[2024-01-24 13:37:15,353] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:15,356] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:15,357] [INFO] DQC Reference Directory: /var/lib/cwl/stg33f01d0c-336a-44e4-a1a6-ed1f6be14f4d/dqc_reference
[2024-01-24 13:37:18,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:18,467] [INFO] Task started: Prodigal
[2024-01-24 13:37:18,468] [INFO] Running command: gunzip -c /var/lib/cwl/stg66b6a094-dea8-4896-9422-5fba000a65c8/GCF_009733925.1_ASM973392v1_genomic.fna.gz | prodigal -d GCF_009733925.1_ASM973392v1_genomic.fna/cds.fna -a GCF_009733925.1_ASM973392v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:20,756] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:20,757] [INFO] Task started: HMMsearch
[2024-01-24 13:37:20,757] [INFO] Running command: hmmsearch --tblout GCF_009733925.1_ASM973392v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33f01d0c-336a-44e4-a1a6-ed1f6be14f4d/dqc_reference/reference_markers.hmm GCF_009733925.1_ASM973392v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:21,093] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:21,095] [INFO] Found 6/6 markers.
[2024-01-24 13:37:21,119] [INFO] Query marker FASTA was written to GCF_009733925.1_ASM973392v1_genomic.fna/markers.fasta
[2024-01-24 13:37:21,121] [INFO] Task started: Blastn
[2024-01-24 13:37:21,121] [INFO] Running command: blastn -query GCF_009733925.1_ASM973392v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33f01d0c-336a-44e4-a1a6-ed1f6be14f4d/dqc_reference/reference_markers.fasta -out GCF_009733925.1_ASM973392v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:24,099] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:24,103] [INFO] Selected 10 target genomes.
[2024-01-24 13:37:24,103] [INFO] Target genome list was writen to GCF_009733925.1_ASM973392v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:24,110] [INFO] Task started: fastANI
[2024-01-24 13:37:24,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg66b6a094-dea8-4896-9422-5fba000a65c8/GCF_009733925.1_ASM973392v1_genomic.fna.gz --refList GCF_009733925.1_ASM973392v1_genomic.fna/target_genomes.txt --output GCF_009733925.1_ASM973392v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:27,585] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:27,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33f01d0c-336a-44e4-a1a6-ed1f6be14f4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:27,588] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33f01d0c-336a-44e4-a1a6-ed1f6be14f4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:27,641] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:27,642] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:27,642] [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
Streptobacillus canis	strain=IHIT1603-19	GCA_009733925.1	2678686	2678686	type	True	100.0	498	500	95	conclusive
Streptobacillus felis	strain=131000547	GCA_001559775.1	1384509	1384509	type	True	84.3645	345	500	95	below_threshold
Streptobacillus ratti	strain=OGS16	GCA_001891165.1	1720557	1720557	type	True	83.691	311	500	95	below_threshold
Streptobacillus moniliformis	strain=DSM 12112	GCA_000024565.1	34105	34105	type	True	83.1997	335	500	95	below_threshold
Caviibacter abscessus	strain=CCUG 39713	GCA_001517835.1	1766719	1766719	type	True	76.767	110	500	95	below_threshold
Sneathia sanguinegens	strain=CCUG41628	GCA_001517935.1	40543	40543	type	True	76.7589	95	500	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	74.8833	62	500	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:27,644] [INFO] DFAST Taxonomy check result was written to GCF_009733925.1_ASM973392v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:27,644] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:27,644] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:27,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33f01d0c-336a-44e4-a1a6-ed1f6be14f4d/dqc_reference/checkm_data
[2024-01-24 13:37:27,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:27,668] [INFO] Task started: CheckM
[2024-01-24 13:37:27,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009733925.1_ASM973392v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009733925.1_ASM973392v1_genomic.fna/checkm_input GCF_009733925.1_ASM973392v1_genomic.fna/checkm_result
[2024-01-24 13:37:48,188] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:48,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:48,214] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:48,214] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:48,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009733925.1_ASM973392v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:48,215] [INFO] Task started: Blastn
[2024-01-24 13:37:48,216] [INFO] Running command: blastn -query GCF_009733925.1_ASM973392v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33f01d0c-336a-44e4-a1a6-ed1f6be14f4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009733925.1_ASM973392v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:49,087] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:49,091] [INFO] Selected 9 target genomes.
[2024-01-24 13:37:49,092] [INFO] Target genome list was writen to GCF_009733925.1_ASM973392v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:49,101] [INFO] Task started: fastANI
[2024-01-24 13:37:49,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg66b6a094-dea8-4896-9422-5fba000a65c8/GCF_009733925.1_ASM973392v1_genomic.fna.gz --refList GCF_009733925.1_ASM973392v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009733925.1_ASM973392v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:52,306] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:52,326] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:52,328] [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_009733925.1	s__Streptobacillus canis	100.0	498	500	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Streptobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001559775.1	s__Streptobacillus felis	84.4317	343	500	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Streptobacillus	95.0	99.40	99.40	0.92	0.92	2	-
GCF_001891165.1	s__Streptobacillus ratti	83.6913	311	500	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Streptobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024565.1	s__Streptobacillus moniliformis	83.2137	334	500	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Streptobacillus	95.0	99.49	99.12	0.94	0.89	25	-
GCF_001612575.1	s__Streptobacillus notomytis	83.1734	305	500	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Streptobacillus	95.0	99.10	99.10	0.95	0.95	3	-
GCA_018060185.1	s__JAGOWQ01 sp018060185	75.9792	82	500	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__JAGOWQ01	95.0	99.67	99.60	0.85	0.80	4	-
GCF_000493815.1	s__Fusobacterium nucleatum_E	75.4036	62	500	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	99.05	99.05	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:52,386] [INFO] GTDB search result was written to GCF_009733925.1_ASM973392v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:52,387] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:52,392] [INFO] DFAST_QC result json was written to GCF_009733925.1_ASM973392v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:52,392] [INFO] DFAST_QC completed!
[2024-01-24 13:37:52,392] [INFO] Total running time: 0h0m37s