[2024-01-24 15:27:11,409] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:11,411] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:11,411] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c936557-8b9d-42c1-a76b-bf5bafaabd7d/dqc_reference
[2024-01-24 15:27:12,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:12,830] [INFO] Task started: Prodigal
[2024-01-24 15:27:12,830] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d68fb24-293c-4f86-99fc-0e7c129fb533/GCF_009711225.1_ASM971122v1_genomic.fna.gz | prodigal -d GCF_009711225.1_ASM971122v1_genomic.fna/cds.fna -a GCF_009711225.1_ASM971122v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:26,731] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:26,731] [INFO] Task started: HMMsearch
[2024-01-24 15:27:26,731] [INFO] Running command: hmmsearch --tblout GCF_009711225.1_ASM971122v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c936557-8b9d-42c1-a76b-bf5bafaabd7d/dqc_reference/reference_markers.hmm GCF_009711225.1_ASM971122v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:27,057] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:27,058] [INFO] Found 6/6 markers.
[2024-01-24 15:27:27,100] [INFO] Query marker FASTA was written to GCF_009711225.1_ASM971122v1_genomic.fna/markers.fasta
[2024-01-24 15:27:27,101] [INFO] Task started: Blastn
[2024-01-24 15:27:27,101] [INFO] Running command: blastn -query GCF_009711225.1_ASM971122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c936557-8b9d-42c1-a76b-bf5bafaabd7d/dqc_reference/reference_markers.fasta -out GCF_009711225.1_ASM971122v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:28,078] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:28,081] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:28,082] [INFO] Target genome list was writen to GCF_009711225.1_ASM971122v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:28,087] [INFO] Task started: fastANI
[2024-01-24 15:27:28,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d68fb24-293c-4f86-99fc-0e7c129fb533/GCF_009711225.1_ASM971122v1_genomic.fna.gz --refList GCF_009711225.1_ASM971122v1_genomic.fna/target_genomes.txt --output GCF_009711225.1_ASM971122v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:41,714] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:41,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c936557-8b9d-42c1-a76b-bf5bafaabd7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:41,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c936557-8b9d-42c1-a76b-bf5bafaabd7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:41,728] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:41,729] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:41,729] [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 aestuariivivens	strain=NBRC 111993	GCA_009711225.1	1820333	1820333	type	True	100.0	1482	1484	95	conclusive
Paracoccus litorisediminis	strain=NBRC 112902	GCA_009711205.1	2006130	2006130	type	True	84.1147	1053	1484	95	below_threshold
Paracoccus ravus	strain=YJ057	GCA_004522175.1	2447760	2447760	type	True	83.401	845	1484	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	81.5649	709	1484	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	81.534	656	1484	95	below_threshold
Paracoccus laeviglucosivorans	strain=DSM 100094	GCA_900182695.1	1197861	1197861	type	True	81.3777	699	1484	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	81.3075	634	1484	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	81.0732	615	1484	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	81.064	675	1484	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	81.0076	626	1484	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	80.9546	638	1484	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	78.7114	382	1484	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	78.6244	424	1484	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.4578	391	1484	95	below_threshold
Paracoccus onubensis	strain=1011MAR3C25	GCA_003591515.1	1675788	1675788	type	True	77.7157	364	1484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:41,731] [INFO] DFAST Taxonomy check result was written to GCF_009711225.1_ASM971122v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:41,732] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:41,732] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:41,732] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c936557-8b9d-42c1-a76b-bf5bafaabd7d/dqc_reference/checkm_data
[2024-01-24 15:27:41,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:41,782] [INFO] Task started: CheckM
[2024-01-24 15:27:41,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009711225.1_ASM971122v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009711225.1_ASM971122v1_genomic.fna/checkm_input GCF_009711225.1_ASM971122v1_genomic.fna/checkm_result
[2024-01-24 15:28:25,549] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:25,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:25,571] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:25,572] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:25,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009711225.1_ASM971122v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:25,572] [INFO] Task started: Blastn
[2024-01-24 15:28:25,573] [INFO] Running command: blastn -query GCF_009711225.1_ASM971122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c936557-8b9d-42c1-a76b-bf5bafaabd7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009711225.1_ASM971122v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:27,160] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:27,163] [INFO] Selected 13 target genomes.
[2024-01-24 15:28:27,163] [INFO] Target genome list was writen to GCF_009711225.1_ASM971122v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:27,172] [INFO] Task started: fastANI
[2024-01-24 15:28:27,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d68fb24-293c-4f86-99fc-0e7c129fb533/GCF_009711225.1_ASM971122v1_genomic.fna.gz --refList GCF_009711225.1_ASM971122v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009711225.1_ASM971122v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:39,293] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:39,308] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:39,308] [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_009711225.1	s__Paracoccus aestuariivivens	100.0	1482	1484	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	84.1078	1054	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.39	97.39	0.92	0.92	2	-
GCF_004522175.1	s__Paracoccus ravus	83.401	845	1484	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	81.6416	724	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009711185.1	s__Paracoccus limosus	81.5595	710	1484	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	81.5342	656	1484	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	81.3934	697	1484	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	81.3075	634	1484	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	81.1622	720	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_900100045.1	s__Paracoccus denitrificans	81.0792	707	1484	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	81.049	671	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_001546115.1	s__Paracoccus aminovorans_B	80.9676	692	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCF_900005615.1	s__Paracoccus aminovorans	80.9536	638	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:39,310] [INFO] GTDB search result was written to GCF_009711225.1_ASM971122v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:39,311] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:39,315] [INFO] DFAST_QC result json was written to GCF_009711225.1_ASM971122v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:39,315] [INFO] DFAST_QC completed!
[2024-01-24 15:28:39,315] [INFO] Total running time: 0h1m28s