[2023-06-29 13:03:23,348] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:03:23,350] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:03:23,351] [INFO] DQC Reference Directory: /var/lib/cwl/stg13210897-7d11-4bc1-b980-beb56ff47910/dqc_reference
[2023-06-29 13:03:24,601] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:03:24,602] [INFO] Task started: Prodigal
[2023-06-29 13:03:24,602] [INFO] Running command: gunzip -c /var/lib/cwl/stg73612e06-f129-42f2-978e-d7d58adabd28/GCA_023404035.1_ASM2340403v1_genomic.fna.gz | prodigal -d GCA_023404035.1_ASM2340403v1_genomic.fna/cds.fna -a GCA_023404035.1_ASM2340403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:03:33,093] [INFO] Task succeeded: Prodigal
[2023-06-29 13:03:33,094] [INFO] Task started: HMMsearch
[2023-06-29 13:03:33,094] [INFO] Running command: hmmsearch --tblout GCA_023404035.1_ASM2340403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13210897-7d11-4bc1-b980-beb56ff47910/dqc_reference/reference_markers.hmm GCA_023404035.1_ASM2340403v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:03:33,357] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:03:33,359] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg73612e06-f129-42f2-978e-d7d58adabd28/GCA_023404035.1_ASM2340403v1_genomic.fna.gz]
[2023-06-29 13:03:33,394] [INFO] Query marker FASTA was written to GCA_023404035.1_ASM2340403v1_genomic.fna/markers.fasta
[2023-06-29 13:03:33,395] [INFO] Task started: Blastn
[2023-06-29 13:03:33,395] [INFO] Running command: blastn -query GCA_023404035.1_ASM2340403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13210897-7d11-4bc1-b980-beb56ff47910/dqc_reference/reference_markers.fasta -out GCA_023404035.1_ASM2340403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:03:34,032] [INFO] Task succeeded: Blastn
[2023-06-29 13:03:34,035] [INFO] Selected 9 target genomes.
[2023-06-29 13:03:34,036] [INFO] Target genome list was writen to GCA_023404035.1_ASM2340403v1_genomic.fna/target_genomes.txt
[2023-06-29 13:03:34,037] [INFO] Task started: fastANI
[2023-06-29 13:03:34,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg73612e06-f129-42f2-978e-d7d58adabd28/GCA_023404035.1_ASM2340403v1_genomic.fna.gz --refList GCA_023404035.1_ASM2340403v1_genomic.fna/target_genomes.txt --output GCA_023404035.1_ASM2340403v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:03:40,920] [INFO] Task succeeded: fastANI
[2023-06-29 13:03:40,921] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13210897-7d11-4bc1-b980-beb56ff47910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:03:40,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13210897-7d11-4bc1-b980-beb56ff47910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:03:40,932] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:03:40,932] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:03:40,933] [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	87.2493	689	926	95	below_threshold
Desulfovibrio legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	79.8243	405	926	95	below_threshold
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	79.6472	353	926	95	below_threshold
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	78.3258	290	926	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	77.5928	170	926	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	77.4753	182	926	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.3407	210	926	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	76.4475	90	926	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:03:40,935] [INFO] DFAST Taxonomy check result was written to GCA_023404035.1_ASM2340403v1_genomic.fna/tc_result.tsv
[2023-06-29 13:03:40,936] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:03:40,936] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:03:40,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13210897-7d11-4bc1-b980-beb56ff47910/dqc_reference/checkm_data
[2023-06-29 13:03:40,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:03:40,969] [INFO] Task started: CheckM
[2023-06-29 13:03:40,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023404035.1_ASM2340403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023404035.1_ASM2340403v1_genomic.fna/checkm_input GCA_023404035.1_ASM2340403v1_genomic.fna/checkm_result
[2023-06-29 13:04:09,982] [INFO] Task succeeded: CheckM
[2023-06-29 13:04:09,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:04:10,008] [INFO] ===== Completeness check finished =====
[2023-06-29 13:04:10,008] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:04:10,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023404035.1_ASM2340403v1_genomic.fna/markers.fasta)
[2023-06-29 13:04:10,009] [INFO] Task started: Blastn
[2023-06-29 13:04:10,009] [INFO] Running command: blastn -query GCA_023404035.1_ASM2340403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13210897-7d11-4bc1-b980-beb56ff47910/dqc_reference/reference_markers_gtdb.fasta -out GCA_023404035.1_ASM2340403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:04:10,959] [INFO] Task succeeded: Blastn
[2023-06-29 13:04:10,964] [INFO] Selected 6 target genomes.
[2023-06-29 13:04:10,965] [INFO] Target genome list was writen to GCA_023404035.1_ASM2340403v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:04:10,972] [INFO] Task started: fastANI
[2023-06-29 13:04:10,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg73612e06-f129-42f2-978e-d7d58adabd28/GCA_023404035.1_ASM2340403v1_genomic.fna.gz --refList GCA_023404035.1_ASM2340403v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023404035.1_ASM2340403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:04:15,836] [INFO] Task succeeded: fastANI
[2023-06-29 13:04:15,846] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:04:15,847] [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_001553605.1	s__Desulfovibrio fairfieldensis	97.2013	836	926	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	97.09	95.23	0.86	0.83	6	conclusive
GCF_009696265.1	s__Desulfovibrio porci	87.2493	689	926	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.64	99.64	0.91	0.91	2	-
GCA_000403945.1	s__Desulfovibrio sp000403945	85.0066	440	926	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	84.6345	524	926	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_011039085.1	s__Desulfovibrio sp011039085	82.055	473	926	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.72	96.72	0.85	0.85	2	-
GCA_015062205.1	s__Desulfovibrio desulfuricans_D	80.067	366	926	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:04:15,849] [INFO] GTDB search result was written to GCA_023404035.1_ASM2340403v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:04:15,849] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:04:15,853] [INFO] DFAST_QC result json was written to GCA_023404035.1_ASM2340403v1_genomic.fna/dqc_result.json
[2023-06-29 13:04:15,853] [INFO] DFAST_QC completed!
[2023-06-29 13:04:15,853] [INFO] Total running time: 0h0m53s