[2024-01-24 13:28:15,910] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:15,912] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:15,912] [INFO] DQC Reference Directory: /var/lib/cwl/stg29592c6b-0aca-4d46-9b4c-c4a9d2191193/dqc_reference
[2024-01-24 13:28:17,150] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:17,151] [INFO] Task started: Prodigal
[2024-01-24 13:28:17,151] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ae0328c-9ac8-44ef-99a2-0a9f012f7959/GCF_000219045.1_ASM21904v1_genomic.fna.gz | prodigal -d GCF_000219045.1_ASM21904v1_genomic.fna/cds.fna -a GCF_000219045.1_ASM21904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:20,857] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:20,857] [INFO] Task started: HMMsearch
[2024-01-24 13:28:20,857] [INFO] Running command: hmmsearch --tblout GCF_000219045.1_ASM21904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29592c6b-0aca-4d46-9b4c-c4a9d2191193/dqc_reference/reference_markers.hmm GCF_000219045.1_ASM21904v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:21,128] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:21,130] [INFO] Found 6/6 markers.
[2024-01-24 13:28:21,170] [INFO] Query marker FASTA was written to GCF_000219045.1_ASM21904v1_genomic.fna/markers.fasta
[2024-01-24 13:28:21,171] [INFO] Task started: Blastn
[2024-01-24 13:28:21,171] [INFO] Running command: blastn -query GCF_000219045.1_ASM21904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29592c6b-0aca-4d46-9b4c-c4a9d2191193/dqc_reference/reference_markers.fasta -out GCF_000219045.1_ASM21904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:21,889] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:21,893] [INFO] Selected 10 target genomes.
[2024-01-24 13:28:21,894] [INFO] Target genome list was writen to GCF_000219045.1_ASM21904v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:21,909] [INFO] Task started: fastANI
[2024-01-24 13:28:21,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ae0328c-9ac8-44ef-99a2-0a9f012f7959/GCF_000219045.1_ASM21904v1_genomic.fna.gz --refList GCF_000219045.1_ASM21904v1_genomic.fna/target_genomes.txt --output GCF_000219045.1_ASM21904v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:26,350] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:26,351] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29592c6b-0aca-4d46-9b4c-c4a9d2191193/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:26,351] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29592c6b-0aca-4d46-9b4c-c4a9d2191193/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:26,358] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:26,358] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:26,358] [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 salina	strain=TX07-7308	GCA_000219045.1	573569	573569	type	True	100.0	677	678	95	conclusive
Francisella philomiragia	strain=O#319L	GCA_000833455.1	28110	28110	type	True	90.8284	568	678	95	below_threshold
Francisella philomiragia	strain=ATCC 25015	GCA_000156715.1	28110	28110	type	True	90.828	580	678	95	below_threshold
Francisella noatunensis subsp. noatunensis	strain=2005/50/F292-6	GCA_009823375.1	360196	657445	type	True	89.6319	449	678	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001608445.1	622488	622488	type	True	82.3092	400	678	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000014645.1	264	263	type	True	81.9648	416	678	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:26,363] [INFO] DFAST Taxonomy check result was written to GCF_000219045.1_ASM21904v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:26,363] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:26,363] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:26,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29592c6b-0aca-4d46-9b4c-c4a9d2191193/dqc_reference/checkm_data
[2024-01-24 13:28:26,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:26,389] [INFO] Task started: CheckM
[2024-01-24 13:28:26,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000219045.1_ASM21904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000219045.1_ASM21904v1_genomic.fna/checkm_input GCF_000219045.1_ASM21904v1_genomic.fna/checkm_result
[2024-01-24 13:28:46,310] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:46,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:46,331] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:46,332] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:46,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000219045.1_ASM21904v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:46,333] [INFO] Task started: Blastn
[2024-01-24 13:28:46,333] [INFO] Running command: blastn -query GCF_000219045.1_ASM21904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29592c6b-0aca-4d46-9b4c-c4a9d2191193/dqc_reference/reference_markers_gtdb.fasta -out GCF_000219045.1_ASM21904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:47,337] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:47,341] [INFO] Selected 7 target genomes.
[2024-01-24 13:28:47,342] [INFO] Target genome list was writen to GCF_000219045.1_ASM21904v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:47,356] [INFO] Task started: fastANI
[2024-01-24 13:28:47,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ae0328c-9ac8-44ef-99a2-0a9f012f7959/GCF_000219045.1_ASM21904v1_genomic.fna.gz --refList GCF_000219045.1_ASM21904v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000219045.1_ASM21904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:50,867] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:50,874] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:50,874] [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_007923265.1	s__Francisella salimarina	97.7478	598	678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	98.26	97.77	0.94	0.91	8	conclusive
GCF_000156715.1	s__Francisella philomiragia	90.828	580	678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	97.81	97.38	0.91	0.88	49	-
GCF_014844275.1	s__Francisella noatunensis	89.4108	507	678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.88	99.78	0.95	0.94	24	-
GCF_001042525.2	s__Francisella orientalis	88.8494	546	678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.91	95.40	0.99	0.93	54	-
GCF_001885235.1	s__Francisella hispaniensis	82.3174	416	678	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	81.5314	403	678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.28	97.47	0.99	0.89	860	-
GCF_000764555.1	s__Francisella sp000764555	80.3625	316	678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:50,876] [INFO] GTDB search result was written to GCF_000219045.1_ASM21904v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:50,877] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:50,879] [INFO] DFAST_QC result json was written to GCF_000219045.1_ASM21904v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:50,879] [INFO] DFAST_QC completed!
[2024-01-24 13:28:50,880] [INFO] Total running time: 0h0m35s