[2024-01-24 13:42:57,535] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:57,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:57,537] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd4bbe93-e76e-40e1-8954-b00a4918ac32/dqc_reference
[2024-01-24 13:42:58,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:58,785] [INFO] Task started: Prodigal
[2024-01-24 13:42:58,785] [INFO] Running command: gunzip -c /var/lib/cwl/stga769d184-7f49-47ca-9fb6-839084b35619/GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/cds.fna -a GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:09,133] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:09,133] [INFO] Task started: HMMsearch
[2024-01-24 13:43:09,133] [INFO] Running command: hmmsearch --tblout GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd4bbe93-e76e-40e1-8954-b00a4918ac32/dqc_reference/reference_markers.hmm GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:09,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:09,403] [INFO] Found 6/6 markers.
[2024-01-24 13:43:09,442] [INFO] Query marker FASTA was written to GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:43:09,443] [INFO] Task started: Blastn
[2024-01-24 13:43:09,443] [INFO] Running command: blastn -query GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd4bbe93-e76e-40e1-8954-b00a4918ac32/dqc_reference/reference_markers.fasta -out GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:10,462] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:10,466] [INFO] Selected 13 target genomes.
[2024-01-24 13:43:10,466] [INFO] Target genome list was writen to GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:43:10,471] [INFO] Task started: fastANI
[2024-01-24 13:43:10,472] [INFO] Running command: fastANI --query /var/lib/cwl/stga769d184-7f49-47ca-9fb6-839084b35619/GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna.gz --refList GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:22,837] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:22,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd4bbe93-e76e-40e1-8954-b00a4918ac32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:22,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd4bbe93-e76e-40e1-8954-b00a4918ac32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:22,849] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:22,850] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:22,850] [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 thiocyanatus	strain=ATCC 700171	GCA_900156255.1	34006	34006	type	True	100.0	1143	1146	95	conclusive
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	90.2664	930	1146	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	90.2278	910	1146	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	89.9685	907	1146	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	89.8566	919	1146	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	89.1387	898	1146	95	below_threshold
Paracoccus denitrificans	strain=DSM 413	GCA_900100045.1	266	266	type	True	89.1107	924	1146	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	88.0908	796	1146	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	84.424	695	1146	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.4576	549	1146	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.0132	532	1146	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.9823	567	1146	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.0952	438	1146	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:22,852] [INFO] DFAST Taxonomy check result was written to GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:43:22,852] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:22,852] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:22,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd4bbe93-e76e-40e1-8954-b00a4918ac32/dqc_reference/checkm_data
[2024-01-24 13:43:22,853] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:22,896] [INFO] Task started: CheckM
[2024-01-24 13:43:22,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/checkm_input GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:43:57,942] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:57,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:57,961] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:57,961] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:57,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:43:57,962] [INFO] Task started: Blastn
[2024-01-24 13:43:57,962] [INFO] Running command: blastn -query GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd4bbe93-e76e-40e1-8954-b00a4918ac32/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:59,926] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:59,933] [INFO] Selected 7 target genomes.
[2024-01-24 13:43:59,933] [INFO] Target genome list was writen to GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:59,938] [INFO] Task started: fastANI
[2024-01-24 13:43:59,938] [INFO] Running command: fastANI --query /var/lib/cwl/stga769d184-7f49-47ca-9fb6-839084b35619/GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna.gz --refList GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:07,749] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:07,761] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:07,761] [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_900156255.1	s__Paracoccus thiocyanatus	100.0	1143	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.14	97.14	0.86	0.86	2	conclusive
GCF_000763885.1	s__Paracoccus versutus	90.2278	910	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_008824185.1	s__Paracoccus pantotrophus	89.8521	920	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_900100045.1	s__Paracoccus denitrificans	89.1087	926	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	-
GCF_001447385.1	s__Paracoccus sp001447385	89.0939	894	1146	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	88.9195	883	1146	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	88.0653	798	1146	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 13:44:07,763] [INFO] GTDB search result was written to GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:07,763] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:07,766] [INFO] DFAST_QC result json was written to GCF_900156255.1_IMG-taxon_2681812813_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:44:07,766] [INFO] DFAST_QC completed!
[2024-01-24 13:44:07,766] [INFO] Total running time: 0h1m10s