[2024-01-24 14:15:02,197] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:02,200] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:02,200] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9a84ff7-4e0a-4a49-9a4e-64c1bbd31f0d/dqc_reference
[2024-01-24 14:15:03,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:03,640] [INFO] Task started: Prodigal
[2024-01-24 14:15:03,641] [INFO] Running command: gunzip -c /var/lib/cwl/stg28a07cb7-f8f4-43b4-a87c-c5f4aa898467/GCF_002006755.1_ASM200675v1_genomic.fna.gz | prodigal -d GCF_002006755.1_ASM200675v1_genomic.fna/cds.fna -a GCF_002006755.1_ASM200675v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:08,824] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:08,824] [INFO] Task started: HMMsearch
[2024-01-24 14:15:08,824] [INFO] Running command: hmmsearch --tblout GCF_002006755.1_ASM200675v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9a84ff7-4e0a-4a49-9a4e-64c1bbd31f0d/dqc_reference/reference_markers.hmm GCF_002006755.1_ASM200675v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:09,091] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:09,093] [INFO] Found 6/6 markers.
[2024-01-24 14:15:09,122] [INFO] Query marker FASTA was written to GCF_002006755.1_ASM200675v1_genomic.fna/markers.fasta
[2024-01-24 14:15:09,123] [INFO] Task started: Blastn
[2024-01-24 14:15:09,123] [INFO] Running command: blastn -query GCF_002006755.1_ASM200675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9a84ff7-4e0a-4a49-9a4e-64c1bbd31f0d/dqc_reference/reference_markers.fasta -out GCF_002006755.1_ASM200675v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:09,768] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:09,774] [INFO] Selected 24 target genomes.
[2024-01-24 14:15:09,774] [INFO] Target genome list was writen to GCF_002006755.1_ASM200675v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:09,789] [INFO] Task started: fastANI
[2024-01-24 14:15:09,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg28a07cb7-f8f4-43b4-a87c-c5f4aa898467/GCF_002006755.1_ASM200675v1_genomic.fna.gz --refList GCF_002006755.1_ASM200675v1_genomic.fna/target_genomes.txt --output GCF_002006755.1_ASM200675v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:21,736] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:21,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9a84ff7-4e0a-4a49-9a4e-64c1bbd31f0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:21,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9a84ff7-4e0a-4a49-9a4e-64c1bbd31f0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:21,741] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:21,741] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:21,741] [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
Wohlfahrtiimonas larvae	strain=kbl006	GCA_002006755.1	1157986	1157986	type	True	100.0	695	708	95	conclusive
Wohlfahrtiimonas populi	strain=34C10-3-10	GCA_002006795.1	1940240	1940240	type	True	86.1588	569	708	95	below_threshold
Wohlfahrtiimonas chitiniclastica	strain=DSM 18708	GCA_000375345.1	400946	400946	type	True	79.2662	235	708	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:21,743] [INFO] DFAST Taxonomy check result was written to GCF_002006755.1_ASM200675v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:21,744] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:21,744] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:21,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9a84ff7-4e0a-4a49-9a4e-64c1bbd31f0d/dqc_reference/checkm_data
[2024-01-24 14:15:21,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:21,782] [INFO] Task started: CheckM
[2024-01-24 14:15:21,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002006755.1_ASM200675v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002006755.1_ASM200675v1_genomic.fna/checkm_input GCF_002006755.1_ASM200675v1_genomic.fna/checkm_result
[2024-01-24 14:15:45,018] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:45,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:45,037] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:45,037] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:45,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002006755.1_ASM200675v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:45,038] [INFO] Task started: Blastn
[2024-01-24 14:15:45,038] [INFO] Running command: blastn -query GCF_002006755.1_ASM200675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9a84ff7-4e0a-4a49-9a4e-64c1bbd31f0d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002006755.1_ASM200675v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:45,833] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:45,836] [INFO] Selected 19 target genomes.
[2024-01-24 14:15:45,836] [INFO] Target genome list was writen to GCF_002006755.1_ASM200675v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:45,865] [INFO] Task started: fastANI
[2024-01-24 14:15:45,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg28a07cb7-f8f4-43b4-a87c-c5f4aa898467/GCF_002006755.1_ASM200675v1_genomic.fna.gz --refList GCF_002006755.1_ASM200675v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002006755.1_ASM200675v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:53,728] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:53,735] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:53,735] [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_002006755.1	s__Wohlfahrtiimonas larvae	100.0	695	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Wohlfahrtiimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002006795.1	s__Wohlfahrtiimonas populi	86.1588	569	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Wohlfahrtiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000375345.1	s__Wohlfahrtiimonas chitiniclastica	79.2463	236	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Wohlfahrtiimonas	95.0	97.18	97.09	0.95	0.93	26	-
GCF_002252155.1	s__Wohlfahrtiimonas sp002252155	79.1528	239	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Wohlfahrtiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:53,737] [INFO] GTDB search result was written to GCF_002006755.1_ASM200675v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:53,737] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:53,739] [INFO] DFAST_QC result json was written to GCF_002006755.1_ASM200675v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:53,739] [INFO] DFAST_QC completed!
[2024-01-24 14:15:53,740] [INFO] Total running time: 0h0m52s