[2024-01-24 11:43:25,070] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,072] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ab9231e-f89a-4ee9-885d-47fd0be7b311/dqc_reference
[2024-01-24 11:43:30,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,059] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,060] [INFO] Running command: gunzip -c /var/lib/cwl/stga91cbac9-dd9e-42e9-903d-0634fbb17383/GCF_023162085.1_ASM2316208v1_genomic.fna.gz | prodigal -d GCF_023162085.1_ASM2316208v1_genomic.fna/cds.fna -a GCF_023162085.1_ASM2316208v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:43,651] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:43,652] [INFO] Task started: HMMsearch
[2024-01-24 11:43:43,652] [INFO] Running command: hmmsearch --tblout GCF_023162085.1_ASM2316208v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ab9231e-f89a-4ee9-885d-47fd0be7b311/dqc_reference/reference_markers.hmm GCF_023162085.1_ASM2316208v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:43,956] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:43,957] [INFO] Found 6/6 markers.
[2024-01-24 11:43:44,003] [INFO] Query marker FASTA was written to GCF_023162085.1_ASM2316208v1_genomic.fna/markers.fasta
[2024-01-24 11:43:44,004] [INFO] Task started: Blastn
[2024-01-24 11:43:44,004] [INFO] Running command: blastn -query GCF_023162085.1_ASM2316208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ab9231e-f89a-4ee9-885d-47fd0be7b311/dqc_reference/reference_markers.fasta -out GCF_023162085.1_ASM2316208v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:45,207] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:45,210] [INFO] Selected 6 target genomes.
[2024-01-24 11:43:45,210] [INFO] Target genome list was writen to GCF_023162085.1_ASM2316208v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:45,213] [INFO] Task started: fastANI
[2024-01-24 11:43:45,213] [INFO] Running command: fastANI --query /var/lib/cwl/stga91cbac9-dd9e-42e9-903d-0634fbb17383/GCF_023162085.1_ASM2316208v1_genomic.fna.gz --refList GCF_023162085.1_ASM2316208v1_genomic.fna/target_genomes.txt --output GCF_023162085.1_ASM2316208v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:51,945] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:51,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ab9231e-f89a-4ee9-885d-47fd0be7b311/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:51,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ab9231e-f89a-4ee9-885d-47fd0be7b311/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:51,953] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:43:51,954] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:51,954] [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
Tomitella gaofuii	strain=HY172	GCA_023162085.1	2760083	2760083	type	True	100.0	1427	1437	95	conclusive
Tomitella gaofuii	strain=HY172	GCA_014126825.1	2760083	2760083	type	True	99.9869	1411	1437	95	conclusive
Tomitella cavernea	strain=JCM 18542	GCA_016599145.1	1387982	1387982	type	True	92.4894	1135	1437	95	below_threshold
Tomitella fengzijianii	strain=HY188	GCA_007559025.1	2597660	2597660	type	True	88.4771	1111	1437	95	below_threshold
Tomitella fengzijianii	strain=HY188	GCA_023162105.1	2597660	2597660	type	True	88.4694	1076	1437	95	below_threshold
Rhodococcus corynebacterioides	strain=NBRC 14404	GCA_001894765.1	53972	53972	suspected-type	True	77.7486	401	1437	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:51,956] [INFO] DFAST Taxonomy check result was written to GCF_023162085.1_ASM2316208v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:51,956] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:51,956] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:51,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ab9231e-f89a-4ee9-885d-47fd0be7b311/dqc_reference/checkm_data
[2024-01-24 11:43:51,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:52,002] [INFO] Task started: CheckM
[2024-01-24 11:43:52,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023162085.1_ASM2316208v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023162085.1_ASM2316208v1_genomic.fna/checkm_input GCF_023162085.1_ASM2316208v1_genomic.fna/checkm_result
[2024-01-24 11:44:43,776] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:43,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:43,797] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:43,798] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:43,798] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023162085.1_ASM2316208v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:43,799] [INFO] Task started: Blastn
[2024-01-24 11:44:43,799] [INFO] Running command: blastn -query GCF_023162085.1_ASM2316208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ab9231e-f89a-4ee9-885d-47fd0be7b311/dqc_reference/reference_markers_gtdb.fasta -out GCF_023162085.1_ASM2316208v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:45,547] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:45,550] [INFO] Selected 14 target genomes.
[2024-01-24 11:44:45,551] [INFO] Target genome list was writen to GCF_023162085.1_ASM2316208v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:45,562] [INFO] Task started: fastANI
[2024-01-24 11:44:45,562] [INFO] Running command: fastANI --query /var/lib/cwl/stga91cbac9-dd9e-42e9-903d-0634fbb17383/GCF_023162085.1_ASM2316208v1_genomic.fna.gz --refList GCF_023162085.1_ASM2316208v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023162085.1_ASM2316208v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:00,708] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:00,720] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:00,720] [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_014126825.1	s__Tomitella sp014126825	99.9869	1411	1437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	97.57	97.57	0.88	0.88	2	conclusive
GCF_016599145.1	s__Tomitella cavernea	92.4894	1135	1437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559025.1	s__Tomitella sp007559025	88.4895	1110	1437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	99.43	99.43	0.96	0.96	2	-
GCF_000524475.1	s__Tomitella biformata	79.1228	605	1437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004011865.1	s__Rhodococcus agglutinans	78.2162	505	1437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013348805.1	s__Rhodococcus sp003350365	78.1178	498	1437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.85	98.85	0.92	0.92	2	-
GCF_015865005.1	s__Rhodococcus sp015865005	78.0411	480	1437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111805.1	s__Rhodococcus_C kroppenstedtii	77.9695	366	1437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_C	95.0	98.58	98.00	0.94	0.91	5	-
GCF_001895025.1	s__Rhodococcus zopfii	77.8273	473	1437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.81	97.81	0.87	0.87	2	-
GCF_001894765.1	s__Rhodococcus_C corynebacterioides	77.7881	396	1437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_C	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900637205.1	s__Mycobacterium chitae	77.7504	386	1437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000308795.1	s__Nocardia thailandica	77.6618	502	1437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477775.1	s__Nocardia abscessus_A	77.5293	450	1437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011801125.1	s__Nocardia brasiliensis_C	77.4056	453	1437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:00,722] [INFO] GTDB search result was written to GCF_023162085.1_ASM2316208v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:00,722] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:00,725] [INFO] DFAST_QC result json was written to GCF_023162085.1_ASM2316208v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:00,726] [INFO] DFAST_QC completed!
[2024-01-24 11:45:00,726] [INFO] Total running time: 0h1m36s