[2023-06-13 15:45:10,273] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:45:10,277] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:45:10,277] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf22ff0e-b860-4b61-a136-63d30f101792/dqc_reference
[2023-06-13 15:45:11,710] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:45:11,711] [INFO] Task started: Prodigal
[2023-06-13 15:45:11,712] [INFO] Running command: gunzip -c /var/lib/cwl/stg7dcb71bd-ce80-4d29-8055-f526af490a3a/GCA_947482105.1_RH-27jun17-421_genomic.fna.gz | prodigal -d GCA_947482105.1_RH-27jun17-421_genomic.fna/cds.fna -a GCA_947482105.1_RH-27jun17-421_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:45:19,713] [INFO] Task succeeded: Prodigal
[2023-06-13 15:45:19,713] [INFO] Task started: HMMsearch
[2023-06-13 15:45:19,714] [INFO] Running command: hmmsearch --tblout GCA_947482105.1_RH-27jun17-421_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf22ff0e-b860-4b61-a136-63d30f101792/dqc_reference/reference_markers.hmm GCA_947482105.1_RH-27jun17-421_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:45:20,013] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:45:20,015] [INFO] Found 6/6 markers.
[2023-06-13 15:45:20,047] [INFO] Query marker FASTA was written to GCA_947482105.1_RH-27jun17-421_genomic.fna/markers.fasta
[2023-06-13 15:45:20,047] [INFO] Task started: Blastn
[2023-06-13 15:45:20,047] [INFO] Running command: blastn -query GCA_947482105.1_RH-27jun17-421_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf22ff0e-b860-4b61-a136-63d30f101792/dqc_reference/reference_markers.fasta -out GCA_947482105.1_RH-27jun17-421_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:45:20,714] [INFO] Task succeeded: Blastn
[2023-06-13 15:45:20,720] [INFO] Selected 27 target genomes.
[2023-06-13 15:45:20,721] [INFO] Target genome list was writen to GCA_947482105.1_RH-27jun17-421_genomic.fna/target_genomes.txt
[2023-06-13 15:45:20,726] [INFO] Task started: fastANI
[2023-06-13 15:45:20,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dcb71bd-ce80-4d29-8055-f526af490a3a/GCA_947482105.1_RH-27jun17-421_genomic.fna.gz --refList GCA_947482105.1_RH-27jun17-421_genomic.fna/target_genomes.txt --output GCA_947482105.1_RH-27jun17-421_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:45:41,752] [INFO] Task succeeded: fastANI
[2023-06-13 15:45:41,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf22ff0e-b860-4b61-a136-63d30f101792/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:45:41,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf22ff0e-b860-4b61-a136-63d30f101792/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:45:41,758] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:45:41,758] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:45:41,759] [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
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	76.7112	52	814	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	76.0365	51	814	95	below_threshold
Polaromonas vacuolata	strain=KCTC 22033	GCA_012584515.1	37448	37448	type	True	75.5795	55	814	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:45:41,761] [INFO] DFAST Taxonomy check result was written to GCA_947482105.1_RH-27jun17-421_genomic.fna/tc_result.tsv
[2023-06-13 15:45:41,761] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:45:41,762] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:45:41,762] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf22ff0e-b860-4b61-a136-63d30f101792/dqc_reference/checkm_data
[2023-06-13 15:45:41,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:45:41,796] [INFO] Task started: CheckM
[2023-06-13 15:45:41,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947482105.1_RH-27jun17-421_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947482105.1_RH-27jun17-421_genomic.fna/checkm_input GCA_947482105.1_RH-27jun17-421_genomic.fna/checkm_result
[2023-06-13 15:46:12,349] [INFO] Task succeeded: CheckM
[2023-06-13 15:46:12,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:46:12,389] [INFO] ===== Completeness check finished =====
[2023-06-13 15:46:12,389] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:46:12,390] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947482105.1_RH-27jun17-421_genomic.fna/markers.fasta)
[2023-06-13 15:46:12,390] [INFO] Task started: Blastn
[2023-06-13 15:46:12,390] [INFO] Running command: blastn -query GCA_947482105.1_RH-27jun17-421_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf22ff0e-b860-4b61-a136-63d30f101792/dqc_reference/reference_markers_gtdb.fasta -out GCA_947482105.1_RH-27jun17-421_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:46:13,546] [INFO] Task succeeded: Blastn
[2023-06-13 15:46:13,552] [INFO] Selected 22 target genomes.
[2023-06-13 15:46:13,552] [INFO] Target genome list was writen to GCA_947482105.1_RH-27jun17-421_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:46:13,562] [INFO] Task started: fastANI
[2023-06-13 15:46:13,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dcb71bd-ce80-4d29-8055-f526af490a3a/GCA_947482105.1_RH-27jun17-421_genomic.fna.gz --refList GCA_947482105.1_RH-27jun17-421_genomic.fna/target_genomes_gtdb.txt --output GCA_947482105.1_RH-27jun17-421_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:46:24,038] [INFO] Task succeeded: fastANI
[2023-06-13 15:46:24,051] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:46:24,052] [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
GCA_009921265.1	s__Limnohabitans sp009921265	99.4508	750	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.67	99.66	0.93	0.90	3	conclusive
GCA_009693305.1	s__Limnohabitans sp009693305	87.765	481	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903956845.1	s__Limnohabitans sp903956845	77.5427	69	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412575.1	s__Limnohabitans_A sp001412575	77.2292	94	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.90	97.72	0.94	0.91	3	-
GCA_903832625.1	s__Limnohabitans sp903832625	77.0162	95	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	97.24	97.19	0.90	0.89	4	-
GCA_903880855.1	s__Limnohabitans sp903880855	76.9388	107	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.14	98.09	0.92	0.91	4	-
GCF_001269365.1	s__Limnohabitans_A sp001269365	76.8981	101	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001269385.1	s__Limnohabitans_A sp001269385	76.619	51	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063415.1	s__Limnohabitans_A sp003063415	76.6154	51	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861115.1	s__Limnohabitans sp903861115	76.484	51	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.34	98.85	0.86	0.79	13	-
GCA_903856875.1	s__Limnohabitans_A sp903856875	76.3961	72	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002778325.1	s__Limnohabitans sp002778325	76.3883	94	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916355.1	s__Limnohabitans_A sp903916355	75.7939	59	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.87	99.87	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-13 15:46:24,055] [INFO] GTDB search result was written to GCA_947482105.1_RH-27jun17-421_genomic.fna/result_gtdb.tsv
[2023-06-13 15:46:24,056] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:46:24,063] [INFO] DFAST_QC result json was written to GCA_947482105.1_RH-27jun17-421_genomic.fna/dqc_result.json
[2023-06-13 15:46:24,063] [INFO] DFAST_QC completed!
[2023-06-13 15:46:24,064] [INFO] Total running time: 0h1m14s