[2024-01-24 14:19:45,306] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:45,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:45,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg02142de9-6540-4249-8e04-2763413342cb/dqc_reference
[2024-01-24 14:19:47,130] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,131] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,132] [INFO] Running command: gunzip -c /var/lib/cwl/stg797098bf-1902-497d-ae99-4eee9c6c7c26/GCF_002761955.1_ASM276195v1_genomic.fna.gz | prodigal -d GCF_002761955.1_ASM276195v1_genomic.fna/cds.fna -a GCF_002761955.1_ASM276195v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:50,498] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:50,498] [INFO] Task started: HMMsearch
[2024-01-24 14:19:50,498] [INFO] Running command: hmmsearch --tblout GCF_002761955.1_ASM276195v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02142de9-6540-4249-8e04-2763413342cb/dqc_reference/reference_markers.hmm GCF_002761955.1_ASM276195v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:50,824] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:50,825] [INFO] Found 6/6 markers.
[2024-01-24 14:19:50,845] [INFO] Query marker FASTA was written to GCF_002761955.1_ASM276195v1_genomic.fna/markers.fasta
[2024-01-24 14:19:50,845] [INFO] Task started: Blastn
[2024-01-24 14:19:50,845] [INFO] Running command: blastn -query GCF_002761955.1_ASM276195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02142de9-6540-4249-8e04-2763413342cb/dqc_reference/reference_markers.fasta -out GCF_002761955.1_ASM276195v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:54,381] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:54,383] [INFO] Selected 7 target genomes.
[2024-01-24 14:19:54,384] [INFO] Target genome list was writen to GCF_002761955.1_ASM276195v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:54,414] [INFO] Task started: fastANI
[2024-01-24 14:19:54,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg797098bf-1902-497d-ae99-4eee9c6c7c26/GCF_002761955.1_ASM276195v1_genomic.fna.gz --refList GCF_002761955.1_ASM276195v1_genomic.fna/target_genomes.txt --output GCF_002761955.1_ASM276195v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:00,928] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:00,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02142de9-6540-4249-8e04-2763413342cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:00,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02142de9-6540-4249-8e04-2763413342cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:00,936] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:00,936] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:00,936] [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 pseudoperiodonticum	strain=KCOM 1259	GCA_002761955.1	2663009	2663009	type	True	100.0	804	804	95	conclusive
Fusobacterium periodonticum	strain=ATCC 33693	GCA_000160475.1	860	860	suspected-type	True	92.6859	632	804	95	below_threshold
Fusobacterium hwasookii	strain=ChDC F128	GCA_000292935.1	1583098	1583098	type	True	86.0103	559	804	95	below_threshold
Fusobacterium hwasookii	strain=KCOM 1249	GCA_014217355.1	1583098	1583098	type	True	85.9615	571	804	95	below_threshold
Fusobacterium nucleatum subsp. polymorphum	strain=ATCC 10953	GCA_000153625.1	76857	851	type	True	85.9037	560	804	95	below_threshold
Fusobacterium nucleatum subsp. polymorphum	strain=NCTC10562	GCA_001457555.1	76857	851	type	True	85.8971	569	804	95	below_threshold
Fusobacterium canifelinum	strain=FDAARGOS_1126	GCA_016724785.1	285729	285729	type	True	85.2666	558	804	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:00,938] [INFO] DFAST Taxonomy check result was written to GCF_002761955.1_ASM276195v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:00,938] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:00,938] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:00,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02142de9-6540-4249-8e04-2763413342cb/dqc_reference/checkm_data
[2024-01-24 14:20:00,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:00,964] [INFO] Task started: CheckM
[2024-01-24 14:20:00,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002761955.1_ASM276195v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002761955.1_ASM276195v1_genomic.fna/checkm_input GCF_002761955.1_ASM276195v1_genomic.fna/checkm_result
[2024-01-24 14:20:20,804] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:20,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:20,820] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:20,820] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:20,820] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002761955.1_ASM276195v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:20,821] [INFO] Task started: Blastn
[2024-01-24 14:20:20,821] [INFO] Running command: blastn -query GCF_002761955.1_ASM276195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02142de9-6540-4249-8e04-2763413342cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002761955.1_ASM276195v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:21,814] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:21,816] [INFO] Selected 6 target genomes.
[2024-01-24 14:20:21,817] [INFO] Target genome list was writen to GCF_002761955.1_ASM276195v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:21,820] [INFO] Task started: fastANI
[2024-01-24 14:20:21,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg797098bf-1902-497d-ae99-4eee9c6c7c26/GCF_002761955.1_ASM276195v1_genomic.fna.gz --refList GCF_002761955.1_ASM276195v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002761955.1_ASM276195v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:27,596] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:27,601] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:20:27,601] [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_002761955.1	s__Fusobacterium pseudoperiodonticum	100.0	804	804	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.1543	96.63	95.97	0.86	0.84	10	inconclusive
GCF_002763915.1	s__Fusobacterium periodonticum_D	95.1784	668	804	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.1543	96.98	95.97	0.86	0.80	11	inconclusive
GCF_000163935.1	s__Fusobacterium periodonticum_B	94.6045	629	804	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000160475.1	s__Fusobacterium periodonticum	92.6859	632	804	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000235465.1	s__Fusobacterium sp000235465	91.156	528	804	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457555.1	s__Fusobacterium polymorphum	85.8897	570	804	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	96.55	95.37	0.85	0.79	30	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:27,602] [INFO] GTDB search result was written to GCF_002761955.1_ASM276195v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:27,603] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:27,605] [INFO] DFAST_QC result json was written to GCF_002761955.1_ASM276195v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:27,605] [INFO] DFAST_QC completed!
[2024-01-24 14:20:27,606] [INFO] Total running time: 0h0m42s