[2024-01-24 11:43:25,070] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,074] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,074] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd0037af-ba25-4a5f-b1dc-a4b88717df17/dqc_reference
[2024-01-24 11:43:30,055] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,056] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,057] [INFO] Running command: gunzip -c /var/lib/cwl/stg005dbf16-b671-4d95-a53a-fc79b7381335/GCF_003337565.1_ASM333756v1_genomic.fna.gz | prodigal -d GCF_003337565.1_ASM333756v1_genomic.fna/cds.fna -a GCF_003337565.1_ASM333756v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:42,278] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:42,278] [INFO] Task started: HMMsearch
[2024-01-24 11:43:42,279] [INFO] Running command: hmmsearch --tblout GCF_003337565.1_ASM333756v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd0037af-ba25-4a5f-b1dc-a4b88717df17/dqc_reference/reference_markers.hmm GCF_003337565.1_ASM333756v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:42,577] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:42,578] [INFO] Found 6/6 markers.
[2024-01-24 11:43:42,620] [INFO] Query marker FASTA was written to GCF_003337565.1_ASM333756v1_genomic.fna/markers.fasta
[2024-01-24 11:43:42,620] [INFO] Task started: Blastn
[2024-01-24 11:43:42,620] [INFO] Running command: blastn -query GCF_003337565.1_ASM333756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd0037af-ba25-4a5f-b1dc-a4b88717df17/dqc_reference/reference_markers.fasta -out GCF_003337565.1_ASM333756v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:43,619] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:43,624] [INFO] Selected 19 target genomes.
[2024-01-24 11:43:43,624] [INFO] Target genome list was writen to GCF_003337565.1_ASM333756v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:43,633] [INFO] Task started: fastANI
[2024-01-24 11:43:43,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg005dbf16-b671-4d95-a53a-fc79b7381335/GCF_003337565.1_ASM333756v1_genomic.fna.gz --refList GCF_003337565.1_ASM333756v1_genomic.fna/target_genomes.txt --output GCF_003337565.1_ASM333756v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:00,392] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:00,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd0037af-ba25-4a5f-b1dc-a4b88717df17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:00,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd0037af-ba25-4a5f-b1dc-a4b88717df17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:00,408] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:00,408] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:00,409] [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 lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	100.0	1346	1351	95	conclusive
Paracoccus halophilus	strain=CGMCC 1.6117	GCA_900111785.1	376733	376733	type	True	84.9728	824	1351	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	84.8555	809	1351	95	below_threshold
Paracoccus halophilus	strain=JCM 14014	GCA_000763905.1	376733	376733	type	True	84.8401	817	1351	95	below_threshold
Paracoccus denitrificans	strain=DSM 413	GCA_900100045.1	266	266	type	True	84.5644	829	1351	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	84.5384	838	1351	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	84.5164	829	1351	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	84.4727	843	1351	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	84.3913	794	1351	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	84.3022	794	1351	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	83.6889	787	1351	95	below_threshold
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	83.6694	770	1351	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	83.1035	707	1351	95	below_threshold
Paracoccus ravus	strain=YJ057	GCA_004522175.1	2447760	2447760	type	True	82.46	693	1351	95	below_threshold
Paracoccus laeviglucosivorans	strain=DSM 100094	GCA_900182695.1	1197861	1197861	type	True	82.324	716	1351	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	80.534	631	1351	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	80.1243	597	1351	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	79.9601	536	1351	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.8441	562	1351	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:00,411] [INFO] DFAST Taxonomy check result was written to GCF_003337565.1_ASM333756v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:00,411] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:00,412] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:00,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd0037af-ba25-4a5f-b1dc-a4b88717df17/dqc_reference/checkm_data
[2024-01-24 11:44:00,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:00,458] [INFO] Task started: CheckM
[2024-01-24 11:44:00,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003337565.1_ASM333756v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003337565.1_ASM333756v1_genomic.fna/checkm_input GCF_003337565.1_ASM333756v1_genomic.fna/checkm_result
[2024-01-24 11:44:42,369] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:42,370] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:42,391] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:42,391] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:42,392] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003337565.1_ASM333756v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:42,392] [INFO] Task started: Blastn
[2024-01-24 11:44:42,392] [INFO] Running command: blastn -query GCF_003337565.1_ASM333756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd0037af-ba25-4a5f-b1dc-a4b88717df17/dqc_reference/reference_markers_gtdb.fasta -out GCF_003337565.1_ASM333756v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:44,292] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:44,296] [INFO] Selected 14 target genomes.
[2024-01-24 11:44:44,297] [INFO] Target genome list was writen to GCF_003337565.1_ASM333756v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:44,307] [INFO] Task started: fastANI
[2024-01-24 11:44:44,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg005dbf16-b671-4d95-a53a-fc79b7381335/GCF_003337565.1_ASM333756v1_genomic.fna.gz --refList GCF_003337565.1_ASM333756v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003337565.1_ASM333756v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:58,026] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:58,043] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:58,044] [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_003337565.1	s__Paracoccus lutimaris	100.0	1346	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018056045.1	s__Paracoccus sp018056045	91.8403	623	1351	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	84.9568	823	1351	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	84.8867	806	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763905.1	s__Paracoccus halophilus	84.8358	818	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001546115.1	s__Paracoccus aminovorans_B	84.551	856	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCF_900100045.1	s__Paracoccus denitrificans	84.5177	835	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	-
GCF_008824185.1	s__Paracoccus pantotrophus	84.5045	831	1351	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	84.4999	832	1351	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	84.3785	815	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_009711185.1	s__Paracoccus limosus	84.3124	793	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156255.1	s__Paracoccus thiocyanatus	84.2249	763	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.14	97.14	0.86	0.86	2	-
GCF_000622145.1	s__Paracoccus yeei	83.6708	787	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	-
GCF_900182695.1	s__Paracoccus laeviglucosivorans	82.3025	719	1351	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 11:44:58,045] [INFO] GTDB search result was written to GCF_003337565.1_ASM333756v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:58,046] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:58,049] [INFO] DFAST_QC result json was written to GCF_003337565.1_ASM333756v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:58,050] [INFO] DFAST_QC completed!
[2024-01-24 11:44:58,050] [INFO] Total running time: 0h1m33s