[2024-01-24 14:03:07,661] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:07,664] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:07,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg9abd4b65-e24f-4cc9-b47b-a20044e4ca48/dqc_reference
[2024-01-24 14:03:09,012] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:09,013] [INFO] Task started: Prodigal
[2024-01-24 14:03:09,013] [INFO] Running command: gunzip -c /var/lib/cwl/stg27ac92c9-b982-4cab-bf4b-2c84c08c7fef/GCF_009696265.1_ASM969626v1_genomic.fna.gz | prodigal -d GCF_009696265.1_ASM969626v1_genomic.fna/cds.fna -a GCF_009696265.1_ASM969626v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:19,564] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:19,565] [INFO] Task started: HMMsearch
[2024-01-24 14:03:19,565] [INFO] Running command: hmmsearch --tblout GCF_009696265.1_ASM969626v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9abd4b65-e24f-4cc9-b47b-a20044e4ca48/dqc_reference/reference_markers.hmm GCF_009696265.1_ASM969626v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:19,913] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:19,915] [INFO] Found 6/6 markers.
[2024-01-24 14:03:19,944] [INFO] Query marker FASTA was written to GCF_009696265.1_ASM969626v1_genomic.fna/markers.fasta
[2024-01-24 14:03:19,944] [INFO] Task started: Blastn
[2024-01-24 14:03:19,945] [INFO] Running command: blastn -query GCF_009696265.1_ASM969626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9abd4b65-e24f-4cc9-b47b-a20044e4ca48/dqc_reference/reference_markers.fasta -out GCF_009696265.1_ASM969626v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:20,652] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:20,655] [INFO] Selected 16 target genomes.
[2024-01-24 14:03:20,655] [INFO] Target genome list was writen to GCF_009696265.1_ASM969626v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:20,666] [INFO] Task started: fastANI
[2024-01-24 14:03:20,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg27ac92c9-b982-4cab-bf4b-2c84c08c7fef/GCF_009696265.1_ASM969626v1_genomic.fna.gz --refList GCF_009696265.1_ASM969626v1_genomic.fna/target_genomes.txt --output GCF_009696265.1_ASM969626v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:30,699] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:30,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9abd4b65-e24f-4cc9-b47b-a20044e4ca48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:30,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9abd4b65-e24f-4cc9-b47b-a20044e4ca48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:30,716] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:30,717] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:30,717] [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
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	100.0	1082	1083	95	conclusive
Desulfovibrio legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	80.2251	468	1083	95	below_threshold
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	79.7177	430	1083	95	below_threshold
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	78.6971	357	1083	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	77.7226	206	1083	95	below_threshold
Mailhella massiliensis	strain=Marseille-P3199	GCA_900155525.1	1903261	1903261	type	True	77.3618	155	1083	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.2759	265	1083	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	76.6621	130	1083	95	below_threshold
Pseudodesulfovibrio cashew	strain=SRB007	GCA_009762795.1	2678688	2678688	type	True	76.5814	103	1083	95	below_threshold
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	76.5714	156	1083	95	below_threshold
Desulfovibrio carbinoliphilus subsp. oakridgensis	strain=FW-101-2B	GCA_000177215.2	694327	345370	type	True	76.5005	135	1083	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	74.9929	51	1083	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:30,721] [INFO] DFAST Taxonomy check result was written to GCF_009696265.1_ASM969626v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:30,722] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:30,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:30,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9abd4b65-e24f-4cc9-b47b-a20044e4ca48/dqc_reference/checkm_data
[2024-01-24 14:03:30,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:30,768] [INFO] Task started: CheckM
[2024-01-24 14:03:30,768] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009696265.1_ASM969626v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009696265.1_ASM969626v1_genomic.fna/checkm_input GCF_009696265.1_ASM969626v1_genomic.fna/checkm_result
[2024-01-24 14:04:04,704] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:04,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:04,732] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:04,733] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:04,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009696265.1_ASM969626v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:04,734] [INFO] Task started: Blastn
[2024-01-24 14:04:04,734] [INFO] Running command: blastn -query GCF_009696265.1_ASM969626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9abd4b65-e24f-4cc9-b47b-a20044e4ca48/dqc_reference/reference_markers_gtdb.fasta -out GCF_009696265.1_ASM969626v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:05,726] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:05,729] [INFO] Selected 6 target genomes.
[2024-01-24 14:04:05,730] [INFO] Target genome list was writen to GCF_009696265.1_ASM969626v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:05,746] [INFO] Task started: fastANI
[2024-01-24 14:04:05,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg27ac92c9-b982-4cab-bf4b-2c84c08c7fef/GCF_009696265.1_ASM969626v1_genomic.fna.gz --refList GCF_009696265.1_ASM969626v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009696265.1_ASM969626v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:10,737] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:10,744] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:10,744] [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_009696265.1	s__Desulfovibrio porci	100.0	1082	1083	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.64	99.64	0.91	0.91	2	conclusive
GCA_000403945.1	s__Desulfovibrio sp000403945	92.0997	525	1083	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575755.1	s__Desulfovibrio sp910575755	88.6455	657	1083	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553605.1	s__Desulfovibrio fairfieldensis	87.4626	837	1083	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	97.09	95.23	0.86	0.83	6	-
GCF_011039085.1	s__Desulfovibrio sp011039085	82.2375	585	1083	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.72	96.72	0.85	0.85	2	-
GCF_900102485.1	s__Desulfovibrio legallii_A	80.5072	504	1083	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.86	99.86	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:10,745] [INFO] GTDB search result was written to GCF_009696265.1_ASM969626v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:10,746] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:10,749] [INFO] DFAST_QC result json was written to GCF_009696265.1_ASM969626v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:10,749] [INFO] DFAST_QC completed!
[2024-01-24 14:04:10,749] [INFO] Total running time: 0h1m3s