[2024-01-24 14:38:49,872] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:49,879] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:49,880] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d4a2e17-65c7-4a42-a868-0a65ea8286fb/dqc_reference
[2024-01-24 14:38:52,373] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:52,374] [INFO] Task started: Prodigal
[2024-01-24 14:38:52,374] [INFO] Running command: gunzip -c /var/lib/cwl/stg1772b7c7-f90a-4a16-b6c2-0c43f8742d9a/GCF_007923265.1_ASM792326v1_genomic.fna.gz | prodigal -d GCF_007923265.1_ASM792326v1_genomic.fna/cds.fna -a GCF_007923265.1_ASM792326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:55,940] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:55,941] [INFO] Task started: HMMsearch
[2024-01-24 14:38:55,941] [INFO] Running command: hmmsearch --tblout GCF_007923265.1_ASM792326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d4a2e17-65c7-4a42-a868-0a65ea8286fb/dqc_reference/reference_markers.hmm GCF_007923265.1_ASM792326v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:56,299] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:56,300] [INFO] Found 6/6 markers.
[2024-01-24 14:38:56,323] [INFO] Query marker FASTA was written to GCF_007923265.1_ASM792326v1_genomic.fna/markers.fasta
[2024-01-24 14:38:56,324] [INFO] Task started: Blastn
[2024-01-24 14:38:56,324] [INFO] Running command: blastn -query GCF_007923265.1_ASM792326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d4a2e17-65c7-4a42-a868-0a65ea8286fb/dqc_reference/reference_markers.fasta -out GCF_007923265.1_ASM792326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:59,123] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:59,127] [INFO] Selected 11 target genomes.
[2024-01-24 14:38:59,128] [INFO] Target genome list was writen to GCF_007923265.1_ASM792326v1_genomic.fna/target_genomes.txt
[2024-01-24 14:38:59,150] [INFO] Task started: fastANI
[2024-01-24 14:38:59,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg1772b7c7-f90a-4a16-b6c2-0c43f8742d9a/GCF_007923265.1_ASM792326v1_genomic.fna.gz --refList GCF_007923265.1_ASM792326v1_genomic.fna/target_genomes.txt --output GCF_007923265.1_ASM792326v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:03,787] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:03,788] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d4a2e17-65c7-4a42-a868-0a65ea8286fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:03,788] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d4a2e17-65c7-4a42-a868-0a65ea8286fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:03,796] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:03,796] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:03,796] [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	97.8046	595	654	95	conclusive
Francisella philomiragia	strain=O#319L	GCA_000833455.1	28110	28110	type	True	90.6476	567	654	95	below_threshold
Francisella philomiragia	strain=ATCC 25015	GCA_000156715.1	28110	28110	type	True	90.6443	576	654	95	below_threshold
Francisella noatunensis subsp. noatunensis	strain=2005/50/F292-6	GCA_009823375.1	360196	657445	type	True	89.8404	442	654	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001608445.1	622488	622488	type	True	82.4258	405	654	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000014645.1	264	263	type	True	81.8148	401	654	95	below_threshold
Francisella halioticida	strain=DSM 23729	GCA_002211785.1	549298	549298	type	True	79.2106	291	654	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:03,798] [INFO] DFAST Taxonomy check result was written to GCF_007923265.1_ASM792326v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:03,799] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:03,799] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:03,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d4a2e17-65c7-4a42-a868-0a65ea8286fb/dqc_reference/checkm_data
[2024-01-24 14:39:03,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:03,827] [INFO] Task started: CheckM
[2024-01-24 14:39:03,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007923265.1_ASM792326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007923265.1_ASM792326v1_genomic.fna/checkm_input GCF_007923265.1_ASM792326v1_genomic.fna/checkm_result
[2024-01-24 14:39:26,171] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:26,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:26,191] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:26,192] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:26,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007923265.1_ASM792326v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:26,192] [INFO] Task started: Blastn
[2024-01-24 14:39:26,192] [INFO] Running command: blastn -query GCF_007923265.1_ASM792326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d4a2e17-65c7-4a42-a868-0a65ea8286fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_007923265.1_ASM792326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:27,608] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:27,611] [INFO] Selected 8 target genomes.
[2024-01-24 14:39:27,611] [INFO] Target genome list was writen to GCF_007923265.1_ASM792326v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:27,618] [INFO] Task started: fastANI
[2024-01-24 14:39:27,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg1772b7c7-f90a-4a16-b6c2-0c43f8742d9a/GCF_007923265.1_ASM792326v1_genomic.fna.gz --refList GCF_007923265.1_ASM792326v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007923265.1_ASM792326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:31,648] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:31,657] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:31,657] [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	100.0	654	654	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	90.6443	576	654	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	89.3683	507	654	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	88.8547	542	654	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	82.4053	413	654	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	81.5441	394	654	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	80.235	318	654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211785.1	s__Francisella halioticida	79.2106	291	654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.38	99.38	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:39:31,659] [INFO] GTDB search result was written to GCF_007923265.1_ASM792326v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:31,660] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:31,664] [INFO] DFAST_QC result json was written to GCF_007923265.1_ASM792326v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:31,665] [INFO] DFAST_QC completed!
[2024-01-24 14:39:31,665] [INFO] Total running time: 0h0m42s