[2024-01-24 14:15:02,610] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:02,612] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:02,613] [INFO] DQC Reference Directory: /var/lib/cwl/stg107ee3ff-0752-4fa6-b7fa-03655439e345/dqc_reference
[2024-01-24 14:15:04,104] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:04,108] [INFO] Task started: Prodigal
[2024-01-24 14:15:04,109] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f9463ce-32eb-4808-a5c6-bc8911b724b2/GCF_002006795.1_ASM200679v1_genomic.fna.gz | prodigal -d GCF_002006795.1_ASM200679v1_genomic.fna/cds.fna -a GCF_002006795.1_ASM200679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:10,944] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:10,944] [INFO] Task started: HMMsearch
[2024-01-24 14:15:10,945] [INFO] Running command: hmmsearch --tblout GCF_002006795.1_ASM200679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg107ee3ff-0752-4fa6-b7fa-03655439e345/dqc_reference/reference_markers.hmm GCF_002006795.1_ASM200679v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:11,217] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:11,219] [INFO] Found 6/6 markers.
[2024-01-24 14:15:11,248] [INFO] Query marker FASTA was written to GCF_002006795.1_ASM200679v1_genomic.fna/markers.fasta
[2024-01-24 14:15:11,249] [INFO] Task started: Blastn
[2024-01-24 14:15:11,249] [INFO] Running command: blastn -query GCF_002006795.1_ASM200679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg107ee3ff-0752-4fa6-b7fa-03655439e345/dqc_reference/reference_markers.fasta -out GCF_002006795.1_ASM200679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:11,976] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:11,979] [INFO] Selected 21 target genomes.
[2024-01-24 14:15:11,980] [INFO] Target genome list was writen to GCF_002006795.1_ASM200679v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:11,991] [INFO] Task started: fastANI
[2024-01-24 14:15:11,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f9463ce-32eb-4808-a5c6-bc8911b724b2/GCF_002006795.1_ASM200679v1_genomic.fna.gz --refList GCF_002006795.1_ASM200679v1_genomic.fna/target_genomes.txt --output GCF_002006795.1_ASM200679v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:24,104] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:24,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg107ee3ff-0752-4fa6-b7fa-03655439e345/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:24,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg107ee3ff-0752-4fa6-b7fa-03655439e345/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:24,110] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:24,110] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:24,110] [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 populi	strain=34C10-3-10	GCA_002006795.1	1940240	1940240	type	True	100.0	895	898	95	conclusive
Wohlfahrtiimonas larvae	strain=kbl006	GCA_002006755.1	1157986	1157986	type	True	86.0007	574	898	95	below_threshold
Wohlfahrtiimonas chitiniclastica	strain=DSM 18708	GCA_000375345.1	400946	400946	type	True	79.1027	293	898	95	below_threshold
Ignatzschineria larvae	strain=DSM 13226	GCA_000510805.1	112009	112009	type	True	75.9164	50	898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:24,112] [INFO] DFAST Taxonomy check result was written to GCF_002006795.1_ASM200679v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:24,120] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:24,120] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:24,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg107ee3ff-0752-4fa6-b7fa-03655439e345/dqc_reference/checkm_data
[2024-01-24 14:15:24,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:24,154] [INFO] Task started: CheckM
[2024-01-24 14:15:24,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002006795.1_ASM200679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002006795.1_ASM200679v1_genomic.fna/checkm_input GCF_002006795.1_ASM200679v1_genomic.fna/checkm_result
[2024-01-24 14:15:50,726] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:50,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:50,747] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:50,748] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:50,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002006795.1_ASM200679v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:50,749] [INFO] Task started: Blastn
[2024-01-24 14:15:50,749] [INFO] Running command: blastn -query GCF_002006795.1_ASM200679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg107ee3ff-0752-4fa6-b7fa-03655439e345/dqc_reference/reference_markers_gtdb.fasta -out GCF_002006795.1_ASM200679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:51,837] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:51,840] [INFO] Selected 12 target genomes.
[2024-01-24 14:15:51,841] [INFO] Target genome list was writen to GCF_002006795.1_ASM200679v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:51,851] [INFO] Task started: fastANI
[2024-01-24 14:15:51,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f9463ce-32eb-4808-a5c6-bc8911b724b2/GCF_002006795.1_ASM200679v1_genomic.fna.gz --refList GCF_002006795.1_ASM200679v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002006795.1_ASM200679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:58,481] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:58,488] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:58,489] [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_002006795.1	s__Wohlfahrtiimonas populi	100.0	895	898	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_002006755.1	s__Wohlfahrtiimonas larvae	85.9922	575	898	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	79.0847	295	898	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	78.8477	287	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Wohlfahrtiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113305.1	s__Ignatzschineria merdigallinarum	75.9235	57	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000510805.1	s__Ignatzschineria larvae	75.9164	50	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:58,490] [INFO] GTDB search result was written to GCF_002006795.1_ASM200679v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:58,491] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:58,494] [INFO] DFAST_QC result json was written to GCF_002006795.1_ASM200679v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:58,494] [INFO] DFAST_QC completed!
[2024-01-24 14:15:58,494] [INFO] Total running time: 0h0m56s