[2024-01-24 13:32:55,498] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:55,500] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:55,500] [INFO] DQC Reference Directory: /var/lib/cwl/stg83666122-fa88-4acc-b0e3-35d5c0e1cbf7/dqc_reference
[2024-01-24 13:32:56,759] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:56,760] [INFO] Task started: Prodigal
[2024-01-24 13:32:56,760] [INFO] Running command: gunzip -c /var/lib/cwl/stg619d1d68-36c8-4046-a967-8559b4f5ed6c/GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/cds.fna -a GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:06,767] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:06,768] [INFO] Task started: HMMsearch
[2024-01-24 13:33:06,768] [INFO] Running command: hmmsearch --tblout GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83666122-fa88-4acc-b0e3-35d5c0e1cbf7/dqc_reference/reference_markers.hmm GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:07,029] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:07,031] [INFO] Found 6/6 markers.
[2024-01-24 13:33:07,061] [INFO] Query marker FASTA was written to GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:33:07,062] [INFO] Task started: Blastn
[2024-01-24 13:33:07,062] [INFO] Running command: blastn -query GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg83666122-fa88-4acc-b0e3-35d5c0e1cbf7/dqc_reference/reference_markers.fasta -out GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:07,692] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:07,696] [INFO] Selected 18 target genomes.
[2024-01-24 13:33:07,697] [INFO] Target genome list was writen to GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:33:07,712] [INFO] Task started: fastANI
[2024-01-24 13:33:07,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg619d1d68-36c8-4046-a967-8559b4f5ed6c/GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna.gz --refList GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:21,797] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:21,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83666122-fa88-4acc-b0e3-35d5c0e1cbf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:21,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83666122-fa88-4acc-b0e3-35d5c0e1cbf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:21,807] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:21,809] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:21,809] [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
Paradesulfovibrio bizertensis	strain=DSM 18034	GCA_900167065.1	376490	376490	type	True	100.0	1073	1076	95	conclusive
Desulfobaculum xiamenense	strain=DSM 24233	GCA_011927665.1	995050	995050	type	True	77.5616	187	1076	95	below_threshold
Maridesulfovibrio salexigens	strain=DSM 2638	GCA_000023445.1	880	880	type	True	76.5563	54	1076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:21,811] [INFO] DFAST Taxonomy check result was written to GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:33:21,812] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:21,812] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:21,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83666122-fa88-4acc-b0e3-35d5c0e1cbf7/dqc_reference/checkm_data
[2024-01-24 13:33:21,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:21,851] [INFO] Task started: CheckM
[2024-01-24 13:33:21,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/checkm_input GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:33:56,599] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:56,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:56,623] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:56,624] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:56,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:33:56,624] [INFO] Task started: Blastn
[2024-01-24 13:33:56,625] [INFO] Running command: blastn -query GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg83666122-fa88-4acc-b0e3-35d5c0e1cbf7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:57,493] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:57,497] [INFO] Selected 21 target genomes.
[2024-01-24 13:33:57,498] [INFO] Target genome list was writen to GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:57,557] [INFO] Task started: fastANI
[2024-01-24 13:33:57,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg619d1d68-36c8-4046-a967-8559b4f5ed6c/GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna.gz --refList GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:11,947] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:11,955] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:11,955] [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_900167065.1	s__Paradesulfovibrio bizertensis	100.0	1073	1076	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Paradesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011927665.1	s__Desulfobaculum xiamenense	77.5453	188	1076	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023445.1	s__Maridesulfovibrio salexigens	76.5563	54	1076	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010470665.1	s__Maridesulfovibrio sp010470665	76.2284	53	1076	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519125.1	s__Desulfocurvus vexinensis	76.1871	60	1076	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfocurvus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:11,958] [INFO] GTDB search result was written to GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:11,959] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:11,972] [INFO] DFAST_QC result json was written to GCF_900167065.1_IMG-taxon_2568526004_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:34:11,973] [INFO] DFAST_QC completed!
[2024-01-24 13:34:11,973] [INFO] Total running time: 0h1m16s