[2024-01-24 14:55:51,342] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:51,344] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:51,344] [INFO] DQC Reference Directory: /var/lib/cwl/stg957b4f2c-04c1-4ea6-9993-e073ae6b23c8/dqc_reference
[2024-01-24 14:55:52,658] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:52,659] [INFO] Task started: Prodigal
[2024-01-24 14:55:52,659] [INFO] Running command: gunzip -c /var/lib/cwl/stg325b53de-385f-4919-842b-2b2683e8b169/GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/cds.fna -a GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:01,192] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:01,192] [INFO] Task started: HMMsearch
[2024-01-24 14:56:01,192] [INFO] Running command: hmmsearch --tblout GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg957b4f2c-04c1-4ea6-9993-e073ae6b23c8/dqc_reference/reference_markers.hmm GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:01,493] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:01,494] [INFO] Found 6/6 markers.
[2024-01-24 14:56:01,525] [INFO] Query marker FASTA was written to GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:56:01,525] [INFO] Task started: Blastn
[2024-01-24 14:56:01,525] [INFO] Running command: blastn -query GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg957b4f2c-04c1-4ea6-9993-e073ae6b23c8/dqc_reference/reference_markers.fasta -out GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:02,237] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:02,242] [INFO] Selected 24 target genomes.
[2024-01-24 14:56:02,243] [INFO] Target genome list was writen to GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:56:02,254] [INFO] Task started: fastANI
[2024-01-24 14:56:02,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg325b53de-385f-4919-842b-2b2683e8b169/GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna.gz --refList GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:15,643] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:15,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg957b4f2c-04c1-4ea6-9993-e073ae6b23c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:15,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg957b4f2c-04c1-4ea6-9993-e073ae6b23c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:15,651] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:15,652] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:15,652] [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
Seinonella peptonophila	strain=DSM 44666	GCA_900129355.1	112248	112248	type	True	100.0	1259	1260	95	conclusive
Shimazuella alba	strain=KC615	GCA_009831235.1	2690964	2690964	type	True	78.2671	54	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:15,654] [INFO] DFAST Taxonomy check result was written to GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:56:15,655] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:15,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:15,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg957b4f2c-04c1-4ea6-9993-e073ae6b23c8/dqc_reference/checkm_data
[2024-01-24 14:56:15,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:15,694] [INFO] Task started: CheckM
[2024-01-24 14:56:15,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/checkm_input GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:56:48,147] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:48,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:48,198] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:48,198] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:48,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:56:48,198] [INFO] Task started: Blastn
[2024-01-24 14:56:48,199] [INFO] Running command: blastn -query GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg957b4f2c-04c1-4ea6-9993-e073ae6b23c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:49,223] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:49,227] [INFO] Selected 26 target genomes.
[2024-01-24 14:56:49,227] [INFO] Target genome list was writen to GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:49,250] [INFO] Task started: fastANI
[2024-01-24 14:56:49,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg325b53de-385f-4919-842b-2b2683e8b169/GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna.gz --refList GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:08,829] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:08,835] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:08,835] [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_900129355.1	s__Seinonella peptonophila	100.0	1259	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Seinonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009831235.1	s__Shimazuella sp009831235	78.3394	53	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Shimazuella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:08,837] [INFO] GTDB search result was written to GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:08,837] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:08,840] [INFO] DFAST_QC result json was written to GCF_900129355.1_IMG-taxon_2695420940_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:57:08,840] [INFO] DFAST_QC completed!
[2024-01-24 14:57:08,840] [INFO] Total running time: 0h1m17s