[2024-01-24 13:31:44,287] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,289] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,290] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7977f86-2b71-4f58-83fa-5111ec5920ef/dqc_reference
[2024-01-24 13:31:45,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,599] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,599] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5450b5a-4120-416a-85ec-068c8dcc61a2/GCF_004365555.1_ASM436555v1_genomic.fna.gz | prodigal -d GCF_004365555.1_ASM436555v1_genomic.fna/cds.fna -a GCF_004365555.1_ASM436555v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:48,271] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:48,272] [INFO] Task started: HMMsearch
[2024-01-24 13:31:48,272] [INFO] Running command: hmmsearch --tblout GCF_004365555.1_ASM436555v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7977f86-2b71-4f58-83fa-5111ec5920ef/dqc_reference/reference_markers.hmm GCF_004365555.1_ASM436555v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:48,582] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:48,583] [INFO] Found 6/6 markers.
[2024-01-24 13:31:48,686] [INFO] Query marker FASTA was written to GCF_004365555.1_ASM436555v1_genomic.fna/markers.fasta
[2024-01-24 13:31:48,686] [INFO] Task started: Blastn
[2024-01-24 13:31:48,687] [INFO] Running command: blastn -query GCF_004365555.1_ASM436555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7977f86-2b71-4f58-83fa-5111ec5920ef/dqc_reference/reference_markers.fasta -out GCF_004365555.1_ASM436555v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:49,398] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:49,402] [INFO] Selected 12 target genomes.
[2024-01-24 13:31:49,403] [INFO] Target genome list was writen to GCF_004365555.1_ASM436555v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:49,409] [INFO] Task started: fastANI
[2024-01-24 13:31:49,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5450b5a-4120-416a-85ec-068c8dcc61a2/GCF_004365555.1_ASM436555v1_genomic.fna.gz --refList GCF_004365555.1_ASM436555v1_genomic.fna/target_genomes.txt --output GCF_004365555.1_ASM436555v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:55,823] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:55,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7977f86-2b71-4f58-83fa-5111ec5920ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:55,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7977f86-2b71-4f58-83fa-5111ec5920ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:55,836] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:31:55,836] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:55,837] [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
Allofrancisella inopinata	strain=DSM 101834	GCA_004365555.1	1085647	1085647	type	True	100.0	543	546	95	conclusive
Allofrancisella inopinata	strain=SYSU YG23	GCA_012222965.1	1085647	1085647	type	True	99.9902	540	546	95	conclusive
Allofrancisella frigidaquae	strain=SYSU 10HL1970	GCA_012222825.1	1085644	1085644	type	True	94.0841	469	546	95	below_threshold
Allofrancisella guangzhouensis	strain=08HL01032	GCA_000815225.1	594679	594679	type	True	87.0301	437	546	95	below_threshold
Francisella opportunistica	strain=PA05-1188	GCA_003347135.1	2016517	2016517	type	True	78.8922	184	546	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000014645.1	264	263	type	True	78.6975	189	546	95	below_threshold
Francisella noatunensis subsp. noatunensis	strain=2005/50/F292-6	GCA_009823375.1	360196	657445	type	True	78.4566	157	546	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001608445.1	622488	622488	type	True	78.4202	206	546	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:55,839] [INFO] DFAST Taxonomy check result was written to GCF_004365555.1_ASM436555v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:55,839] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:55,840] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:55,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7977f86-2b71-4f58-83fa-5111ec5920ef/dqc_reference/checkm_data
[2024-01-24 13:31:55,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:55,871] [INFO] Task started: CheckM
[2024-01-24 13:31:55,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004365555.1_ASM436555v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004365555.1_ASM436555v1_genomic.fna/checkm_input GCF_004365555.1_ASM436555v1_genomic.fna/checkm_result
[2024-01-24 13:32:13,759] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:13,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:13,802] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:13,803] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:13,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004365555.1_ASM436555v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:13,803] [INFO] Task started: Blastn
[2024-01-24 13:32:13,803] [INFO] Running command: blastn -query GCF_004365555.1_ASM436555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7977f86-2b71-4f58-83fa-5111ec5920ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_004365555.1_ASM436555v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:14,750] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:14,756] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:14,756] [INFO] Target genome list was writen to GCF_004365555.1_ASM436555v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:14,771] [INFO] Task started: fastANI
[2024-01-24 13:32:14,771] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5450b5a-4120-416a-85ec-068c8dcc61a2/GCF_004365555.1_ASM436555v1_genomic.fna.gz --refList GCF_004365555.1_ASM436555v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004365555.1_ASM436555v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:21,083] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:21,108] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:21,109] [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_012222965.1	s__Allofrancisella inopinata	99.9902	540	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Allofrancisella	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_012222825.1	s__Allofrancisella frigidaquae	94.0841	469	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Allofrancisella	95.0	98.33	98.33	0.93	0.93	2	-
GCF_000815225.1	s__Allofrancisella guangzhouensis	87.0829	435	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Allofrancisella	95.0	99.92	99.90	0.98	0.96	4	-
GCF_003347135.1	s__Francisella opportunistica	78.8894	184	546	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	78.6983	194	546	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	78.6135	197	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000008985.1	s__Francisella tularensis	78.554	185	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.28	97.47	0.99	0.89	860	-
GCF_008711465.1	s__Francisella sp008711465	78.4962	201	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885235.1	s__Francisella hispaniensis	78.42	212	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	98.55	97.74	0.95	0.92	4	-
GCF_014844275.1	s__Francisella noatunensis	78.3369	156	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.88	99.78	0.95	0.94	24	-
GCF_002211785.1	s__Francisella halioticida	78.2865	178	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.38	99.38	0.93	0.93	2	-
GCF_001042525.2	s__Francisella orientalis	78.2848	164	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.91	95.40	0.99	0.93	54	-
GCF_002095075.1	s__Francisella sp002095075	78.1457	175	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	98.09	96.18	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:21,111] [INFO] GTDB search result was written to GCF_004365555.1_ASM436555v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:21,112] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:21,115] [INFO] DFAST_QC result json was written to GCF_004365555.1_ASM436555v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:21,115] [INFO] DFAST_QC completed!
[2024-01-24 13:32:21,115] [INFO] Total running time: 0h0m37s