[2024-01-24 13:31:27,394] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:27,397] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:27,397] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3a89c85-05c2-429a-bdda-1a4d5f660344/dqc_reference
[2024-01-24 13:31:28,599] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:28,600] [INFO] Task started: Prodigal
[2024-01-24 13:31:28,600] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bc0f254-3894-495f-a25b-a60afab909dd/GCF_001894945.1_ASM189494v1_genomic.fna.gz | prodigal -d GCF_001894945.1_ASM189494v1_genomic.fna/cds.fna -a GCF_001894945.1_ASM189494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:44,915] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:44,916] [INFO] Task started: HMMsearch
[2024-01-24 13:31:44,916] [INFO] Running command: hmmsearch --tblout GCF_001894945.1_ASM189494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3a89c85-05c2-429a-bdda-1a4d5f660344/dqc_reference/reference_markers.hmm GCF_001894945.1_ASM189494v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:45,205] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:45,207] [INFO] Found 6/6 markers.
[2024-01-24 13:31:45,258] [INFO] Query marker FASTA was written to GCF_001894945.1_ASM189494v1_genomic.fna/markers.fasta
[2024-01-24 13:31:45,259] [INFO] Task started: Blastn
[2024-01-24 13:31:45,259] [INFO] Running command: blastn -query GCF_001894945.1_ASM189494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3a89c85-05c2-429a-bdda-1a4d5f660344/dqc_reference/reference_markers.fasta -out GCF_001894945.1_ASM189494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:46,479] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:46,482] [INFO] Selected 10 target genomes.
[2024-01-24 13:31:46,483] [INFO] Target genome list was writen to GCF_001894945.1_ASM189494v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:46,574] [INFO] Task started: fastANI
[2024-01-24 13:31:46,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bc0f254-3894-495f-a25b-a60afab909dd/GCF_001894945.1_ASM189494v1_genomic.fna.gz --refList GCF_001894945.1_ASM189494v1_genomic.fna/target_genomes.txt --output GCF_001894945.1_ASM189494v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:59,837] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:59,837] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3a89c85-05c2-429a-bdda-1a4d5f660344/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:59,837] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3a89c85-05c2-429a-bdda-1a4d5f660344/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:59,847] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:31:59,847] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:59,847] [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
Rhodococcus ruber	strain=NBRC 15591	GCA_001894945.1	1830	1830	type	True	100.0	1750	1753	95	conclusive
Rhodococcus ruber	strain=DSM 43338	GCA_001646835.1	1830	1830	type	True	99.9385	1652	1753	95	conclusive
Rhodococcus aetherivorans	strain=JCM 14343	GCA_009176285.1	191292	191292	type	True	92.0019	1518	1753	95	below_threshold
Rhodococcus aetherivorans	strain=DSM 44752	GCA_011058165.1	191292	191292	type	True	91.9537	1475	1753	95	below_threshold
Rhodococcus zopfii	strain=NBRC 100606	GCA_001895025.1	43772	43772	type	True	82.0502	1043	1753	95	below_threshold
Rhodococcus phenolicus	strain=DSM 44812	GCA_001646785.1	263849	263849	type	True	81.7446	991	1753	95	below_threshold
Rhodococcus rhodochrous	strain=DSM 43241	GCA_001646825.1	1829	1829	suspected-type	True	81.1611	942	1753	95	below_threshold
Rhodococcus yananensis	strain=FBM22-1	GCA_020515525.1	2879464	2879464	type	True	80.7107	799	1753	95	below_threshold
Nocardia amamiensis	strain=NBRC 102102	GCA_001612745.1	404578	404578	type	True	78.467	576	1753	95	below_threshold
Mycolicibacterium insubricum	strain=JCM 16366	GCA_010731615.1	444597	444597	type	True	78.1297	433	1753	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:59,849] [INFO] DFAST Taxonomy check result was written to GCF_001894945.1_ASM189494v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:59,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:59,850] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:59,850] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3a89c85-05c2-429a-bdda-1a4d5f660344/dqc_reference/checkm_data
[2024-01-24 13:31:59,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:59,909] [INFO] Task started: CheckM
[2024-01-24 13:31:59,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001894945.1_ASM189494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001894945.1_ASM189494v1_genomic.fna/checkm_input GCF_001894945.1_ASM189494v1_genomic.fna/checkm_result
[2024-01-24 13:32:59,326] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:59,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:59,347] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:59,348] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:59,348] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001894945.1_ASM189494v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:59,349] [INFO] Task started: Blastn
[2024-01-24 13:32:59,349] [INFO] Running command: blastn -query GCF_001894945.1_ASM189494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3a89c85-05c2-429a-bdda-1a4d5f660344/dqc_reference/reference_markers_gtdb.fasta -out GCF_001894945.1_ASM189494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:01,196] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:01,201] [INFO] Selected 13 target genomes.
[2024-01-24 13:33:01,201] [INFO] Target genome list was writen to GCF_001894945.1_ASM189494v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:01,268] [INFO] Task started: fastANI
[2024-01-24 13:33:01,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bc0f254-3894-495f-a25b-a60afab909dd/GCF_001894945.1_ASM189494v1_genomic.fna.gz --refList GCF_001894945.1_ASM189494v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001894945.1_ASM189494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:18,219] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:18,230] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:18,230] [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_001894945.1	s__Rhodococcus ruber	100.0	1750	1753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.84	95.07	0.94	0.85	19	conclusive
GCF_011058165.1	s__Rhodococcus aetherivorans	91.9565	1475	1753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.92	95.74	0.88	0.78	18	-
GCF_015865005.1	s__Rhodococcus sp015865005	82.2009	1029	1753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001895025.1	s__Rhodococcus zopfii	82.0436	1042	1753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.81	97.81	0.87	0.87	2	-
GCF_001646785.1	s__Rhodococcus phenolicus	81.7668	988	1753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105195.1	s__Rhodococcus pyridinivorans	81.1583	950	1753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.16	95.17	0.90	0.84	21	-
GCF_900187265.1	s__Rhodococcus rhodochrous	81.1429	965	1753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.52	95.51	0.91	0.84	11	-
GCF_001646655.1	s__Rhodococcus gordoniae	81.1169	907	1753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.98	98.16	0.95	0.93	4	-
GCF_013602415.1	s__Rhodococcus sp013602415	80.9757	963	1753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012726195.1	s__Rhodococcus sp012726195	79.74	763	1753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612745.1	s__Nocardia amamiensis	78.4628	576	1753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731615.1	s__Mycobacterium insubricum	78.0713	440	1753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000230935.1	s__Mycobacterium rhodesiae_B	77.4409	450	1753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:18,232] [INFO] GTDB search result was written to GCF_001894945.1_ASM189494v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:18,233] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:18,236] [INFO] DFAST_QC result json was written to GCF_001894945.1_ASM189494v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:18,237] [INFO] DFAST_QC completed!
[2024-01-24 13:33:18,237] [INFO] Total running time: 0h1m51s