[2024-01-25 17:55:05,437] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:55:05,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:55:05,438] [INFO] DQC Reference Directory: /var/lib/cwl/stgecb8136a-9f0c-423a-bcd0-e391b619017e/dqc_reference
[2024-01-25 17:55:06,555] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:55:06,555] [INFO] Task started: Prodigal
[2024-01-25 17:55:06,556] [INFO] Running command: gunzip -c /var/lib/cwl/stg15ea6c5b-f03a-4455-a8e5-67e923f331e9/GCF_009711205.1_ASM971120v1_genomic.fna.gz | prodigal -d GCF_009711205.1_ASM971120v1_genomic.fna/cds.fna -a GCF_009711205.1_ASM971120v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:55:20,723] [INFO] Task succeeded: Prodigal
[2024-01-25 17:55:20,723] [INFO] Task started: HMMsearch
[2024-01-25 17:55:20,723] [INFO] Running command: hmmsearch --tblout GCF_009711205.1_ASM971120v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecb8136a-9f0c-423a-bcd0-e391b619017e/dqc_reference/reference_markers.hmm GCF_009711205.1_ASM971120v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:55:21,046] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:55:21,047] [INFO] Found 6/6 markers.
[2024-01-25 17:55:21,092] [INFO] Query marker FASTA was written to GCF_009711205.1_ASM971120v1_genomic.fna/markers.fasta
[2024-01-25 17:55:21,092] [INFO] Task started: Blastn
[2024-01-25 17:55:21,092] [INFO] Running command: blastn -query GCF_009711205.1_ASM971120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecb8136a-9f0c-423a-bcd0-e391b619017e/dqc_reference/reference_markers.fasta -out GCF_009711205.1_ASM971120v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:55:22,021] [INFO] Task succeeded: Blastn
[2024-01-25 17:55:22,024] [INFO] Selected 20 target genomes.
[2024-01-25 17:55:22,025] [INFO] Target genome list was writen to GCF_009711205.1_ASM971120v1_genomic.fna/target_genomes.txt
[2024-01-25 17:55:22,034] [INFO] Task started: fastANI
[2024-01-25 17:55:22,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg15ea6c5b-f03a-4455-a8e5-67e923f331e9/GCF_009711205.1_ASM971120v1_genomic.fna.gz --refList GCF_009711205.1_ASM971120v1_genomic.fna/target_genomes.txt --output GCF_009711205.1_ASM971120v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:55:40,080] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:40,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecb8136a-9f0c-423a-bcd0-e391b619017e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:55:40,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecb8136a-9f0c-423a-bcd0-e391b619017e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:55:40,094] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:55:40,094] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:55:40,095] [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 litorisediminis	strain=NBRC 112902	GCA_009711205.1	2006130	2006130	type	True	100.0	1749	1753	95	conclusive
Paracoccus ravus	strain=YJ057	GCA_004522175.1	2447760	2447760	type	True	84.4955	923	1753	95	below_threshold
Paracoccus aestuariivivens	strain=NBRC 111993	GCA_009711225.1	1820333	1820333	type	True	84.1612	1054	1753	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	83.307	755	1753	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	83.1589	803	1753	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	82.9562	760	1753	95	below_threshold
Paracoccus denitrificans	strain=DSM 413	GCA_900100045.1	266	266	type	True	82.8058	820	1753	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	82.7715	821	1753	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	82.7325	829	1753	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	82.7069	720	1753	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	82.6725	824	1753	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	82.636	821	1753	95	below_threshold
Paracoccus laeviglucosivorans	strain=DSM 100094	GCA_900182695.1	1197861	1197861	type	True	82.5616	827	1753	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	82.5253	744	1753	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	82.4345	771	1753	95	below_threshold
Paracoccus sulfuroxidans	strain=CGMCC 1.5364	GCA_007830335.1	384678	384678	type	True	81.6088	738	1753	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	79.9863	631	1753	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.6473	587	1753	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	78.9855	496	1753	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.607	494	1753	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:55:40,097] [INFO] DFAST Taxonomy check result was written to GCF_009711205.1_ASM971120v1_genomic.fna/tc_result.tsv
[2024-01-25 17:55:40,098] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:55:40,098] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:55:40,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecb8136a-9f0c-423a-bcd0-e391b619017e/dqc_reference/checkm_data
[2024-01-25 17:55:40,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:55:40,159] [INFO] Task started: CheckM
[2024-01-25 17:55:40,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009711205.1_ASM971120v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009711205.1_ASM971120v1_genomic.fna/checkm_input GCF_009711205.1_ASM971120v1_genomic.fna/checkm_result
[2024-01-25 17:56:29,132] [INFO] Task succeeded: CheckM
[2024-01-25 17:56:29,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:56:29,154] [INFO] ===== Completeness check finished =====
[2024-01-25 17:56:29,154] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:56:29,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009711205.1_ASM971120v1_genomic.fna/markers.fasta)
[2024-01-25 17:56:29,156] [INFO] Task started: Blastn
[2024-01-25 17:56:29,156] [INFO] Running command: blastn -query GCF_009711205.1_ASM971120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecb8136a-9f0c-423a-bcd0-e391b619017e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009711205.1_ASM971120v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:56:30,994] [INFO] Task succeeded: Blastn
[2024-01-25 17:56:30,998] [INFO] Selected 17 target genomes.
[2024-01-25 17:56:30,998] [INFO] Target genome list was writen to GCF_009711205.1_ASM971120v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:56:31,013] [INFO] Task started: fastANI
[2024-01-25 17:56:31,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg15ea6c5b-f03a-4455-a8e5-67e923f331e9/GCF_009711205.1_ASM971120v1_genomic.fna.gz --refList GCF_009711205.1_ASM971120v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009711205.1_ASM971120v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:56:47,483] [INFO] Task succeeded: fastANI
[2024-01-25 17:56:47,494] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:56:47,494] [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_009711205.1	s__Paracoccus litorisediminis	100.0	1749	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.39	97.39	0.92	0.92	2	conclusive
GCF_004522175.1	s__Paracoccus ravus	84.5143	921	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711225.1	s__Paracoccus aestuariivivens	84.1703	1053	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337565.1	s__Paracoccus lutimaris	83.3269	753	1753	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	83.1658	803	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711265.1	s__Paracoccus sp009711265	83.131	815	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000518925.1	s__Paracoccus sp000518925	83.0081	827	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_016446475.1	s__Paracoccus binzhouensis	82.9281	763	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100045.1	s__Paracoccus denitrificans	82.805	818	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	-
GCF_000763885.1	s__Paracoccus versutus	82.6822	824	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_001546115.1	s__Paracoccus aminovorans_B	82.6422	834	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCF_008824185.1	s__Paracoccus pantotrophus	82.6321	820	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_001447385.1	s__Paracoccus sp001447385	82.6309	834	1753	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	82.5615	827	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018056045.1	s__Paracoccus sp018056045	82.467	486	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900005615.1	s__Paracoccus aminovorans	82.4518	769	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_007830335.1	s__Paracoccus sulfuroxidans	81.5859	740	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:56:47,497] [INFO] GTDB search result was written to GCF_009711205.1_ASM971120v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:56:47,498] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:56:47,502] [INFO] DFAST_QC result json was written to GCF_009711205.1_ASM971120v1_genomic.fna/dqc_result.json
[2024-01-25 17:56:47,502] [INFO] DFAST_QC completed!
[2024-01-25 17:56:47,502] [INFO] Total running time: 0h1m42s