[2024-01-24 15:27:12,295] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:12,297] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:12,298] [INFO] DQC Reference Directory: /var/lib/cwl/stgc56f77fe-8985-469c-94f3-a959656ef963/dqc_reference
[2024-01-24 15:27:13,703] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:13,704] [INFO] Task started: Prodigal
[2024-01-24 15:27:13,704] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3ee51fc-97d2-453d-a5c8-f3ac08aac063/GCF_900450765.1_42650_B02_genomic.fna.gz | prodigal -d GCF_900450765.1_42650_B02_genomic.fna/cds.fna -a GCF_900450765.1_42650_B02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:16,796] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:16,797] [INFO] Task started: HMMsearch
[2024-01-24 15:27:16,797] [INFO] Running command: hmmsearch --tblout GCF_900450765.1_42650_B02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc56f77fe-8985-469c-94f3-a959656ef963/dqc_reference/reference_markers.hmm GCF_900450765.1_42650_B02_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:17,095] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:17,096] [INFO] Found 6/6 markers.
[2024-01-24 15:27:17,123] [INFO] Query marker FASTA was written to GCF_900450765.1_42650_B02_genomic.fna/markers.fasta
[2024-01-24 15:27:17,123] [INFO] Task started: Blastn
[2024-01-24 15:27:17,124] [INFO] Running command: blastn -query GCF_900450765.1_42650_B02_genomic.fna/markers.fasta -db /var/lib/cwl/stgc56f77fe-8985-469c-94f3-a959656ef963/dqc_reference/reference_markers.fasta -out GCF_900450765.1_42650_B02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:18,599] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:18,602] [INFO] Selected 14 target genomes.
[2024-01-24 15:27:18,602] [INFO] Target genome list was writen to GCF_900450765.1_42650_B02_genomic.fna/target_genomes.txt
[2024-01-24 15:27:18,633] [INFO] Task started: fastANI
[2024-01-24 15:27:18,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3ee51fc-97d2-453d-a5c8-f3ac08aac063/GCF_900450765.1_42650_B02_genomic.fna.gz --refList GCF_900450765.1_42650_B02_genomic.fna/target_genomes.txt --output GCF_900450765.1_42650_B02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:25,027] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:25,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc56f77fe-8985-469c-94f3-a959656ef963/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:25,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc56f77fe-8985-469c-94f3-a959656ef963/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:25,039] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:25,039] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:25,039] [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 necrogenes	strain=NCTC10723	GCA_900450765.1	858	858	type	True	100.0	668	669	95	conclusive
Fusobacterium ulcerans	strain=ATCC 49185	GCA_003019675.1	861	861	type	True	78.8681	253	669	95	below_threshold
Fusobacterium varium	strain=NCTC10560	GCA_900637705.1	856	856	type	True	78.6745	272	669	95	below_threshold
Fusobacterium necrophorum subsp. necrophorum	strain=ATCC 25286	GCA_004006635.1	143388	859	type	True	78.6527	59	669	95	below_threshold
Fusobacterium ulcerans	strain=ATCC 49185	GCA_000158315.2	861	861	type	True	78.5511	242	669	95	below_threshold
Fusobacterium hwasookii	strain=KCOM 1249	GCA_014217355.1	1583098	1583098	type	True	77.3562	134	669	95	below_threshold
Fusobacterium nucleatum subsp. polymorphum	strain=NCTC10562	GCA_001457555.1	76857	851	type	True	77.204	135	669	95	below_threshold
Fusobacterium periodonticum	strain=ATCC 33693	GCA_000160475.1	860	860	suspected-type	True	77.1315	131	669	95	below_threshold
Psychrilyobacter atlanticus	strain=DSM 19335	GCA_000426625.1	271091	271091	type	True	77.0789	81	669	95	below_threshold
Fusobacterium nucleatum subsp. polymorphum	strain=ATCC 10953	GCA_000153625.1	76857	851	type	True	76.89	134	669	95	below_threshold
Cetobacterium somerae	strain=ATCC BAA-474	GCA_000479045.1	188913	188913	type	True	76.6721	149	669	95	below_threshold
Fusobacterium necrophorum	strain=ATCC 25286	GCA_900104395.1	859	859	type	True	76.6521	55	669	95	below_threshold
Fusobacterium hwasookii	strain=ChDC F128	GCA_000292935.1	1583098	1583098	type	True	76.6151	132	669	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:25,050] [INFO] DFAST Taxonomy check result was written to GCF_900450765.1_42650_B02_genomic.fna/tc_result.tsv
[2024-01-24 15:27:25,051] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:25,051] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:25,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc56f77fe-8985-469c-94f3-a959656ef963/dqc_reference/checkm_data
[2024-01-24 15:27:25,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:25,081] [INFO] Task started: CheckM
[2024-01-24 15:27:25,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900450765.1_42650_B02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900450765.1_42650_B02_genomic.fna/checkm_input GCF_900450765.1_42650_B02_genomic.fna/checkm_result
[2024-01-24 15:27:46,181] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:46,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:46,219] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:46,220] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:46,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900450765.1_42650_B02_genomic.fna/markers.fasta)
[2024-01-24 15:27:46,221] [INFO] Task started: Blastn
[2024-01-24 15:27:46,221] [INFO] Running command: blastn -query GCF_900450765.1_42650_B02_genomic.fna/markers.fasta -db /var/lib/cwl/stgc56f77fe-8985-469c-94f3-a959656ef963/dqc_reference/reference_markers_gtdb.fasta -out GCF_900450765.1_42650_B02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:47,293] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:47,297] [INFO] Selected 7 target genomes.
[2024-01-24 15:27:47,297] [INFO] Target genome list was writen to GCF_900450765.1_42650_B02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:47,304] [INFO] Task started: fastANI
[2024-01-24 15:27:47,305] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3ee51fc-97d2-453d-a5c8-f3ac08aac063/GCF_900450765.1_42650_B02_genomic.fna.gz --refList GCF_900450765.1_42650_B02_genomic.fna/target_genomes_gtdb.txt --output GCF_900450765.1_42650_B02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:52,208] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:52,215] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:52,216] [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_900450765.1	s__Fusobacterium_A necrogenes	100.0	668	669	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000158195.2	s__Fusobacterium_A mortiferum	88.9338	469	669	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.16	98.67	0.92	0.88	9	-
GCA_905193685.1	s__Fusobacterium_A sp900555485	83.3627	421	669	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016900045.1	s__Fusobacterium_A sp900549465	82.7477	415	669	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	98.59	98.37	0.86	0.84	6	-
GCA_900764925.1	s__Fusobacterium_A sp900764925	82.3683	335	669	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.98	99.98	0.98	0.98	2	-
GCA_019012925.1	s__Fusobacterium_A sp019012925	80.61	352	669	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_003019675.1	s__Fusobacterium_A ulcerans	78.9291	252	669	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.20	98.24	0.93	0.85	7	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:52,218] [INFO] GTDB search result was written to GCF_900450765.1_42650_B02_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:52,219] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:52,228] [INFO] DFAST_QC result json was written to GCF_900450765.1_42650_B02_genomic.fna/dqc_result.json
[2024-01-24 15:27:52,228] [INFO] DFAST_QC completed!
[2024-01-24 15:27:52,229] [INFO] Total running time: 0h0m40s