[2023-06-04 20:02:04,748] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:02:04,750] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:02:04,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg22d01b70-e1d6-4d15-977b-2acc9ddf2fb9/dqc_reference
[2023-06-04 20:02:05,992] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:02:05,993] [INFO] Task started: Prodigal
[2023-06-04 20:02:05,993] [INFO] Running command: gunzip -c /var/lib/cwl/stga840cf84-7da5-452b-8eaf-2e808209f9b3/GCA_004964455.1_ASM496445v1_genomic.fna.gz | prodigal -d GCA_004964455.1_ASM496445v1_genomic.fna/cds.fna -a GCA_004964455.1_ASM496445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:02:12,885] [INFO] Task succeeded: Prodigal
[2023-06-04 20:02:12,885] [INFO] Task started: HMMsearch
[2023-06-04 20:02:12,885] [INFO] Running command: hmmsearch --tblout GCA_004964455.1_ASM496445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22d01b70-e1d6-4d15-977b-2acc9ddf2fb9/dqc_reference/reference_markers.hmm GCA_004964455.1_ASM496445v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:02:13,122] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:02:13,123] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga840cf84-7da5-452b-8eaf-2e808209f9b3/GCA_004964455.1_ASM496445v1_genomic.fna.gz]
[2023-06-04 20:02:13,164] [INFO] Query marker FASTA was written to GCA_004964455.1_ASM496445v1_genomic.fna/markers.fasta
[2023-06-04 20:02:13,164] [INFO] Task started: Blastn
[2023-06-04 20:02:13,164] [INFO] Running command: blastn -query GCA_004964455.1_ASM496445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22d01b70-e1d6-4d15-977b-2acc9ddf2fb9/dqc_reference/reference_markers.fasta -out GCA_004964455.1_ASM496445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:02:13,870] [INFO] Task succeeded: Blastn
[2023-06-04 20:02:13,875] [INFO] Selected 11 target genomes.
[2023-06-04 20:02:13,876] [INFO] Target genome list was writen to GCA_004964455.1_ASM496445v1_genomic.fna/target_genomes.txt
[2023-06-04 20:02:13,879] [INFO] Task started: fastANI
[2023-06-04 20:02:13,879] [INFO] Running command: fastANI --query /var/lib/cwl/stga840cf84-7da5-452b-8eaf-2e808209f9b3/GCA_004964455.1_ASM496445v1_genomic.fna.gz --refList GCA_004964455.1_ASM496445v1_genomic.fna/target_genomes.txt --output GCA_004964455.1_ASM496445v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:02:23,407] [INFO] Task succeeded: fastANI
[2023-06-04 20:02:23,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22d01b70-e1d6-4d15-977b-2acc9ddf2fb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:02:23,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22d01b70-e1d6-4d15-977b-2acc9ddf2fb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:02:23,415] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:02:23,415] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 20:02:23,415] [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
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	86.5367	53	124	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	84.7792	57	124	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	84.0625	56	124	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	83.2214	58	124	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	82.4764	51	124	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	82.0853	55	124	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 20:02:23,419] [INFO] DFAST Taxonomy check result was written to GCA_004964455.1_ASM496445v1_genomic.fna/tc_result.tsv
[2023-06-04 20:02:23,420] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:02:23,420] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:02:23,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22d01b70-e1d6-4d15-977b-2acc9ddf2fb9/dqc_reference/checkm_data
[2023-06-04 20:02:23,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:02:23,461] [INFO] Task started: CheckM
[2023-06-04 20:02:23,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004964455.1_ASM496445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004964455.1_ASM496445v1_genomic.fna/checkm_input GCA_004964455.1_ASM496445v1_genomic.fna/checkm_result
[2023-06-04 20:02:49,832] [INFO] Task succeeded: CheckM
[2023-06-04 20:02:49,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.01%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:02:49,860] [INFO] ===== Completeness check finished =====
[2023-06-04 20:02:49,860] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:02:49,860] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004964455.1_ASM496445v1_genomic.fna/markers.fasta)
[2023-06-04 20:02:49,861] [INFO] Task started: Blastn
[2023-06-04 20:02:49,861] [INFO] Running command: blastn -query GCA_004964455.1_ASM496445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22d01b70-e1d6-4d15-977b-2acc9ddf2fb9/dqc_reference/reference_markers_gtdb.fasta -out GCA_004964455.1_ASM496445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:02:51,028] [INFO] Task succeeded: Blastn
[2023-06-04 20:02:51,033] [INFO] Selected 12 target genomes.
[2023-06-04 20:02:51,033] [INFO] Target genome list was writen to GCA_004964455.1_ASM496445v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:02:51,068] [INFO] Task started: fastANI
[2023-06-04 20:02:51,068] [INFO] Running command: fastANI --query /var/lib/cwl/stga840cf84-7da5-452b-8eaf-2e808209f9b3/GCA_004964455.1_ASM496445v1_genomic.fna.gz --refList GCA_004964455.1_ASM496445v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004964455.1_ASM496445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:03:00,823] [INFO] Task succeeded: fastANI
[2023-06-04 20:03:00,838] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:03:00,838] [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_003952425.1	s__Mesorhizobium sp003952425	95.9959	102	124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.51	95.02	0.90	0.84	19	conclusive
GCF_004016445.2	s__Mesorhizobium sp004016445	92.3651	80	124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	96.92	0.94	0.90	3	-
GCA_004017535.1	s__Mesorhizobium sp004017535	92.0932	82	124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.05	98.03	0.89	0.85	7	-
GCA_004020875.1	s__Mesorhizobium sp004020875	91.1129	69	124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.89	99.01	0.98	0.89	11	-
GCA_000824845.1	s__Mesorhizobium sp000824845	88.397	60	124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002295065.1	s__Mesorhizobium sp002295065	87.3938	61	124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289965.1	s__Mesorhizobium atlanticum	86.5367	53	124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016591715.1	s__Mesorhizobium sp016591715	85.1879	53	124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006440775.1	s__Mesorhizobium sp006440775	84.0189	55	124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.82	97.16	0.94	0.92	4	-
--------------------------------------------------------------------------------
[2023-06-04 20:03:00,841] [INFO] GTDB search result was written to GCA_004964455.1_ASM496445v1_genomic.fna/result_gtdb.tsv
[2023-06-04 20:03:00,841] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:03:00,845] [INFO] DFAST_QC result json was written to GCA_004964455.1_ASM496445v1_genomic.fna/dqc_result.json
[2023-06-04 20:03:00,845] [INFO] DFAST_QC completed!
[2023-06-04 20:03:00,846] [INFO] Total running time: 0h0m56s