[2024-01-24 12:40:08,011] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:08,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:08,013] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6d47e2c-eb0d-49c2-8516-e39eefe03d8f/dqc_reference
[2024-01-24 12:40:09,338] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:09,339] [INFO] Task started: Prodigal
[2024-01-24 12:40:09,339] [INFO] Running command: gunzip -c /var/lib/cwl/stg4511ada8-6e65-4658-ab7a-f62f572c98cb/GCF_000024405.1_ASM2440v1_genomic.fna.gz | prodigal -d GCF_000024405.1_ASM2440v1_genomic.fna/cds.fna -a GCF_000024405.1_ASM2440v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:17,677] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:17,677] [INFO] Task started: HMMsearch
[2024-01-24 12:40:17,677] [INFO] Running command: hmmsearch --tblout GCF_000024405.1_ASM2440v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6d47e2c-eb0d-49c2-8516-e39eefe03d8f/dqc_reference/reference_markers.hmm GCF_000024405.1_ASM2440v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:18,019] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:18,020] [INFO] Found 6/6 markers.
[2024-01-24 12:40:18,075] [INFO] Query marker FASTA was written to GCF_000024405.1_ASM2440v1_genomic.fna/markers.fasta
[2024-01-24 12:40:18,076] [INFO] Task started: Blastn
[2024-01-24 12:40:18,076] [INFO] Running command: blastn -query GCF_000024405.1_ASM2440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6d47e2c-eb0d-49c2-8516-e39eefe03d8f/dqc_reference/reference_markers.fasta -out GCF_000024405.1_ASM2440v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:18,681] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:18,685] [INFO] Selected 11 target genomes.
[2024-01-24 12:40:18,686] [INFO] Target genome list was writen to GCF_000024405.1_ASM2440v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:18,691] [INFO] Task started: fastANI
[2024-01-24 12:40:18,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg4511ada8-6e65-4658-ab7a-f62f572c98cb/GCF_000024405.1_ASM2440v1_genomic.fna.gz --refList GCF_000024405.1_ASM2440v1_genomic.fna/target_genomes.txt --output GCF_000024405.1_ASM2440v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:25,426] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:25,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6d47e2c-eb0d-49c2-8516-e39eefe03d8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:25,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6d47e2c-eb0d-49c2-8516-e39eefe03d8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:25,436] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:25,437] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:25,437] [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
Sebaldella termitidis	strain=ATCC 33386	GCA_000024405.1	826	826	type	True	100.0	1492	1494	95	conclusive
Sebaldella termitidis	strain=NCTC11300	GCA_900456835.1	826	826	type	True	99.9976	1492	1494	95	conclusive
Leptotrichia hofstadii	strain=JCM16775	GCA_007990525.1	157688	157688	type	True	76.9186	80	1494	95	below_threshold
Pseudoleptotrichia goodfellowii	strain=JCM16774	GCA_007990505.1	157692	157692	type	True	76.7191	121	1494	95	below_threshold
Pseudoleptotrichia goodfellowii	strain=DSM 19756	GCA_000516535.1	157692	157692	type	True	76.4487	118	1494	95	below_threshold
Fusobacterium ulcerans	strain=ATCC 49185	GCA_003019675.1	861	861	type	True	76.0042	78	1494	95	below_threshold
Leptotrichia hofstadii	strain=DSM 21651	GCA_000428965.1	157688	157688	type	True	75.9776	75	1494	95	below_threshold
Leptotrichia trevisanii	strain=DSM 22070	GCA_000482505.1	109328	109328	type	True	75.6801	90	1494	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:25,439] [INFO] DFAST Taxonomy check result was written to GCF_000024405.1_ASM2440v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:25,439] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:25,439] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:25,440] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6d47e2c-eb0d-49c2-8516-e39eefe03d8f/dqc_reference/checkm_data
[2024-01-24 12:40:25,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:25,491] [INFO] Task started: CheckM
[2024-01-24 12:40:25,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024405.1_ASM2440v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024405.1_ASM2440v1_genomic.fna/checkm_input GCF_000024405.1_ASM2440v1_genomic.fna/checkm_result
[2024-01-24 12:40:55,250] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:55,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:55,275] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:55,276] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:55,276] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024405.1_ASM2440v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:55,276] [INFO] Task started: Blastn
[2024-01-24 12:40:55,277] [INFO] Running command: blastn -query GCF_000024405.1_ASM2440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6d47e2c-eb0d-49c2-8516-e39eefe03d8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024405.1_ASM2440v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:56,010] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:56,016] [INFO] Selected 19 target genomes.
[2024-01-24 12:40:56,016] [INFO] Target genome list was writen to GCF_000024405.1_ASM2440v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:56,030] [INFO] Task started: fastANI
[2024-01-24 12:40:56,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg4511ada8-6e65-4658-ab7a-f62f572c98cb/GCF_000024405.1_ASM2440v1_genomic.fna.gz --refList GCF_000024405.1_ASM2440v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024405.1_ASM2440v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:04,877] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:04,891] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:04,891] [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_000024405.1	s__Sebaldella termitidis	100.0	1490	1494	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Sebaldella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_018058425.1	s__Sebaldella sp018058425	78.0573	346	1494	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Sebaldella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990635.1	s__Leptotrichia hongkongensis	76.9525	76	1494	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274535.1	s__Leptotrichia_A sp001274535	76.7793	123	1494	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia_A	95.0	97.10	97.10	0.94	0.94	2	-
GCF_007990525.1	s__Leptotrichia hofstadii	76.7312	78	1494	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	98.32	96.65	0.96	0.92	3	-
GCF_007990505.1	s__Pseudoleptotrichia goodfellowii	76.7132	120	1494	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Pseudoleptotrichia	95.0	98.75	97.51	0.96	0.93	3	-
GCF_000469505.1	s__Leptotrichia_A sp000469505	76.2932	98	1494	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003019675.1	s__Fusobacterium_A ulcerans	75.9418	78	1494	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.20	98.24	0.93	0.85	7	-
GCF_002356455.1	s__Fusobacterium_A varium_A	75.6961	110	1494	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.56	99.56	0.92	0.92	2	-
GCA_910588715.1	s__Clostridium sp910588715	74.6422	51	1494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:04,893] [INFO] GTDB search result was written to GCF_000024405.1_ASM2440v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:04,894] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:04,897] [INFO] DFAST_QC result json was written to GCF_000024405.1_ASM2440v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:04,897] [INFO] DFAST_QC completed!
[2024-01-24 12:41:04,898] [INFO] Total running time: 0h0m57s