[2024-01-24 12:21:56,865] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:56,868] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:56,868] [INFO] DQC Reference Directory: /var/lib/cwl/stg917a52a0-0906-4c75-85fb-1eaee20284d0/dqc_reference
[2024-01-24 12:21:58,170] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:58,171] [INFO] Task started: Prodigal
[2024-01-24 12:21:58,172] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f0942ae-47b5-4746-9be1-d2e1238bfc88/GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/cds.fna -a GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:09,563] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:09,564] [INFO] Task started: HMMsearch
[2024-01-24 12:22:09,564] [INFO] Running command: hmmsearch --tblout GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg917a52a0-0906-4c75-85fb-1eaee20284d0/dqc_reference/reference_markers.hmm GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:09,858] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:09,859] [INFO] Found 6/6 markers.
[2024-01-24 12:22:09,893] [INFO] Query marker FASTA was written to GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:22:09,893] [INFO] Task started: Blastn
[2024-01-24 12:22:09,893] [INFO] Running command: blastn -query GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg917a52a0-0906-4c75-85fb-1eaee20284d0/dqc_reference/reference_markers.fasta -out GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:10,944] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:10,947] [INFO] Selected 14 target genomes.
[2024-01-24 12:22:10,948] [INFO] Target genome list was writen to GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:22:10,966] [INFO] Task started: fastANI
[2024-01-24 12:22:10,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f0942ae-47b5-4746-9be1-d2e1238bfc88/GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna.gz --refList GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:26,105] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:26,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg917a52a0-0906-4c75-85fb-1eaee20284d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:26,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg917a52a0-0906-4c75-85fb-1eaee20284d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:26,117] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:26,118] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:26,118] [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 aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	100.0	1265	1270	95	conclusive
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	99.983	1264	1270	95	conclusive
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	88.1801	875	1270	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	87.624	907	1270	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	87.6184	882	1270	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	87.2486	870	1270	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	87.2283	863	1270	95	below_threshold
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	85.3366	797	1270	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	85.2746	831	1270	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	84.8787	753	1270	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.2514	530	1270	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.0489	528	1270	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.6446	554	1270	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.973	479	1270	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:26,120] [INFO] DFAST Taxonomy check result was written to GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:22:26,120] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:26,120] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:26,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg917a52a0-0906-4c75-85fb-1eaee20284d0/dqc_reference/checkm_data
[2024-01-24 12:22:26,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:26,165] [INFO] Task started: CheckM
[2024-01-24 12:22:26,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/checkm_input GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:23:04,315] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:04,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:04,333] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:04,334] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:04,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:23:04,334] [INFO] Task started: Blastn
[2024-01-24 12:23:04,335] [INFO] Running command: blastn -query GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg917a52a0-0906-4c75-85fb-1eaee20284d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:06,408] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:06,413] [INFO] Selected 9 target genomes.
[2024-01-24 12:23:06,413] [INFO] Target genome list was writen to GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:06,420] [INFO] Task started: fastANI
[2024-01-24 12:23:06,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f0942ae-47b5-4746-9be1-d2e1238bfc88/GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna.gz --refList GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:16,817] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:16,831] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:16,832] [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_900005615.1	s__Paracoccus aminovorans	99.983	1264	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_001546115.1	s__Paracoccus aminovorans_B	90.1543	986	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCF_016446475.1	s__Paracoccus binzhouensis	88.1454	877	1270	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	87.9064	899	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_000763885.1	s__Paracoccus versutus	87.6008	883	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_001447385.1	s__Paracoccus sp001447385	87.2723	884	1270	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	87.2563	870	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_000622145.1	s__Paracoccus yeei	85.2001	838	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	-
GCF_003285265.1	s__Paracoccus mutanolyticus	84.9088	751	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:16,834] [INFO] GTDB search result was written to GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:16,834] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:16,851] [INFO] DFAST_QC result json was written to GCF_900113565.1_IMG-taxon_2615840720_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:23:16,851] [INFO] DFAST_QC completed!
[2024-01-24 12:23:16,852] [INFO] Total running time: 0h1m20s