[2023-06-18 21:39:33,943] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:39:33,945] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:39:33,945] [INFO] DQC Reference Directory: /var/lib/cwl/stg269d2522-1c60-473b-bfe5-d610f382f196/dqc_reference
[2023-06-18 21:39:35,314] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:39:35,315] [INFO] Task started: Prodigal
[2023-06-18 21:39:35,315] [INFO] Running command: gunzip -c /var/lib/cwl/stga19ba7eb-b652-4989-965c-825b6b63915b/GCA_013314855.1_ASM1331485v1_genomic.fna.gz | prodigal -d GCA_013314855.1_ASM1331485v1_genomic.fna/cds.fna -a GCA_013314855.1_ASM1331485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:39:43,846] [INFO] Task succeeded: Prodigal
[2023-06-18 21:39:43,847] [INFO] Task started: HMMsearch
[2023-06-18 21:39:43,847] [INFO] Running command: hmmsearch --tblout GCA_013314855.1_ASM1331485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg269d2522-1c60-473b-bfe5-d610f382f196/dqc_reference/reference_markers.hmm GCA_013314855.1_ASM1331485v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:39:44,191] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:39:44,193] [INFO] Found 6/6 markers.
[2023-06-18 21:39:44,241] [INFO] Query marker FASTA was written to GCA_013314855.1_ASM1331485v1_genomic.fna/markers.fasta
[2023-06-18 21:39:44,241] [INFO] Task started: Blastn
[2023-06-18 21:39:44,242] [INFO] Running command: blastn -query GCA_013314855.1_ASM1331485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg269d2522-1c60-473b-bfe5-d610f382f196/dqc_reference/reference_markers.fasta -out GCA_013314855.1_ASM1331485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:39:44,841] [INFO] Task succeeded: Blastn
[2023-06-18 21:39:44,845] [INFO] Selected 13 target genomes.
[2023-06-18 21:39:44,846] [INFO] Target genome list was writen to GCA_013314855.1_ASM1331485v1_genomic.fna/target_genomes.txt
[2023-06-18 21:39:44,850] [INFO] Task started: fastANI
[2023-06-18 21:39:44,850] [INFO] Running command: fastANI --query /var/lib/cwl/stga19ba7eb-b652-4989-965c-825b6b63915b/GCA_013314855.1_ASM1331485v1_genomic.fna.gz --refList GCA_013314855.1_ASM1331485v1_genomic.fna/target_genomes.txt --output GCA_013314855.1_ASM1331485v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:39:52,678] [INFO] Task succeeded: fastANI
[2023-06-18 21:39:52,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg269d2522-1c60-473b-bfe5-d610f382f196/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:39:52,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg269d2522-1c60-473b-bfe5-d610f382f196/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:39:52,684] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 21:39:52,684] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 21:39:52,684] [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
Acetivibrio clariflavus	strain=DSM 19732	GCA_000237085.1	288965	288965	type	True	76.735	63	1351	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 21:39:52,687] [INFO] DFAST Taxonomy check result was written to GCA_013314855.1_ASM1331485v1_genomic.fna/tc_result.tsv
[2023-06-18 21:39:52,687] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:39:52,687] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:39:52,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg269d2522-1c60-473b-bfe5-d610f382f196/dqc_reference/checkm_data
[2023-06-18 21:39:52,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:39:52,761] [INFO] Task started: CheckM
[2023-06-18 21:39:52,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013314855.1_ASM1331485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013314855.1_ASM1331485v1_genomic.fna/checkm_input GCA_013314855.1_ASM1331485v1_genomic.fna/checkm_result
[2023-06-18 21:40:24,345] [INFO] Task succeeded: CheckM
[2023-06-18 21:40:24,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:40:24,378] [INFO] ===== Completeness check finished =====
[2023-06-18 21:40:24,378] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:40:24,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013314855.1_ASM1331485v1_genomic.fna/markers.fasta)
[2023-06-18 21:40:24,379] [INFO] Task started: Blastn
[2023-06-18 21:40:24,380] [INFO] Running command: blastn -query GCA_013314855.1_ASM1331485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg269d2522-1c60-473b-bfe5-d610f382f196/dqc_reference/reference_markers_gtdb.fasta -out GCA_013314855.1_ASM1331485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:40:25,149] [INFO] Task succeeded: Blastn
[2023-06-18 21:40:25,155] [INFO] Selected 26 target genomes.
[2023-06-18 21:40:25,156] [INFO] Target genome list was writen to GCA_013314855.1_ASM1331485v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:40:25,188] [INFO] Task started: fastANI
[2023-06-18 21:40:25,188] [INFO] Running command: fastANI --query /var/lib/cwl/stga19ba7eb-b652-4989-965c-825b6b63915b/GCA_013314855.1_ASM1331485v1_genomic.fna.gz --refList GCA_013314855.1_ASM1331485v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013314855.1_ASM1331485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:40:37,997] [INFO] Task succeeded: fastANI
[2023-06-18 21:40:38,002] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:40:38,002] [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
GCA_013314855.1	s__Ch48 sp013314855	100.0	1330	1351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DUMC01;g__Ch48	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000237085.1	s__Acetivibrio clariflavus	76.7682	62	1351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Acetivibrio	95.0	98.23	96.28	0.88	0.88	4	-
--------------------------------------------------------------------------------
[2023-06-18 21:40:38,004] [INFO] GTDB search result was written to GCA_013314855.1_ASM1331485v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:40:38,005] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:40:38,008] [INFO] DFAST_QC result json was written to GCA_013314855.1_ASM1331485v1_genomic.fna/dqc_result.json
[2023-06-18 21:40:38,008] [INFO] DFAST_QC completed!
[2023-06-18 21:40:38,008] [INFO] Total running time: 0h1m4s