[2024-01-24 13:22:40,506] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:40,507] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:40,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg063b3f83-7fd9-47d8-b028-73f6e9dbe9ea/dqc_reference
[2024-01-24 13:22:41,889] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:41,890] [INFO] Task started: Prodigal
[2024-01-24 13:22:41,890] [INFO] Running command: gunzip -c /var/lib/cwl/stgb89a432a-36c8-419d-8862-941c1b63ddbe/GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/cds.fna -a GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:05,286] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:05,286] [INFO] Task started: HMMsearch
[2024-01-24 13:23:05,286] [INFO] Running command: hmmsearch --tblout GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg063b3f83-7fd9-47d8-b028-73f6e9dbe9ea/dqc_reference/reference_markers.hmm GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:05,585] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:05,587] [INFO] Found 6/6 markers.
[2024-01-24 13:23:05,636] [INFO] Query marker FASTA was written to GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:23:05,636] [INFO] Task started: Blastn
[2024-01-24 13:23:05,636] [INFO] Running command: blastn -query GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg063b3f83-7fd9-47d8-b028-73f6e9dbe9ea/dqc_reference/reference_markers.fasta -out GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:06,258] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:06,262] [INFO] Selected 27 target genomes.
[2024-01-24 13:23:06,263] [INFO] Target genome list was writen to GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:23:06,284] [INFO] Task started: fastANI
[2024-01-24 13:23:06,284] [INFO] Running command: fastANI --query /var/lib/cwl/stgb89a432a-36c8-419d-8862-941c1b63ddbe/GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna.gz --refList GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:30,822] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:30,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg063b3f83-7fd9-47d8-b028-73f6e9dbe9ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:30,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg063b3f83-7fd9-47d8-b028-73f6e9dbe9ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:30,830] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:30,830] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:30,830] [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
Reichenbachiella faecimaris	strain=DSM 26133	GCA_900176375.1	692418	692418	type	True	100.0	1563	1566	95	conclusive
Reichenbachiella agariperforans	strain=DSM 26134	GCA_900142205.1	156994	156994	type	True	77.9193	97	1566	95	below_threshold
Reichenbachiella versicolor	strain=DC003	GCA_003171675.1	1821036	1821036	type	True	76.8552	68	1566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:30,832] [INFO] DFAST Taxonomy check result was written to GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:23:30,833] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:30,833] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:30,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg063b3f83-7fd9-47d8-b028-73f6e9dbe9ea/dqc_reference/checkm_data
[2024-01-24 13:23:30,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:30,883] [INFO] Task started: CheckM
[2024-01-24 13:23:30,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/checkm_input GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:24:35,073] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:35,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:35,096] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:35,097] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:35,097] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:24:35,097] [INFO] Task started: Blastn
[2024-01-24 13:24:35,098] [INFO] Running command: blastn -query GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg063b3f83-7fd9-47d8-b028-73f6e9dbe9ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:35,827] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:35,831] [INFO] Selected 26 target genomes.
[2024-01-24 13:24:35,831] [INFO] Target genome list was writen to GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:36,544] [INFO] Task started: fastANI
[2024-01-24 13:24:36,545] [INFO] Running command: fastANI --query /var/lib/cwl/stgb89a432a-36c8-419d-8862-941c1b63ddbe/GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna.gz --refList GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:56,585] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:56,594] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:56,595] [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_900176375.1	s__Reichenbachiella faecimaris	100.0	1564	1566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Reichenbachiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900142205.1	s__Reichenbachiella agariperforans	77.9193	97	1566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Reichenbachiella	95.0	98.48	98.45	0.94	0.94	3	-
GCF_002742335.1	s__Reichenbachiella sp002742335	77.4864	99	1566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Reichenbachiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003171675.1	s__Reichenbachiella versicolor	76.8552	68	1566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Reichenbachiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:56,597] [INFO] GTDB search result was written to GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:56,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:56,601] [INFO] DFAST_QC result json was written to GCF_900176375.1_IMG-taxon_2619619645_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:24:56,602] [INFO] DFAST_QC completed!
[2024-01-24 13:24:56,602] [INFO] Total running time: 0h2m16s