[2024-01-25 17:52:05,524] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:52:05,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:52:05,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg40a7b23d-addf-466b-8c27-5fbf23fd0c2d/dqc_reference
[2024-01-25 17:52:06,723] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:52:06,723] [INFO] Task started: Prodigal
[2024-01-25 17:52:06,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ba1fe23-f446-4447-ab31-0fd815626945/GCF_014195445.1_ASM1419544v1_genomic.fna.gz | prodigal -d GCF_014195445.1_ASM1419544v1_genomic.fna/cds.fna -a GCF_014195445.1_ASM1419544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:12,776] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:12,776] [INFO] Task started: HMMsearch
[2024-01-25 17:52:12,776] [INFO] Running command: hmmsearch --tblout GCF_014195445.1_ASM1419544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40a7b23d-addf-466b-8c27-5fbf23fd0c2d/dqc_reference/reference_markers.hmm GCF_014195445.1_ASM1419544v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:12,953] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:12,954] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9ba1fe23-f446-4447-ab31-0fd815626945/GCF_014195445.1_ASM1419544v1_genomic.fna.gz]
[2024-01-25 17:52:12,975] [INFO] Query marker FASTA was written to GCF_014195445.1_ASM1419544v1_genomic.fna/markers.fasta
[2024-01-25 17:52:12,976] [INFO] Task started: Blastn
[2024-01-25 17:52:12,976] [INFO] Running command: blastn -query GCF_014195445.1_ASM1419544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40a7b23d-addf-466b-8c27-5fbf23fd0c2d/dqc_reference/reference_markers.fasta -out GCF_014195445.1_ASM1419544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:13,790] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:13,793] [INFO] Selected 16 target genomes.
[2024-01-25 17:52:13,793] [INFO] Target genome list was writen to GCF_014195445.1_ASM1419544v1_genomic.fna/target_genomes.txt
[2024-01-25 17:52:13,808] [INFO] Task started: fastANI
[2024-01-25 17:52:13,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ba1fe23-f446-4447-ab31-0fd815626945/GCF_014195445.1_ASM1419544v1_genomic.fna.gz --refList GCF_014195445.1_ASM1419544v1_genomic.fna/target_genomes.txt --output GCF_014195445.1_ASM1419544v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:24,332] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:24,333] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40a7b23d-addf-466b-8c27-5fbf23fd0c2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:24,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40a7b23d-addf-466b-8c27-5fbf23fd0c2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:24,343] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:52:24,343] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:52:24,343] [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
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	100.0	727	735	95	conclusive
Nesterenkonia populi	strain=DSM 27959	GCA_007994735.1	1591087	1591087	type	True	79.5998	273	735	95	below_threshold
Nesterenkonia alkaliphila	strain=CGMCC 1.12781	GCA_014639295.1	1463631	1463631	type	True	79.5544	332	735	95	below_threshold
Nesterenkonia alkaliphila	strain=F10	GCA_009758175.1	1463631	1463631	type	True	79.5187	329	735	95	below_threshold
Nesterenkonia cremea	strain=CGMCC 1.15388	GCA_014642675.1	1882340	1882340	type	True	79.5014	303	735	95	below_threshold
Nesterenkonia sandarakina	strain=DSM 15664	GCA_013410215.1	272918	272918	type	True	79.3571	293	735	95	below_threshold
Nesterenkonia sedimenti	strain=MY13	GCA_012641515.1	1463632	1463632	type	True	79.35	296	735	95	below_threshold
Nesterenkonia lacusekhoensis	strain=DSM 12544	GCA_017876395.1	150832	150832	type	True	79.3084	294	735	95	below_threshold
Nesterenkonia muleiensis	strain=RB2	GCA_003600155.1	2282648	2282648	type	True	79.2466	321	735	95	below_threshold
Nesterenkonia ebinurensis	strain=MD2	GCA_008711175.1	2608252	2608252	type	True	79.1859	322	735	95	below_threshold
Nesterenkonia jeotgali	strain=DSM 19081	GCA_014138825.1	317018	317018	type	True	79.1826	303	735	95	below_threshold
Nesterenkonia halophila	strain=DSM 16378	GCA_009467795.1	302044	302044	type	True	79.0681	239	735	95	below_threshold
Nesterenkonia massiliensis	strain=NP1	GCA_000455245.1	1232429	1232429	type	True	78.7631	252	735	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.3033	101	735	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	76.9533	167	735	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	76.1381	88	735	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:24,345] [INFO] DFAST Taxonomy check result was written to GCF_014195445.1_ASM1419544v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:24,345] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:24,346] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:24,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40a7b23d-addf-466b-8c27-5fbf23fd0c2d/dqc_reference/checkm_data
[2024-01-25 17:52:24,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:24,372] [INFO] Task started: CheckM
[2024-01-25 17:52:24,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014195445.1_ASM1419544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014195445.1_ASM1419544v1_genomic.fna/checkm_input GCF_014195445.1_ASM1419544v1_genomic.fna/checkm_result
[2024-01-25 17:52:46,200] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:46,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:46,220] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:46,220] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:46,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014195445.1_ASM1419544v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:46,221] [INFO] Task started: Blastn
[2024-01-25 17:52:46,221] [INFO] Running command: blastn -query GCF_014195445.1_ASM1419544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40a7b23d-addf-466b-8c27-5fbf23fd0c2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014195445.1_ASM1419544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:47,453] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:47,456] [INFO] Selected 15 target genomes.
[2024-01-25 17:52:47,456] [INFO] Target genome list was writen to GCF_014195445.1_ASM1419544v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:47,480] [INFO] Task started: fastANI
[2024-01-25 17:52:47,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ba1fe23-f446-4447-ab31-0fd815626945/GCF_014195445.1_ASM1419544v1_genomic.fna.gz --refList GCF_014195445.1_ASM1419544v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014195445.1_ASM1419544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:55,751] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:55,761] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:55,762] [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_014195445.1	s__Nesterenkonia koreensis	100.0	728	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014642675.1	s__Nesterenkonia cremea	79.544	300	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758175.1	s__Nesterenkonia alkaliphila	79.5263	329	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007994735.1	s__Nesterenkonia populi	79.526	270	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641515.1	s__Nesterenkonia sp012641515	79.3883	295	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876395.1	s__Nesterenkonia lacusekhoensis	79.3084	294	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410215.1	s__Nesterenkonia sandarakina	79.2877	293	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	97.10	97.05	0.88	0.86	3	-
GCF_003600155.1	s__Nesterenkonia muleiensis	79.2466	321	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008711175.1	s__Nesterenkonia sp008711175	79.2005	321	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364585.1	s__Nesterenkonia aurantiaca	79.1248	299	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_009467795.1	s__Nesterenkonia halophila	79.0902	237	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003175.1	s__Nesterenkonia sandarakina_A	79.0876	305	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017347085.1	s__Nesterenkonia sp017347085	79.036	300	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000455245.1	s__Nesterenkonia massiliensis	78.7806	251	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_019173455.1	s__Nesterenkonia sp019173455	78.5271	273	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:55,763] [INFO] GTDB search result was written to GCF_014195445.1_ASM1419544v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:55,764] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:55,767] [INFO] DFAST_QC result json was written to GCF_014195445.1_ASM1419544v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:55,767] [INFO] DFAST_QC completed!
[2024-01-25 17:52:55,767] [INFO] Total running time: 0h0m50s