[2023-06-30 19:53:17,537] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:53:17,554] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:53:17,555] [INFO] DQC Reference Directory: /var/lib/cwl/stg7343bfab-b119-47e4-83b3-6f5dd5f66a16/dqc_reference
[2023-06-30 19:53:19,166] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:53:19,166] [INFO] Task started: Prodigal
[2023-06-30 19:53:19,167] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e3b0d6a-b148-41c1-bd44-b19d49abaa99/GCA_024648745.1_ASM2464874v1_genomic.fna.gz | prodigal -d GCA_024648745.1_ASM2464874v1_genomic.fna/cds.fna -a GCA_024648745.1_ASM2464874v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:53:21,719] [INFO] Task succeeded: Prodigal
[2023-06-30 19:53:21,719] [INFO] Task started: HMMsearch
[2023-06-30 19:53:21,719] [INFO] Running command: hmmsearch --tblout GCA_024648745.1_ASM2464874v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7343bfab-b119-47e4-83b3-6f5dd5f66a16/dqc_reference/reference_markers.hmm GCA_024648745.1_ASM2464874v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:53:21,944] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:53:21,946] [INFO] Found 6/6 markers.
[2023-06-30 19:53:21,967] [INFO] Query marker FASTA was written to GCA_024648745.1_ASM2464874v1_genomic.fna/markers.fasta
[2023-06-30 19:53:21,968] [INFO] Task started: Blastn
[2023-06-30 19:53:21,968] [INFO] Running command: blastn -query GCA_024648745.1_ASM2464874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7343bfab-b119-47e4-83b3-6f5dd5f66a16/dqc_reference/reference_markers.fasta -out GCA_024648745.1_ASM2464874v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:53:23,190] [INFO] Task succeeded: Blastn
[2023-06-30 19:53:23,195] [INFO] Selected 30 target genomes.
[2023-06-30 19:53:23,196] [INFO] Target genome list was writen to GCA_024648745.1_ASM2464874v1_genomic.fna/target_genomes.txt
[2023-06-30 19:53:23,201] [INFO] Task started: fastANI
[2023-06-30 19:53:23,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e3b0d6a-b148-41c1-bd44-b19d49abaa99/GCA_024648745.1_ASM2464874v1_genomic.fna.gz --refList GCA_024648745.1_ASM2464874v1_genomic.fna/target_genomes.txt --output GCA_024648745.1_ASM2464874v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:53:42,026] [INFO] Task succeeded: fastANI
[2023-06-30 19:53:42,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7343bfab-b119-47e4-83b3-6f5dd5f66a16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:53:42,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7343bfab-b119-47e4-83b3-6f5dd5f66a16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:53:42,038] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:53:42,039] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 19:53:42,039] [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
Sodalis ligni	strain=159R	GCA_004346745.1	2697027	2697027	type	True	77.4231	57	382	95	below_threshold
Sodalis ligni	strain=dw23	GCA_016865525.2	2697027	2697027	type	True	77.3424	58	382	95	below_threshold
Brenneria goodwinii	strain=FRB141	GCA_002291445.1	1109412	1109412	type	True	77.1088	50	382	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	76.5221	51	382	95	below_threshold
Pectobacterium carotovorum subsp. carotovorum	strain=ICMP 5702	GCA_001039055.1	555	554	suspected-type	True	76.2821	53	382	95	below_threshold
Brenneria roseae subsp. americana	strain=LMG 27715	GCA_003115815.1	1508507	1509241	type	True	76.1464	53	382	95	below_threshold
Pectobacterium carotovorum	strain=DSM 30168	GCA_900129615.1	554	554	type	True	75.9619	53	382	95	below_threshold
Brenneria roseae subsp. roseae	strain=LMG 27714	GCA_003115845.1	1508506	1509241	type	True	75.9481	51	382	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 19:53:42,041] [INFO] DFAST Taxonomy check result was written to GCA_024648745.1_ASM2464874v1_genomic.fna/tc_result.tsv
[2023-06-30 19:53:42,041] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:53:42,041] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:53:42,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7343bfab-b119-47e4-83b3-6f5dd5f66a16/dqc_reference/checkm_data
[2023-06-30 19:53:42,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:53:42,058] [INFO] Task started: CheckM
[2023-06-30 19:53:42,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024648745.1_ASM2464874v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024648745.1_ASM2464874v1_genomic.fna/checkm_input GCA_024648745.1_ASM2464874v1_genomic.fna/checkm_result
[2023-06-30 19:53:57,621] [INFO] Task succeeded: CheckM
[2023-06-30 19:53:57,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 19:53:57,641] [INFO] ===== Completeness check finished =====
[2023-06-30 19:53:57,641] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:53:57,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024648745.1_ASM2464874v1_genomic.fna/markers.fasta)
[2023-06-30 19:53:57,642] [INFO] Task started: Blastn
[2023-06-30 19:53:57,642] [INFO] Running command: blastn -query GCA_024648745.1_ASM2464874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7343bfab-b119-47e4-83b3-6f5dd5f66a16/dqc_reference/reference_markers_gtdb.fasta -out GCA_024648745.1_ASM2464874v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:53:58,736] [INFO] Task succeeded: Blastn
[2023-06-30 19:53:58,742] [INFO] Selected 20 target genomes.
[2023-06-30 19:53:58,742] [INFO] Target genome list was writen to GCA_024648745.1_ASM2464874v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:53:58,752] [INFO] Task started: fastANI
[2023-06-30 19:53:58,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e3b0d6a-b148-41c1-bd44-b19d49abaa99/GCA_024648745.1_ASM2464874v1_genomic.fna.gz --refList GCA_024648745.1_ASM2464874v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024648745.1_ASM2464874v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:54:11,520] [INFO] Task succeeded: fastANI
[2023-06-30 19:54:11,529] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 19:54:11,529] [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_000517405.1	s__Sodalis_A pierantonius	78.1317	157	382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Sodalis_A	96.0224	N/A	N/A	N/A	N/A	1	-
GCF_000517425.1	s__Sodalis_A praecaptivus	78.0137	175	382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Sodalis_A	96.0224	N/A	N/A	N/A	N/A	1	-
GCA_000010085.1	s__Sodalis glossinidius	77.7634	160	382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Sodalis	95.0	99.91	99.91	0.97	0.97	2	-
GCF_900143145.1	s__SoCistrobi sp900143145	77.6785	147	382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__SoCistrobi	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018777395.1	s__Sodalis_B endolongispinus	77.6492	161	382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Sodalis_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002291445.1	s__Brenneria goodwinii	77.0569	51	382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.30	98.94	0.94	0.91	4	-
--------------------------------------------------------------------------------
[2023-06-30 19:54:11,531] [INFO] GTDB search result was written to GCA_024648745.1_ASM2464874v1_genomic.fna/result_gtdb.tsv
[2023-06-30 19:54:11,532] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:54:11,535] [INFO] DFAST_QC result json was written to GCA_024648745.1_ASM2464874v1_genomic.fna/dqc_result.json
[2023-06-30 19:54:11,536] [INFO] DFAST_QC completed!
[2023-06-30 19:54:11,536] [INFO] Total running time: 0h0m54s