[2024-01-24 13:09:27,332] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:27,333] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:27,333] [INFO] DQC Reference Directory: /var/lib/cwl/stga73f4b6b-e1a2-4a30-8daf-c5443b55fdd6/dqc_reference
[2024-01-24 13:09:28,514] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:28,514] [INFO] Task started: Prodigal
[2024-01-24 13:09:28,515] [INFO] Running command: gunzip -c /var/lib/cwl/stge07bd5fb-4103-4e82-bf5a-58da0b49beac/GCF_003347135.1_ASM334713v1_genomic.fna.gz | prodigal -d GCF_003347135.1_ASM334713v1_genomic.fna/cds.fna -a GCF_003347135.1_ASM334713v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:31,609] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:31,609] [INFO] Task started: HMMsearch
[2024-01-24 13:09:31,609] [INFO] Running command: hmmsearch --tblout GCF_003347135.1_ASM334713v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga73f4b6b-e1a2-4a30-8daf-c5443b55fdd6/dqc_reference/reference_markers.hmm GCF_003347135.1_ASM334713v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:31,827] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:31,829] [INFO] Found 6/6 markers.
[2024-01-24 13:09:31,849] [INFO] Query marker FASTA was written to GCF_003347135.1_ASM334713v1_genomic.fna/markers.fasta
[2024-01-24 13:09:31,849] [INFO] Task started: Blastn
[2024-01-24 13:09:31,849] [INFO] Running command: blastn -query GCF_003347135.1_ASM334713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga73f4b6b-e1a2-4a30-8daf-c5443b55fdd6/dqc_reference/reference_markers.fasta -out GCF_003347135.1_ASM334713v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:32,480] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:32,490] [INFO] Selected 12 target genomes.
[2024-01-24 13:09:32,490] [INFO] Target genome list was writen to GCF_003347135.1_ASM334713v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:32,534] [INFO] Task started: fastANI
[2024-01-24 13:09:32,535] [INFO] Running command: fastANI --query /var/lib/cwl/stge07bd5fb-4103-4e82-bf5a-58da0b49beac/GCF_003347135.1_ASM334713v1_genomic.fna.gz --refList GCF_003347135.1_ASM334713v1_genomic.fna/target_genomes.txt --output GCF_003347135.1_ASM334713v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:38,191] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:38,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga73f4b6b-e1a2-4a30-8daf-c5443b55fdd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:38,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga73f4b6b-e1a2-4a30-8daf-c5443b55fdd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:38,199] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:38,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:38,200] [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
Francisella opportunistica	strain=PA05-1188	GCA_003347135.1	2016517	2016517	type	True	100.0	613	613	95	conclusive
Francisella persica	strain=FSC845	GCA_001275365.1	954	954	type	True	88.2543	445	613	95	below_threshold
Francisella persica	strain=ATCC VR-331	GCA_001653955.1	954	954	type	True	88.1646	454	613	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001885235.1	622488	622488	type	True	86.81	499	613	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001608445.1	622488	622488	type	True	86.791	482	613	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000833375.1	264	263	type	True	86.6189	509	613	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000014645.1	264	263	type	True	86.5718	509	613	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:38,202] [INFO] DFAST Taxonomy check result was written to GCF_003347135.1_ASM334713v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:38,202] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:38,202] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:38,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga73f4b6b-e1a2-4a30-8daf-c5443b55fdd6/dqc_reference/checkm_data
[2024-01-24 13:09:38,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:38,230] [INFO] Task started: CheckM
[2024-01-24 13:09:38,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003347135.1_ASM334713v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003347135.1_ASM334713v1_genomic.fna/checkm_input GCF_003347135.1_ASM334713v1_genomic.fna/checkm_result
[2024-01-24 13:09:55,396] [INFO] Task succeeded: CheckM
[2024-01-24 13:09:55,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:09:55,423] [INFO] ===== Completeness check finished =====
[2024-01-24 13:09:55,424] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:09:55,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003347135.1_ASM334713v1_genomic.fna/markers.fasta)
[2024-01-24 13:09:55,424] [INFO] Task started: Blastn
[2024-01-24 13:09:55,425] [INFO] Running command: blastn -query GCF_003347135.1_ASM334713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga73f4b6b-e1a2-4a30-8daf-c5443b55fdd6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003347135.1_ASM334713v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:56,395] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:56,398] [INFO] Selected 5 target genomes.
[2024-01-24 13:09:56,398] [INFO] Target genome list was writen to GCF_003347135.1_ASM334713v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:09:56,439] [INFO] Task started: fastANI
[2024-01-24 13:09:56,439] [INFO] Running command: fastANI --query /var/lib/cwl/stge07bd5fb-4103-4e82-bf5a-58da0b49beac/GCF_003347135.1_ASM334713v1_genomic.fna.gz --refList GCF_003347135.1_ASM334713v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003347135.1_ASM334713v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:09:59,013] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:59,021] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:09:59,022] [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_003347135.1	s__Francisella opportunistica	100.0	613	613	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.87	99.85	1.00	0.99	4	conclusive
GCF_002095075.1	s__Francisella sp002095075	88.8386	460	613	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	98.09	96.18	0.98	0.96	3	-
GCF_001653955.1	s__Francisella persica	88.1706	452	613	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001885235.1	s__Francisella hispaniensis	86.81	499	613	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	98.55	97.74	0.95	0.92	4	-
GCF_000008985.1	s__Francisella tularensis	86.335	493	613	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.28	97.47	0.99	0.89	860	-
--------------------------------------------------------------------------------
[2024-01-24 13:09:59,023] [INFO] GTDB search result was written to GCF_003347135.1_ASM334713v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:09:59,024] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:09:59,028] [INFO] DFAST_QC result json was written to GCF_003347135.1_ASM334713v1_genomic.fna/dqc_result.json
[2024-01-24 13:09:59,028] [INFO] DFAST_QC completed!
[2024-01-24 13:09:59,028] [INFO] Total running time: 0h0m32s