[2024-01-24 13:40:34,713] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,715] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a2ac87f-1505-40db-8e7f-bc3f6ec7fbcf/dqc_reference
[2024-01-24 13:40:36,150] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,151] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,151] [INFO] Running command: gunzip -c /var/lib/cwl/stgd08fe248-1ef6-416b-b22f-2a1476185ce6/GCF_004006635.1_ASM400663v1_genomic.fna.gz | prodigal -d GCF_004006635.1_ASM400663v1_genomic.fna/cds.fna -a GCF_004006635.1_ASM400663v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:42,319] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:42,320] [INFO] Task started: HMMsearch
[2024-01-24 13:40:42,320] [INFO] Running command: hmmsearch --tblout GCF_004006635.1_ASM400663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a2ac87f-1505-40db-8e7f-bc3f6ec7fbcf/dqc_reference/reference_markers.hmm GCF_004006635.1_ASM400663v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:42,643] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:42,644] [INFO] Found 6/6 markers.
[2024-01-24 13:40:42,672] [INFO] Query marker FASTA was written to GCF_004006635.1_ASM400663v1_genomic.fna/markers.fasta
[2024-01-24 13:40:42,673] [INFO] Task started: Blastn
[2024-01-24 13:40:42,673] [INFO] Running command: blastn -query GCF_004006635.1_ASM400663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a2ac87f-1505-40db-8e7f-bc3f6ec7fbcf/dqc_reference/reference_markers.fasta -out GCF_004006635.1_ASM400663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:43,267] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:43,270] [INFO] Selected 5 target genomes.
[2024-01-24 13:40:43,270] [INFO] Target genome list was writen to GCF_004006635.1_ASM400663v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:43,273] [INFO] Task started: fastANI
[2024-01-24 13:40:43,273] [INFO] Running command: fastANI --query /var/lib/cwl/stgd08fe248-1ef6-416b-b22f-2a1476185ce6/GCF_004006635.1_ASM400663v1_genomic.fna.gz --refList GCF_004006635.1_ASM400663v1_genomic.fna/target_genomes.txt --output GCF_004006635.1_ASM400663v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:46,672] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:46,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a2ac87f-1505-40db-8e7f-bc3f6ec7fbcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:46,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a2ac87f-1505-40db-8e7f-bc3f6ec7fbcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:46,679] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:40:46,679] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:46,679] [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 necrophorum subsp. necrophorum	strain=ATCC 25286	GCA_004006635.1	143388	859	type	True	100.0	889	892	95	conclusive
Fusobacterium necrophorum	strain=ATCC 25286	GCA_900104395.1	859	859	type	True	99.8592	802	892	95	conclusive
Fusobacterium necrophorum subsp. funduliforme	strain=ATCC 51357	GCA_000262225.1	143387	859	type	True	97.0751	591	892	95	conclusive
Fusobacterium necrophorum subsp. funduliforme	strain=CCUG 42162	GCA_008801775.1	143387	859	type	True	96.9653	611	892	95	conclusive
Fusobacterium gonidiaformans	strain=ATCC 25563	GCA_003019695.1	849	849	type	True	82.6273	426	892	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:46,681] [INFO] DFAST Taxonomy check result was written to GCF_004006635.1_ASM400663v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:46,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:46,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:46,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a2ac87f-1505-40db-8e7f-bc3f6ec7fbcf/dqc_reference/checkm_data
[2024-01-24 13:40:46,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:46,717] [INFO] Task started: CheckM
[2024-01-24 13:40:46,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004006635.1_ASM400663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004006635.1_ASM400663v1_genomic.fna/checkm_input GCF_004006635.1_ASM400663v1_genomic.fna/checkm_result
[2024-01-24 13:41:12,093] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:12,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:12,116] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:12,116] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:12,117] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004006635.1_ASM400663v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:12,117] [INFO] Task started: Blastn
[2024-01-24 13:41:12,117] [INFO] Running command: blastn -query GCF_004006635.1_ASM400663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a2ac87f-1505-40db-8e7f-bc3f6ec7fbcf/dqc_reference/reference_markers_gtdb.fasta -out GCF_004006635.1_ASM400663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:12,987] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:12,991] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:12,992] [INFO] Target genome list was writen to GCF_004006635.1_ASM400663v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:13,004] [INFO] Task started: fastANI
[2024-01-24 13:41:13,005] [INFO] Running command: fastANI --query /var/lib/cwl/stgd08fe248-1ef6-416b-b22f-2a1476185ce6/GCF_004006635.1_ASM400663v1_genomic.fna.gz --refList GCF_004006635.1_ASM400663v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004006635.1_ASM400663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:20,156] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:20,166] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:20,166] [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_004006635.1	s__Fusobacterium_C necrophorum	100.0	889	892	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_C	95.0	97.54	95.37	0.87	0.77	49	conclusive
GCF_003019695.1	s__Fusobacterium_C gonidiaformans	82.756	425	892	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_C	95.0	98.88	98.56	0.91	0.87	6	-
GCA_000182945.1	s__Fusobacterium vincentii	78.6909	100	892	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	97.44	96.10	0.85	0.73	18	-
GCF_900450765.1	s__Fusobacterium_A necrogenes	78.6572	65	892	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016724785.1	s__Fusobacterium canifelinum	77.9264	122	892	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.22	98.13	0.90	0.87	3	-
GCF_000158275.2	s__Fusobacterium animalis	77.8921	139	892	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	97.57	95.72	0.88	0.80	29	-
GCF_008633215.1	s__Fusobacterium nucleatum_J	77.1917	110	892	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.47	98.47	0.86	0.86	2	-
GCF_000493815.1	s__Fusobacterium nucleatum_E	77.0223	132	892	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	99.05	99.05	0.94	0.94	2	-
GCF_016900045.1	s__Fusobacterium_A sp900549465	76.6244	55	892	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	98.59	98.37	0.86	0.84	6	-
GCF_000622245.1	s__Fusobacterium_B perfoetens	75.7904	66	892	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_012843705.1	s__Fusobacterium_B sp012843705	75.7616	56	892	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 13:41:20,168] [INFO] GTDB search result was written to GCF_004006635.1_ASM400663v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:20,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:20,172] [INFO] DFAST_QC result json was written to GCF_004006635.1_ASM400663v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:20,172] [INFO] DFAST_QC completed!
[2024-01-24 13:41:20,172] [INFO] Total running time: 0h0m45s