[2024-01-24 14:56:34,474] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:34,479] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:34,480] [INFO] DQC Reference Directory: /var/lib/cwl/stga78df678-4645-42bd-8d33-402ef83705a8/dqc_reference
[2024-01-24 14:56:40,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:40,426] [INFO] Task started: Prodigal
[2024-01-24 14:56:40,426] [INFO] Running command: gunzip -c /var/lib/cwl/stgeca73c04-238d-4474-bb19-5f409785bbf0/GCF_001653955.1_ASM165395v1_genomic.fna.gz | prodigal -d GCF_001653955.1_ASM165395v1_genomic.fna/cds.fna -a GCF_001653955.1_ASM165395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:43,265] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:43,265] [INFO] Task started: HMMsearch
[2024-01-24 14:56:43,265] [INFO] Running command: hmmsearch --tblout GCF_001653955.1_ASM165395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga78df678-4645-42bd-8d33-402ef83705a8/dqc_reference/reference_markers.hmm GCF_001653955.1_ASM165395v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:43,553] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:43,554] [INFO] Found 6/6 markers.
[2024-01-24 14:56:43,583] [INFO] Query marker FASTA was written to GCF_001653955.1_ASM165395v1_genomic.fna/markers.fasta
[2024-01-24 14:56:43,584] [INFO] Task started: Blastn
[2024-01-24 14:56:43,584] [INFO] Running command: blastn -query GCF_001653955.1_ASM165395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga78df678-4645-42bd-8d33-402ef83705a8/dqc_reference/reference_markers.fasta -out GCF_001653955.1_ASM165395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:48,229] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:48,237] [INFO] Selected 12 target genomes.
[2024-01-24 14:56:48,237] [INFO] Target genome list was writen to GCF_001653955.1_ASM165395v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:48,293] [INFO] Task started: fastANI
[2024-01-24 14:56:48,293] [INFO] Running command: fastANI --query /var/lib/cwl/stgeca73c04-238d-4474-bb19-5f409785bbf0/GCF_001653955.1_ASM165395v1_genomic.fna.gz --refList GCF_001653955.1_ASM165395v1_genomic.fna/target_genomes.txt --output GCF_001653955.1_ASM165395v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:55,264] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:55,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga78df678-4645-42bd-8d33-402ef83705a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:55,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga78df678-4645-42bd-8d33-402ef83705a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:55,279] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:56:55,280] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:55,280] [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 persica	strain=ATCC VR-331	GCA_001653955.1	954	954	type	True	100.0	511	513	95	conclusive
Francisella persica	strain=FSC845	GCA_001275365.1	954	954	type	True	99.9612	505	513	95	conclusive
Francisella opportunistica	strain=PA05-1188	GCA_003347135.1	2016517	2016517	type	True	88.5	448	513	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001885235.1	622488	622488	type	True	86.5415	436	513	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001608445.1	622488	622488	type	True	86.5172	431	513	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000014645.1	264	263	type	True	86.4848	441	513	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000833375.1	264	263	type	True	86.4335	448	513	95	below_threshold
Francisella noatunensis subsp. noatunensis	strain=2005/50/F292-6	GCA_009823375.1	360196	657445	type	True	79.7028	274	513	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:55,282] [INFO] DFAST Taxonomy check result was written to GCF_001653955.1_ASM165395v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:55,282] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:55,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:55,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga78df678-4645-42bd-8d33-402ef83705a8/dqc_reference/checkm_data
[2024-01-24 14:56:55,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:55,310] [INFO] Task started: CheckM
[2024-01-24 14:56:55,311] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001653955.1_ASM165395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001653955.1_ASM165395v1_genomic.fna/checkm_input GCF_001653955.1_ASM165395v1_genomic.fna/checkm_result
[2024-01-24 14:57:20,061] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:20,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:20,094] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:20,095] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:20,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001653955.1_ASM165395v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:20,097] [INFO] Task started: Blastn
[2024-01-24 14:57:20,097] [INFO] Running command: blastn -query GCF_001653955.1_ASM165395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga78df678-4645-42bd-8d33-402ef83705a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_001653955.1_ASM165395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:21,741] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:21,745] [INFO] Selected 5 target genomes.
[2024-01-24 14:57:21,745] [INFO] Target genome list was writen to GCF_001653955.1_ASM165395v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:21,752] [INFO] Task started: fastANI
[2024-01-24 14:57:21,752] [INFO] Running command: fastANI --query /var/lib/cwl/stgeca73c04-238d-4474-bb19-5f409785bbf0/GCF_001653955.1_ASM165395v1_genomic.fna.gz --refList GCF_001653955.1_ASM165395v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001653955.1_ASM165395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:24,065] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:24,071] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:24,071] [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_001653955.1	s__Francisella persica	100.0	510	513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_002095075.1	s__Francisella sp002095075	93.5818	474	513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	98.09	96.18	0.98	0.96	3	-
GCF_003347135.1	s__Francisella opportunistica	88.4932	451	513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.87	99.85	1.00	0.99	4	-
GCF_001885235.1	s__Francisella hispaniensis	86.5375	436	513	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	86.3131	427	513	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 14:57:24,073] [INFO] GTDB search result was written to GCF_001653955.1_ASM165395v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:24,073] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:24,076] [INFO] DFAST_QC result json was written to GCF_001653955.1_ASM165395v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:24,080] [INFO] DFAST_QC completed!
[2024-01-24 14:57:24,081] [INFO] Total running time: 0h0m50s