[2024-01-24 15:27:20,822] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:20,825] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:20,826] [INFO] DQC Reference Directory: /var/lib/cwl/stg0495084c-9ce7-433f-9085-7e6985d721f6/dqc_reference
[2024-01-24 15:27:23,298] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:23,300] [INFO] Task started: Prodigal
[2024-01-24 15:27:23,300] [INFO] Running command: gunzip -c /var/lib/cwl/stg21a37789-e7a2-45d6-aa5f-a417ca4e1054/GCF_003290445.1_ASM329044v1_genomic.fna.gz | prodigal -d GCF_003290445.1_ASM329044v1_genomic.fna/cds.fna -a GCF_003290445.1_ASM329044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:26,881] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:26,882] [INFO] Task started: HMMsearch
[2024-01-24 15:27:26,882] [INFO] Running command: hmmsearch --tblout GCF_003290445.1_ASM329044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0495084c-9ce7-433f-9085-7e6985d721f6/dqc_reference/reference_markers.hmm GCF_003290445.1_ASM329044v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:27,107] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:27,109] [INFO] Found 6/6 markers.
[2024-01-24 15:27:27,131] [INFO] Query marker FASTA was written to GCF_003290445.1_ASM329044v1_genomic.fna/markers.fasta
[2024-01-24 15:27:27,131] [INFO] Task started: Blastn
[2024-01-24 15:27:27,132] [INFO] Running command: blastn -query GCF_003290445.1_ASM329044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0495084c-9ce7-433f-9085-7e6985d721f6/dqc_reference/reference_markers.fasta -out GCF_003290445.1_ASM329044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:30,368] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:30,372] [INFO] Selected 20 target genomes.
[2024-01-24 15:27:30,372] [INFO] Target genome list was writen to GCF_003290445.1_ASM329044v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:30,495] [INFO] Task started: fastANI
[2024-01-24 15:27:30,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg21a37789-e7a2-45d6-aa5f-a417ca4e1054/GCF_003290445.1_ASM329044v1_genomic.fna.gz --refList GCF_003290445.1_ASM329044v1_genomic.fna/target_genomes.txt --output GCF_003290445.1_ASM329044v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:38,347] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:38,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0495084c-9ce7-433f-9085-7e6985d721f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:38,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0495084c-9ce7-433f-9085-7e6985d721f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:38,363] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:38,363] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:38,363] [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 adeliensis	strain=FDC440	GCA_003290445.1	2007306	2007306	type	True	100.0	683	684	95	conclusive
Francisella uliginis	strain=TX07-7310	GCA_001895265.1	573570	573570	type	True	78.9387	232	684	95	below_threshold
Francisella philomiragia	strain=O#319L	GCA_000833455.1	28110	28110	type	True	78.6662	189	684	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000014645.1	264	263	type	True	78.5407	187	684	95	below_threshold
Francisella noatunensis subsp. noatunensis	strain=2005/50/F292-6	GCA_009823375.1	360196	657445	type	True	78.5022	165	684	95	below_threshold
Francisella philomiragia	strain=ATCC 25015	GCA_000156715.1	28110	28110	type	True	78.3696	189	684	95	below_threshold
Francisella persica	strain=FSC845	GCA_001275365.1	954	954	type	True	78.2935	129	684	95	below_threshold
Francisella opportunistica	strain=PA05-1188	GCA_003347135.1	2016517	2016517	type	True	78.2528	154	684	95	below_threshold
Francisella salina	strain=TX07-7308	GCA_000219045.1	573569	573569	type	True	78.1957	211	684	95	below_threshold
Francisella persica	strain=ATCC VR-331	GCA_001653955.1	954	954	type	True	78.1136	131	684	95	below_threshold
Allofrancisella inopinata	strain=SYSU YG23	GCA_012222965.1	1085647	1085647	type	True	78.1071	138	684	95	below_threshold
Allofrancisella inopinata	strain=DSM 101834	GCA_004365555.1	1085647	1085647	type	True	77.7293	134	684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:38,365] [INFO] DFAST Taxonomy check result was written to GCF_003290445.1_ASM329044v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:38,365] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:38,365] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:38,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0495084c-9ce7-433f-9085-7e6985d721f6/dqc_reference/checkm_data
[2024-01-24 15:27:38,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:38,394] [INFO] Task started: CheckM
[2024-01-24 15:27:38,395] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003290445.1_ASM329044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003290445.1_ASM329044v1_genomic.fna/checkm_input GCF_003290445.1_ASM329044v1_genomic.fna/checkm_result
[2024-01-24 15:27:58,607] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:58,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:58,628] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:58,629] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:58,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003290445.1_ASM329044v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:58,630] [INFO] Task started: Blastn
[2024-01-24 15:27:58,630] [INFO] Running command: blastn -query GCF_003290445.1_ASM329044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0495084c-9ce7-433f-9085-7e6985d721f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003290445.1_ASM329044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:59,639] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:59,643] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:59,643] [INFO] Target genome list was writen to GCF_003290445.1_ASM329044v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:59,655] [INFO] Task started: fastANI
[2024-01-24 15:27:59,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg21a37789-e7a2-45d6-aa5f-a417ca4e1054/GCF_003290445.1_ASM329044v1_genomic.fna.gz --refList GCF_003290445.1_ASM329044v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003290445.1_ASM329044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:06,753] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:06,766] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:06,766] [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_003290445.1	s__Francisella_A adeliensis	100.0	683	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella_A	95.0	98.86	95.45	0.98	0.93	5	conclusive
GCF_001895265.1	s__Francisella uliginis	78.958	231	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012224145.1	s__Francisella sp012224145	78.7793	212	684	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	78.7476	182	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.38	99.38	0.93	0.93	2	-
GCF_000764555.1	s__Francisella sp000764555	78.7331	226	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014844275.1	s__Francisella noatunensis	78.7316	174	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.88	99.78	0.95	0.94	24	-
GCF_000156715.1	s__Francisella philomiragia	78.3696	189	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	97.81	97.38	0.91	0.88	49	-
GCF_001042525.2	s__Francisella orientalis	78.3003	179	684	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	78.1676	201	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	98.26	97.77	0.94	0.91	8	-
GCF_003347135.1	s__Francisella opportunistica	78.1246	154	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.87	99.85	1.00	0.99	4	-
GCF_001880225.1	s__Pseudofrancisella frigiditurris	78.0772	135	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Pseudofrancisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653955.1	s__Francisella persica	77.9905	130	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002095075.1	s__Francisella sp002095075	77.6801	133	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	98.09	96.18	0.98	0.96	3	-
GCF_012222825.1	s__Allofrancisella frigidaquae	77.6773	154	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Allofrancisella	95.0	98.33	98.33	0.93	0.93	2	-
GCF_003574475.2	s__Pseudofrancisella aestuarii	77.3492	139	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Pseudofrancisella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:06,768] [INFO] GTDB search result was written to GCF_003290445.1_ASM329044v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:06,769] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:06,773] [INFO] DFAST_QC result json was written to GCF_003290445.1_ASM329044v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:06,773] [INFO] DFAST_QC completed!
[2024-01-24 15:28:06,773] [INFO] Total running time: 0h0m46s