[2024-01-24 14:56:22,694] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:22,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:22,698] [INFO] DQC Reference Directory: /var/lib/cwl/stg017fd717-a79e-4f08-b94b-254a3dc888d0/dqc_reference
[2024-01-24 14:56:26,557] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:26,558] [INFO] Task started: Prodigal
[2024-01-24 14:56:26,559] [INFO] Running command: gunzip -c /var/lib/cwl/stge20a5960-9dc8-4714-bd06-bb39c8f5e5a0/GCF_004063735.1_ASM406373v1_genomic.fna.gz | prodigal -d GCF_004063735.1_ASM406373v1_genomic.fna/cds.fna -a GCF_004063735.1_ASM406373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:43,508] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:43,508] [INFO] Task started: HMMsearch
[2024-01-24 14:56:43,508] [INFO] Running command: hmmsearch --tblout GCF_004063735.1_ASM406373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg017fd717-a79e-4f08-b94b-254a3dc888d0/dqc_reference/reference_markers.hmm GCF_004063735.1_ASM406373v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:43,952] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:43,953] [INFO] Found 6/6 markers.
[2024-01-24 14:56:44,001] [INFO] Query marker FASTA was written to GCF_004063735.1_ASM406373v1_genomic.fna/markers.fasta
[2024-01-24 14:56:44,002] [INFO] Task started: Blastn
[2024-01-24 14:56:44,002] [INFO] Running command: blastn -query GCF_004063735.1_ASM406373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg017fd717-a79e-4f08-b94b-254a3dc888d0/dqc_reference/reference_markers.fasta -out GCF_004063735.1_ASM406373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:45,129] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:45,133] [INFO] Selected 13 target genomes.
[2024-01-24 14:56:45,133] [INFO] Target genome list was writen to GCF_004063735.1_ASM406373v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:45,137] [INFO] Task started: fastANI
[2024-01-24 14:56:45,137] [INFO] Running command: fastANI --query /var/lib/cwl/stge20a5960-9dc8-4714-bd06-bb39c8f5e5a0/GCF_004063735.1_ASM406373v1_genomic.fna.gz --refList GCF_004063735.1_ASM406373v1_genomic.fna/target_genomes.txt --output GCF_004063735.1_ASM406373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:57:01,704] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:01,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg017fd717-a79e-4f08-b94b-254a3dc888d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:57:01,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg017fd717-a79e-4f08-b94b-254a3dc888d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:57:01,717] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:57:01,717] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:57:01,717] [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 denitrificans	strain=DSM 413	GCA_900100045.1	266	266	type	True	99.9601	1669	1745	95	conclusive
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	99.9207	1613	1745	95	conclusive
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	91.4009	1141	1745	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	91.3992	1131	1745	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	91.1099	1172	1745	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	91.0998	1215	1745	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	89.1314	998	1745	95	below_threshold
Paracoccus thiocyanatus	strain=ATCC 700171	GCA_900156255.1	34006	34006	type	True	88.9317	936	1745	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	84.4303	818	1745	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.2236	706	1745	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.3495	575	1745	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.7619	642	1745	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.1041	528	1745	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:57:01,719] [INFO] DFAST Taxonomy check result was written to GCF_004063735.1_ASM406373v1_genomic.fna/tc_result.tsv
[2024-01-24 14:57:01,719] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:57:01,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:57:01,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg017fd717-a79e-4f08-b94b-254a3dc888d0/dqc_reference/checkm_data
[2024-01-24 14:57:01,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:57:01,776] [INFO] Task started: CheckM
[2024-01-24 14:57:01,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004063735.1_ASM406373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004063735.1_ASM406373v1_genomic.fna/checkm_input GCF_004063735.1_ASM406373v1_genomic.fna/checkm_result
[2024-01-24 14:58:04,085] [INFO] Task succeeded: CheckM
[2024-01-24 14:58:04,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:58:04,107] [INFO] ===== Completeness check finished =====
[2024-01-24 14:58:04,107] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:58:04,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004063735.1_ASM406373v1_genomic.fna/markers.fasta)
[2024-01-24 14:58:04,109] [INFO] Task started: Blastn
[2024-01-24 14:58:04,109] [INFO] Running command: blastn -query GCF_004063735.1_ASM406373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg017fd717-a79e-4f08-b94b-254a3dc888d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_004063735.1_ASM406373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:58:06,330] [INFO] Task succeeded: Blastn
[2024-01-24 14:58:06,334] [INFO] Selected 7 target genomes.
[2024-01-24 14:58:06,334] [INFO] Target genome list was writen to GCF_004063735.1_ASM406373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:58:06,337] [INFO] Task started: fastANI
[2024-01-24 14:58:06,337] [INFO] Running command: fastANI --query /var/lib/cwl/stge20a5960-9dc8-4714-bd06-bb39c8f5e5a0/GCF_004063735.1_ASM406373v1_genomic.fna.gz --refList GCF_004063735.1_ASM406373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004063735.1_ASM406373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:58:15,705] [INFO] Task succeeded: fastANI
[2024-01-24 14:58:15,715] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:58:15,715] [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_900100045.1	s__Paracoccus denitrificans	99.96	1668	1745	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	conclusive
GCF_001447385.1	s__Paracoccus sp001447385	91.9659	1153	1745	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	91.4053	1140	1745	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_000518925.1	s__Paracoccus sp000518925	91.1157	1092	1745	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	91.0901	1173	1745	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_016446475.1	s__Paracoccus binzhouensis	89.1558	997	1745	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	88.9726	933	1745	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.14	97.14	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:58:15,719] [INFO] GTDB search result was written to GCF_004063735.1_ASM406373v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:58:15,720] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:58:15,723] [INFO] DFAST_QC result json was written to GCF_004063735.1_ASM406373v1_genomic.fna/dqc_result.json
[2024-01-24 14:58:15,723] [INFO] DFAST_QC completed!
[2024-01-24 14:58:15,724] [INFO] Total running time: 0h1m53s