[2024-01-24 13:46:01,368] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,370] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a917652-0e16-40dc-846c-4f5f60e9622d/dqc_reference
[2024-01-24 13:46:02,662] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,663] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,663] [INFO] Running command: gunzip -c /var/lib/cwl/stge9d1886c-2149-4743-8767-f5560b905188/GCF_009684755.1_ASM968475v1_genomic.fna.gz | prodigal -d GCF_009684755.1_ASM968475v1_genomic.fna/cds.fna -a GCF_009684755.1_ASM968475v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:14,964] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:14,965] [INFO] Task started: HMMsearch
[2024-01-24 13:46:14,965] [INFO] Running command: hmmsearch --tblout GCF_009684755.1_ASM968475v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a917652-0e16-40dc-846c-4f5f60e9622d/dqc_reference/reference_markers.hmm GCF_009684755.1_ASM968475v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:15,241] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:15,242] [INFO] Found 6/6 markers.
[2024-01-24 13:46:15,269] [INFO] Query marker FASTA was written to GCF_009684755.1_ASM968475v1_genomic.fna/markers.fasta
[2024-01-24 13:46:15,269] [INFO] Task started: Blastn
[2024-01-24 13:46:15,269] [INFO] Running command: blastn -query GCF_009684755.1_ASM968475v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a917652-0e16-40dc-846c-4f5f60e9622d/dqc_reference/reference_markers.fasta -out GCF_009684755.1_ASM968475v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:15,882] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:15,887] [INFO] Selected 15 target genomes.
[2024-01-24 13:46:15,888] [INFO] Target genome list was writen to GCF_009684755.1_ASM968475v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:15,922] [INFO] Task started: fastANI
[2024-01-24 13:46:15,923] [INFO] Running command: fastANI --query /var/lib/cwl/stge9d1886c-2149-4743-8767-f5560b905188/GCF_009684755.1_ASM968475v1_genomic.fna.gz --refList GCF_009684755.1_ASM968475v1_genomic.fna/target_genomes.txt --output GCF_009684755.1_ASM968475v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:23,990] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:23,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a917652-0e16-40dc-846c-4f5f60e9622d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:23,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a917652-0e16-40dc-846c-4f5f60e9622d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:23,999] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:23,999] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:24,000] [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
Capnocytophaga felis	strain=KC07070	GCA_009684755.1	2267611	2267611	type	True	100.0	939	941	95	conclusive
Capnocytophaga cynodegmi	strain=E6447	GCA_000379185.1	28189	28189	type	True	83.5794	683	941	95	below_threshold
Capnocytophaga canimorsus	strain=NCTC12242	GCA_900460905.1	28188	28188	type	True	80.9098	267	941	95	below_threshold
Capnocytophaga canimorsus	strain=7120	GCA_002302565.1	28188	28188	type	True	80.9092	267	941	95	below_threshold
Capnocytophaga canimorsus	strain=DSM 19204	GCA_002797785.1	28188	28188	type	True	80.8177	275	941	95	below_threshold
Capnocytophaga canis	strain=CcD38	GCA_000827555.1	1848903	1848903	type	True	80.0961	253	941	95	below_threshold
Flavobacterium sufflavum	strain=BBQ-12	GCA_004016525.1	1921138	1921138	type	True	75.9066	55	941	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_902804475.1	2704140	2704140	type	True	75.6333	57	941	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	75.4923	58	941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:24,001] [INFO] DFAST Taxonomy check result was written to GCF_009684755.1_ASM968475v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:24,001] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:24,002] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:24,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a917652-0e16-40dc-846c-4f5f60e9622d/dqc_reference/checkm_data
[2024-01-24 13:46:24,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:24,032] [INFO] Task started: CheckM
[2024-01-24 13:46:24,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009684755.1_ASM968475v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009684755.1_ASM968475v1_genomic.fna/checkm_input GCF_009684755.1_ASM968475v1_genomic.fna/checkm_result
[2024-01-24 13:47:03,175] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:03,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:03,195] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:03,195] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:03,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009684755.1_ASM968475v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:03,196] [INFO] Task started: Blastn
[2024-01-24 13:47:03,196] [INFO] Running command: blastn -query GCF_009684755.1_ASM968475v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a917652-0e16-40dc-846c-4f5f60e9622d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009684755.1_ASM968475v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:04,018] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:04,023] [INFO] Selected 12 target genomes.
[2024-01-24 13:47:04,023] [INFO] Target genome list was writen to GCF_009684755.1_ASM968475v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:04,078] [INFO] Task started: fastANI
[2024-01-24 13:47:04,079] [INFO] Running command: fastANI --query /var/lib/cwl/stge9d1886c-2149-4743-8767-f5560b905188/GCF_009684755.1_ASM968475v1_genomic.fna.gz --refList GCF_009684755.1_ASM968475v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009684755.1_ASM968475v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:11,060] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:11,068] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:11,068] [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_009684755.1	s__Capnocytophaga felis	100.0	939	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	99.93	99.93	0.99	0.99	2	conclusive
GCF_002302635.1	s__Capnocytophaga stomatis	90.219	758	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.71	97.65	0.92	0.91	4	-
GCF_000379185.1	s__Capnocytophaga cynodegmi	83.5621	684	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.53	96.05	0.91	0.86	7	-
GCF_002302565.1	s__Capnocytophaga canimorsus	80.8997	267	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	98.20	97.29	0.93	0.87	15	-
GCF_000827555.1	s__Capnocytophaga canis	80.0745	254	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	98.20	97.91	0.92	0.88	11	-
GCF_004016525.1	s__Flavobacterium sufflavum	75.9066	55	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902804475.1	s__Flavobacterium bizetiae	75.6556	56	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.96	99.94	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:11,070] [INFO] GTDB search result was written to GCF_009684755.1_ASM968475v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:11,071] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:11,074] [INFO] DFAST_QC result json was written to GCF_009684755.1_ASM968475v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:11,074] [INFO] DFAST_QC completed!
[2024-01-24 13:47:11,074] [INFO] Total running time: 0h1m10s