[2024-01-24 14:56:23,833] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:23,835] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:23,835] [INFO] DQC Reference Directory: /var/lib/cwl/stga50ad232-a7b2-49ec-b9b4-36d3c903cf47/dqc_reference
[2024-01-24 14:56:26,563] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:26,564] [INFO] Task started: Prodigal
[2024-01-24 14:56:26,564] [INFO] Running command: gunzip -c /var/lib/cwl/stg90bdfffd-00a9-4f5c-bd6e-42154c271b14/GCF_004522175.1_ASM452217v1_genomic.fna.gz | prodigal -d GCF_004522175.1_ASM452217v1_genomic.fna/cds.fna -a GCF_004522175.1_ASM452217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:39,943] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:39,944] [INFO] Task started: HMMsearch
[2024-01-24 14:56:39,944] [INFO] Running command: hmmsearch --tblout GCF_004522175.1_ASM452217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga50ad232-a7b2-49ec-b9b4-36d3c903cf47/dqc_reference/reference_markers.hmm GCF_004522175.1_ASM452217v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:40,310] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:40,312] [INFO] Found 6/6 markers.
[2024-01-24 14:56:40,368] [INFO] Query marker FASTA was written to GCF_004522175.1_ASM452217v1_genomic.fna/markers.fasta
[2024-01-24 14:56:40,369] [INFO] Task started: Blastn
[2024-01-24 14:56:40,369] [INFO] Running command: blastn -query GCF_004522175.1_ASM452217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga50ad232-a7b2-49ec-b9b4-36d3c903cf47/dqc_reference/reference_markers.fasta -out GCF_004522175.1_ASM452217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:41,406] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:41,410] [INFO] Selected 18 target genomes.
[2024-01-24 14:56:41,411] [INFO] Target genome list was writen to GCF_004522175.1_ASM452217v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:41,420] [INFO] Task started: fastANI
[2024-01-24 14:56:41,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg90bdfffd-00a9-4f5c-bd6e-42154c271b14/GCF_004522175.1_ASM452217v1_genomic.fna.gz --refList GCF_004522175.1_ASM452217v1_genomic.fna/target_genomes.txt --output GCF_004522175.1_ASM452217v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:57,584] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:57,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga50ad232-a7b2-49ec-b9b4-36d3c903cf47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:57,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga50ad232-a7b2-49ec-b9b4-36d3c903cf47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:57,599] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:57,600] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:57,600] [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 ravus	strain=YJ057	GCA_004522175.1	2447760	2447760	type	True	100.0	1352	1358	95	conclusive
Paracoccus litorisediminis	strain=NBRC 112902	GCA_009711205.1	2006130	2006130	type	True	84.5115	904	1358	95	below_threshold
Paracoccus aestuariivivens	strain=NBRC 111993	GCA_009711225.1	1820333	1820333	type	True	83.4587	841	1358	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	82.5157	693	1358	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	82.3988	722	1358	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	82.1997	702	1358	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	82.1962	733	1358	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	82.1175	731	1358	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	81.8817	671	1358	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	81.8773	685	1358	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	81.7524	651	1358	95	below_threshold
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	81.715	693	1358	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	81.6715	713	1358	95	below_threshold
Paracoccus laeviglucosivorans	strain=DSM 100094	GCA_900182695.1	1197861	1197861	type	True	81.5476	710	1358	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	79.6893	521	1358	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.0603	526	1358	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	78.9129	424	1358	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.4989	424	1358	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:57,602] [INFO] DFAST Taxonomy check result was written to GCF_004522175.1_ASM452217v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:57,602] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:57,603] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:57,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga50ad232-a7b2-49ec-b9b4-36d3c903cf47/dqc_reference/checkm_data
[2024-01-24 14:56:57,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:57,649] [INFO] Task started: CheckM
[2024-01-24 14:56:57,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004522175.1_ASM452217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004522175.1_ASM452217v1_genomic.fna/checkm_input GCF_004522175.1_ASM452217v1_genomic.fna/checkm_result
[2024-01-24 14:57:38,244] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:38,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:38,269] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:38,269] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:38,270] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004522175.1_ASM452217v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:38,270] [INFO] Task started: Blastn
[2024-01-24 14:57:38,271] [INFO] Running command: blastn -query GCF_004522175.1_ASM452217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga50ad232-a7b2-49ec-b9b4-36d3c903cf47/dqc_reference/reference_markers_gtdb.fasta -out GCF_004522175.1_ASM452217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:40,070] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:40,073] [INFO] Selected 15 target genomes.
[2024-01-24 14:57:40,073] [INFO] Target genome list was writen to GCF_004522175.1_ASM452217v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:40,084] [INFO] Task started: fastANI
[2024-01-24 14:57:40,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg90bdfffd-00a9-4f5c-bd6e-42154c271b14/GCF_004522175.1_ASM452217v1_genomic.fna.gz --refList GCF_004522175.1_ASM452217v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004522175.1_ASM452217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:56,744] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:56,758] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:56,758] [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_004522175.1	s__Paracoccus ravus	100.0	1352	1358	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_009711205.1	s__Paracoccus litorisediminis	84.5056	903	1358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.39	97.39	0.92	0.92	2	-
GCF_009711225.1	s__Paracoccus aestuariivivens	83.4666	840	1358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518925.1	s__Paracoccus sp000518925	82.5898	727	1358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_003337565.1	s__Paracoccus lutimaris	82.5191	693	1358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711185.1	s__Paracoccus limosus	82.4234	720	1358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001546115.1	s__Paracoccus aminovorans_B	82.2515	731	1358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCF_000763885.1	s__Paracoccus versutus	82.2353	710	1358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_016446475.1	s__Paracoccus binzhouensis	82.2044	700	1358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447385.1	s__Paracoccus sp001447385	82.1833	700	1358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008824185.1	s__Paracoccus pantotrophus	82.179	735	1358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_900005615.1	s__Paracoccus aminovorans	81.8842	684	1358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000622145.1	s__Paracoccus yeei	81.6875	712	1358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	-
GCA_018056045.1	s__Paracoccus sp018056045	81.6249	432	1358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182695.1	s__Paracoccus laeviglucosivorans	81.5475	710	1358	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 14:57:56,760] [INFO] GTDB search result was written to GCF_004522175.1_ASM452217v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:56,760] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:56,765] [INFO] DFAST_QC result json was written to GCF_004522175.1_ASM452217v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:56,765] [INFO] DFAST_QC completed!
[2024-01-24 14:57:56,765] [INFO] Total running time: 0h1m33s