[2024-01-24 13:32:32,590] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:32,592] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:32,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg6364c47d-eccc-45db-ac33-f012e3ac372b/dqc_reference
[2024-01-24 13:32:33,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:33,929] [INFO] Task started: Prodigal
[2024-01-24 13:32:33,929] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4de3901-f57c-4f53-9894-70213a765334/GCF_000024565.1_ASM2456v1_genomic.fna.gz | prodigal -d GCF_000024565.1_ASM2456v1_genomic.fna/cds.fna -a GCF_000024565.1_ASM2456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:36,464] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:36,465] [INFO] Task started: HMMsearch
[2024-01-24 13:32:36,465] [INFO] Running command: hmmsearch --tblout GCF_000024565.1_ASM2456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6364c47d-eccc-45db-ac33-f012e3ac372b/dqc_reference/reference_markers.hmm GCF_000024565.1_ASM2456v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:36,739] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:36,740] [INFO] Found 6/6 markers.
[2024-01-24 13:32:36,770] [INFO] Query marker FASTA was written to GCF_000024565.1_ASM2456v1_genomic.fna/markers.fasta
[2024-01-24 13:32:36,770] [INFO] Task started: Blastn
[2024-01-24 13:32:36,770] [INFO] Running command: blastn -query GCF_000024565.1_ASM2456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6364c47d-eccc-45db-ac33-f012e3ac372b/dqc_reference/reference_markers.fasta -out GCF_000024565.1_ASM2456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:37,376] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:37,380] [INFO] Selected 9 target genomes.
[2024-01-24 13:32:37,381] [INFO] Target genome list was writen to GCF_000024565.1_ASM2456v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:37,390] [INFO] Task started: fastANI
[2024-01-24 13:32:37,390] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4de3901-f57c-4f53-9894-70213a765334/GCF_000024565.1_ASM2456v1_genomic.fna.gz --refList GCF_000024565.1_ASM2456v1_genomic.fna/target_genomes.txt --output GCF_000024565.1_ASM2456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:41,041] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:41,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6364c47d-eccc-45db-ac33-f012e3ac372b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:41,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6364c47d-eccc-45db-ac33-f012e3ac372b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:41,049] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:41,049] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:41,049] [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 moniliformis	strain=DSM 12112	GCA_000024565.1	34105	34105	type	True	100.0	556	557	95	conclusive
Streptobacillus ratti	strain=OGS16	GCA_001891165.1	1720557	1720557	type	True	90.2617	377	557	95	below_threshold
Streptobacillus canis	strain=IHIT1603-19	GCA_009733925.1	2678686	2678686	type	True	83.3581	327	557	95	below_threshold
Streptobacillus felis	strain=131000547	GCA_001559775.1	1384509	1384509	type	True	83.0046	322	557	95	below_threshold
Leptotrichia buccalis	strain=DSM 1135	GCA_000023905.1	40542	40542	type	True	78.1658	64	557	95	below_threshold
Oceanivirga miroungae	strain=ES3154-GLU	GCA_902505095.1	1130046	1130046	type	True	77.7533	108	557	95	below_threshold
Sneathia sanguinegens	strain=CCUG41628	GCA_001517935.1	40543	40543	type	True	76.9195	109	557	95	below_threshold
Fusobacterium russii	strain=593A	GCA_000381725.1	854	854	type	True	75.4987	61	557	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:41,051] [INFO] DFAST Taxonomy check result was written to GCF_000024565.1_ASM2456v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:41,051] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:41,051] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:41,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6364c47d-eccc-45db-ac33-f012e3ac372b/dqc_reference/checkm_data
[2024-01-24 13:32:41,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:41,071] [INFO] Task started: CheckM
[2024-01-24 13:32:41,072] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024565.1_ASM2456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024565.1_ASM2456v1_genomic.fna/checkm_input GCF_000024565.1_ASM2456v1_genomic.fna/checkm_result
[2024-01-24 13:32:58,230] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:58,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:58,249] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:58,249] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:58,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024565.1_ASM2456v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:58,250] [INFO] Task started: Blastn
[2024-01-24 13:32:58,250] [INFO] Running command: blastn -query GCF_000024565.1_ASM2456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6364c47d-eccc-45db-ac33-f012e3ac372b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024565.1_ASM2456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:59,150] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:59,153] [INFO] Selected 7 target genomes.
[2024-01-24 13:32:59,154] [INFO] Target genome list was writen to GCF_000024565.1_ASM2456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:59,162] [INFO] Task started: fastANI
[2024-01-24 13:32:59,162] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4de3901-f57c-4f53-9894-70213a765334/GCF_000024565.1_ASM2456v1_genomic.fna.gz --refList GCF_000024565.1_ASM2456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024565.1_ASM2456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:02,866] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:02,873] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:02,873] [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_000024565.1	s__Streptobacillus moniliformis	100.0	555	557	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Streptobacillus	95.0	99.49	99.12	0.94	0.89	25	conclusive
GCF_001891165.1	s__Streptobacillus ratti	90.2617	377	557	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Streptobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612575.1	s__Streptobacillus notomytis	89.5178	397	557	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Streptobacillus	95.0	99.10	99.10	0.95	0.95	3	-
GCF_009733925.1	s__Streptobacillus canis	83.4144	325	557	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Streptobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001559775.1	s__Streptobacillus felis	83.0241	320	557	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Streptobacillus	95.0	99.40	99.40	0.92	0.92	2	-
GCA_018058425.1	s__Sebaldella sp018058425	75.8522	77	557	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Sebaldella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:02,875] [INFO] GTDB search result was written to GCF_000024565.1_ASM2456v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:02,875] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:02,878] [INFO] DFAST_QC result json was written to GCF_000024565.1_ASM2456v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:02,878] [INFO] DFAST_QC completed!
[2024-01-24 13:33:02,878] [INFO] Total running time: 0h0m30s