[2024-01-24 13:48:43,127] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:43,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:43,129] [INFO] DQC Reference Directory: /var/lib/cwl/stg38179958-017b-4b79-af02-b66a5d662c7d/dqc_reference
[2024-01-24 13:48:44,380] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,381] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,382] [INFO] Running command: gunzip -c /var/lib/cwl/stg89a55a3f-f4c3-41b2-9a84-e0c2222702bc/GCF_003019695.1_ASM301969v1_genomic.fna.gz | prodigal -d GCF_003019695.1_ASM301969v1_genomic.fna/cds.fna -a GCF_003019695.1_ASM301969v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:48:47,700] [INFO] Task succeeded: Prodigal
[2024-01-24 13:48:47,700] [INFO] Task started: HMMsearch
[2024-01-24 13:48:47,700] [INFO] Running command: hmmsearch --tblout GCF_003019695.1_ASM301969v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38179958-017b-4b79-af02-b66a5d662c7d/dqc_reference/reference_markers.hmm GCF_003019695.1_ASM301969v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:48:47,923] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:48:47,924] [INFO] Found 6/6 markers.
[2024-01-24 13:48:47,945] [INFO] Query marker FASTA was written to GCF_003019695.1_ASM301969v1_genomic.fna/markers.fasta
[2024-01-24 13:48:47,945] [INFO] Task started: Blastn
[2024-01-24 13:48:47,945] [INFO] Running command: blastn -query GCF_003019695.1_ASM301969v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38179958-017b-4b79-af02-b66a5d662c7d/dqc_reference/reference_markers.fasta -out GCF_003019695.1_ASM301969v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:48,520] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:48,524] [INFO] Selected 6 target genomes.
[2024-01-24 13:48:48,524] [INFO] Target genome list was writen to GCF_003019695.1_ASM301969v1_genomic.fna/target_genomes.txt
[2024-01-24 13:48:48,529] [INFO] Task started: fastANI
[2024-01-24 13:48:48,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg89a55a3f-f4c3-41b2-9a84-e0c2222702bc/GCF_003019695.1_ASM301969v1_genomic.fna.gz --refList GCF_003019695.1_ASM301969v1_genomic.fna/target_genomes.txt --output GCF_003019695.1_ASM301969v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:48:51,169] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:51,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38179958-017b-4b79-af02-b66a5d662c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:48:51,170] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38179958-017b-4b79-af02-b66a5d662c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:48:51,177] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:48:51,177] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:48:51,177] [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
Fusobacterium gonidiaformans	strain=ATCC 25563	GCA_003019695.1	849	849	type	True	100.0	558	559	95	conclusive
Fusobacterium gonidiaformans	strain=ATCC 25563	GCA_000158835.2	849	849	type	True	99.9517	543	559	95	conclusive
Fusobacterium necrophorum subsp. necrophorum	strain=ATCC 25286	GCA_004006635.1	143388	859	type	True	82.7673	422	559	95	below_threshold
Fusobacterium necrophorum subsp. funduliforme	strain=CCUG 42162	GCA_008801775.1	143387	859	type	True	82.4925	421	559	95	below_threshold
Fusobacterium necrophorum	strain=ATCC 25286	GCA_900104395.1	859	859	type	True	82.4623	413	559	95	below_threshold
Fusobacterium necrophorum subsp. funduliforme	strain=ATCC 51357	GCA_000262225.1	143387	859	type	True	82.3635	417	559	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:48:51,179] [INFO] DFAST Taxonomy check result was written to GCF_003019695.1_ASM301969v1_genomic.fna/tc_result.tsv
[2024-01-24 13:48:51,179] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:48:51,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:48:51,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38179958-017b-4b79-af02-b66a5d662c7d/dqc_reference/checkm_data
[2024-01-24 13:48:51,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:48:51,200] [INFO] Task started: CheckM
[2024-01-24 13:48:51,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003019695.1_ASM301969v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003019695.1_ASM301969v1_genomic.fna/checkm_input GCF_003019695.1_ASM301969v1_genomic.fna/checkm_result
[2024-01-24 13:49:09,011] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:09,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:09,031] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:09,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:09,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003019695.1_ASM301969v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:09,033] [INFO] Task started: Blastn
[2024-01-24 13:49:09,033] [INFO] Running command: blastn -query GCF_003019695.1_ASM301969v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38179958-017b-4b79-af02-b66a5d662c7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003019695.1_ASM301969v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:09,864] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:09,868] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:09,869] [INFO] Target genome list was writen to GCF_003019695.1_ASM301969v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:09,882] [INFO] Task started: fastANI
[2024-01-24 13:49:09,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg89a55a3f-f4c3-41b2-9a84-e0c2222702bc/GCF_003019695.1_ASM301969v1_genomic.fna.gz --refList GCF_003019695.1_ASM301969v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003019695.1_ASM301969v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:15,648] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:15,662] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:15,662] [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_003019695.1	s__Fusobacterium_C gonidiaformans	100.0	559	559	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_C	95.0	98.88	98.56	0.91	0.87	6	conclusive
GCF_004006635.1	s__Fusobacterium_C necrophorum	82.7556	421	559	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_C	95.0	97.54	95.37	0.87	0.77	49	-
GCF_002761955.1	s__Fusobacterium pseudoperiodonticum	78.7716	113	559	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.1543	96.63	95.97	0.86	0.84	10	-
GCF_001457555.1	s__Fusobacterium polymorphum	77.9138	124	559	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	96.55	95.37	0.85	0.79	30	-
GCF_000235465.1	s__Fusobacterium sp000235465	77.5551	109	559	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000163935.1	s__Fusobacterium periodonticum_B	77.4757	110	559	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900095705.1	s__Fusobacterium massiliense	77.4731	116	559	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000381725.1	s__Fusobacterium russii	76.9682	100	559	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012843705.1	s__Fusobacterium_B sp012843705	76.5707	84	559	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010367435.1	s__Fusobacterium_B sp010367435	76.4878	66	559	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622245.1	s__Fusobacterium_B perfoetens	76.3705	98	559	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:15,668] [INFO] GTDB search result was written to GCF_003019695.1_ASM301969v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:15,669] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:15,672] [INFO] DFAST_QC result json was written to GCF_003019695.1_ASM301969v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:15,672] [INFO] DFAST_QC completed!
[2024-01-24 13:49:15,672] [INFO] Total running time: 0h0m33s