:14:55,464] [INFO] GTDB search result was written to GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:55,465] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:55,469] [INFO] DFAST_QC result json was written to GCF_900106665.1_IMG-taxon_2693429863_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:14:55,470] [INFO] DFAST_QC completed!
[2024-01-24 13:14:55,470] [INFO] Total running time: 0h1m16s