[2024-01-24 13:57:31,807] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:31,809] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:31,809] [INFO] DQC Reference Directory: /var/lib/cwl/stga041b1dc-8cac-48e1-b855-1d1313ed5809/dqc_reference
[2024-01-24 13:57:33,175] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:33,176] [INFO] Task started: Prodigal
[2024-01-24 13:57:33,177] [INFO] Running command: gunzip -c /var/lib/cwl/stg65b94c7d-c04e-4eee-9e4a-0a3f9f89f63b/GCF_000024365.1_ASM2436v1_genomic.fna.gz | prodigal -d GCF_000024365.1_ASM2436v1_genomic.fna/cds.fna -a GCF_000024365.1_ASM2436v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:53,212] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:53,212] [INFO] Task started: HMMsearch
[2024-01-24 13:57:53,212] [INFO] Running command: hmmsearch --tblout GCF_000024365.1_ASM2436v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga041b1dc-8cac-48e1-b855-1d1313ed5809/dqc_reference/reference_markers.hmm GCF_000024365.1_ASM2436v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:53,490] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:53,491] [INFO] Found 6/6 markers.
[2024-01-24 13:57:53,539] [INFO] Query marker FASTA was written to GCF_000024365.1_ASM2436v1_genomic.fna/markers.fasta
[2024-01-24 13:57:53,540] [INFO] Task started: Blastn
[2024-01-24 13:57:53,540] [INFO] Running command: blastn -query GCF_000024365.1_ASM2436v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga041b1dc-8cac-48e1-b855-1d1313ed5809/dqc_reference/reference_markers.fasta -out GCF_000024365.1_ASM2436v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:54,786] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:54,789] [INFO] Selected 10 target genomes.
[2024-01-24 13:57:54,790] [INFO] Target genome list was writen to GCF_000024365.1_ASM2436v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:54,794] [INFO] Task started: fastANI
[2024-01-24 13:57:54,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg65b94c7d-c04e-4eee-9e4a-0a3f9f89f63b/GCF_000024365.1_ASM2436v1_genomic.fna.gz --refList GCF_000024365.1_ASM2436v1_genomic.fna/target_genomes.txt --output GCF_000024365.1_ASM2436v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:07,225] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:07,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga041b1dc-8cac-48e1-b855-1d1313ed5809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:07,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga041b1dc-8cac-48e1-b855-1d1313ed5809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:07,236] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:07,236] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:07,236] [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
Nakamurella multipartita	strain=DSM 44233	GCA_000024365.1	53461	53461	type	True	100.0	2020	2020	95	conclusive
Nakamurella flava	strain=N5BH11	GCA_005298075.1	2576308	2576308	type	True	79.9385	791	2020	95	below_threshold
Nakamurella flavida	strain=KCTC 19127	GCA_016918095.1	363630	363630	type	True	79.2473	636	2020	95	below_threshold
Nakamurella leprariae	strain=YIM 132084	GCA_016918035.1	2803911	2803911	type	True	79.2356	641	2020	95	below_threshold
Nakamurella endophytica	strain=CGMCC 4.7308	GCA_014646215.1	1748367	1748367	type	True	78.6138	686	2020	95	below_threshold
Nakamurella deserti	strain=12Sc4-1	GCA_003260015.1	2164074	2164074	type	True	78.4273	617	2020	95	below_threshold
Nakamurella lactea	strain=DSM 19367	GCA_000426645.1	459515	459515	type	True	77.8857	597	2020	95	below_threshold
Nakamurella aerolata	strain=DB0629	GCA_013002705.1	1656892	1656892	type	True	77.829	467	2020	95	below_threshold
Pseudonocardia antarctica	strain=DSM 44749	GCA_013408715.1	237656	237656	type	True	76.7241	570	2020	95	below_threshold
Actinoalloteichus cyanogriseus	strain=DSM 43889	GCA_000429185.2	65497	65497	type	True	76.3922	372	2020	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:07,238] [INFO] DFAST Taxonomy check result was written to GCF_000024365.1_ASM2436v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:07,238] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:07,238] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:07,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga041b1dc-8cac-48e1-b855-1d1313ed5809/dqc_reference/checkm_data
[2024-01-24 13:58:07,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:07,296] [INFO] Task started: CheckM
[2024-01-24 13:58:07,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024365.1_ASM2436v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024365.1_ASM2436v1_genomic.fna/checkm_input GCF_000024365.1_ASM2436v1_genomic.fna/checkm_result
[2024-01-24 13:59:49,752] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:49,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:49,773] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:49,773] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:49,773] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024365.1_ASM2436v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:49,774] [INFO] Task started: Blastn
[2024-01-24 13:59:49,774] [INFO] Running command: blastn -query GCF_000024365.1_ASM2436v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga041b1dc-8cac-48e1-b855-1d1313ed5809/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024365.1_ASM2436v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:51,474] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:51,477] [INFO] Selected 13 target genomes.
[2024-01-24 13:59:51,478] [INFO] Target genome list was writen to GCF_000024365.1_ASM2436v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:51,490] [INFO] Task started: fastANI
[2024-01-24 13:59:51,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg65b94c7d-c04e-4eee-9e4a-0a3f9f89f63b/GCF_000024365.1_ASM2436v1_genomic.fna.gz --refList GCF_000024365.1_ASM2436v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024365.1_ASM2436v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:05,873] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:05,883] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:05,884] [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_000024365.1	s__Nakamurella multipartita	100.0	2018	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005298075.1	s__Nakamurella flava	79.9101	795	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918095.1	s__Nakamurella flavida	79.2588	636	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918035.1	s__Nakamurella sp016918035	79.2196	643	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882715.1	s__Nakamurella sp017882715	78.9115	576	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707545.1	s__Nakamurella sp009707545	78.7381	708	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646215.1	s__Nakamurella endophytica	78.6757	676	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104535.1	s__Nakamurella panacisegetis	78.5804	580	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426645.1	s__Nakamurella lactea	77.8626	601	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002813375.1	s__Pseudonocardia alni	76.6764	559	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.52	96.72	0.89	0.85	6	-
GCF_001420995.1	s__Pseudonocardia sp001420995	76.4237	574	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.03	98.66	0.91	0.86	8	-
GCF_013410565.1	s__Streptomonospora nanhaiensis	76.0797	487	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
GCA_017882655.1	s__Fen-668 sp017882655	75.725	122	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Fen-668	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:05,885] [INFO] GTDB search result was written to GCF_000024365.1_ASM2436v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:05,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:05,889] [INFO] DFAST_QC result json was written to GCF_000024365.1_ASM2436v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:05,890] [INFO] DFAST_QC completed!
[2024-01-24 14:00:05,890] [INFO] Total running time: 0h2m34s