[2024-01-25 18:11:35,737] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:35,739] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:35,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg35af9632-1213-4049-9d5f-5ad53d8ca505/dqc_reference
[2024-01-25 18:11:36,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:36,895] [INFO] Task started: Prodigal
[2024-01-25 18:11:36,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg1692a7a7-79b9-4d28-bbc4-260efb7d6a98/GCF_000833455.1_ASM83345v1_genomic.fna.gz | prodigal -d GCF_000833455.1_ASM83345v1_genomic.fna/cds.fna -a GCF_000833455.1_ASM83345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:40,053] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:40,053] [INFO] Task started: HMMsearch
[2024-01-25 18:11:40,053] [INFO] Running command: hmmsearch --tblout GCF_000833455.1_ASM83345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35af9632-1213-4049-9d5f-5ad53d8ca505/dqc_reference/reference_markers.hmm GCF_000833455.1_ASM83345v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:40,257] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:40,259] [INFO] Found 6/6 markers.
[2024-01-25 18:11:40,281] [INFO] Query marker FASTA was written to GCF_000833455.1_ASM83345v1_genomic.fna/markers.fasta
[2024-01-25 18:11:40,281] [INFO] Task started: Blastn
[2024-01-25 18:11:40,281] [INFO] Running command: blastn -query GCF_000833455.1_ASM83345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35af9632-1213-4049-9d5f-5ad53d8ca505/dqc_reference/reference_markers.fasta -out GCF_000833455.1_ASM83345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:40,853] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:40,859] [INFO] Selected 12 target genomes.
[2024-01-25 18:11:40,860] [INFO] Target genome list was writen to GCF_000833455.1_ASM83345v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:40,872] [INFO] Task started: fastANI
[2024-01-25 18:11:40,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg1692a7a7-79b9-4d28-bbc4-260efb7d6a98/GCF_000833455.1_ASM83345v1_genomic.fna.gz --refList GCF_000833455.1_ASM83345v1_genomic.fna/target_genomes.txt --output GCF_000833455.1_ASM83345v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:46,099] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:46,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35af9632-1213-4049-9d5f-5ad53d8ca505/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:46,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35af9632-1213-4049-9d5f-5ad53d8ca505/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:46,106] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:11:46,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:11:46,107] [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 philomiragia	strain=O#319L	GCA_000833455.1	28110	28110	type	True	100.0	672	672	95	conclusive
Francisella philomiragia	strain=ATCC 25015	GCA_000156715.1	28110	28110	type	True	99.9453	660	672	95	conclusive
Francisella noatunensis subsp. noatunensis	strain=2005/50/F292-6	GCA_009823375.1	360196	657445	type	True	94.8501	467	672	95	below_threshold
Francisella salina	strain=TX07-7308	GCA_000219045.1	573569	573569	type	True	90.8049	574	672	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001608445.1	622488	622488	type	True	83.2367	403	672	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000833375.1	264	263	type	True	82.7833	432	672	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000014645.1	264	263	type	True	82.6638	431	672	95	below_threshold
Francisella opportunistica	strain=PA05-1188	GCA_003347135.1	2016517	2016517	type	True	80.1909	361	672	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:46,108] [INFO] DFAST Taxonomy check result was written to GCF_000833455.1_ASM83345v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:46,108] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:46,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:46,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35af9632-1213-4049-9d5f-5ad53d8ca505/dqc_reference/checkm_data
[2024-01-25 18:11:46,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:46,131] [INFO] Task started: CheckM
[2024-01-25 18:11:46,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000833455.1_ASM83345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000833455.1_ASM83345v1_genomic.fna/checkm_input GCF_000833455.1_ASM83345v1_genomic.fna/checkm_result
[2024-01-25 18:12:01,826] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:01,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:01,847] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:01,847] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:01,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000833455.1_ASM83345v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:01,847] [INFO] Task started: Blastn
[2024-01-25 18:12:01,847] [INFO] Running command: blastn -query GCF_000833455.1_ASM83345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35af9632-1213-4049-9d5f-5ad53d8ca505/dqc_reference/reference_markers_gtdb.fasta -out GCF_000833455.1_ASM83345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:02,774] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:02,776] [INFO] Selected 8 target genomes.
[2024-01-25 18:12:02,776] [INFO] Target genome list was writen to GCF_000833455.1_ASM83345v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:02,784] [INFO] Task started: fastANI
[2024-01-25 18:12:02,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg1692a7a7-79b9-4d28-bbc4-260efb7d6a98/GCF_000833455.1_ASM83345v1_genomic.fna.gz --refList GCF_000833455.1_ASM83345v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000833455.1_ASM83345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:06,563] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:06,570] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:06,570] [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_000156715.1	s__Francisella philomiragia	99.9453	660	672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	97.81	97.38	0.91	0.88	49	conclusive
GCF_014844275.1	s__Francisella noatunensis	94.3581	537	672	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	93.1319	563	672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.91	95.40	0.99	0.93	54	-
GCF_007923265.1	s__Francisella salimarina	90.811	556	672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	98.26	97.77	0.94	0.91	8	-
GCF_001885235.1	s__Francisella hispaniensis	83.3744	411	672	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	82.4633	417	672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.28	97.47	0.99	0.89	860	-
GCF_003347135.1	s__Francisella opportunistica	80.1908	361	672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.87	99.85	1.00	0.99	4	-
GCF_000764555.1	s__Francisella sp000764555	80.1438	323	672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:06,572] [INFO] GTDB search result was written to GCF_000833455.1_ASM83345v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:06,572] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:06,576] [INFO] DFAST_QC result json was written to GCF_000833455.1_ASM83345v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:06,576] [INFO] DFAST_QC completed!
[2024-01-25 18:12:06,576] [INFO] Total running time: 0h0m31s