[2024-01-25 18:51:35,554] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:35,555] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:35,555] [INFO] DQC Reference Directory: /var/lib/cwl/stg671f13e9-7b88-46f4-a627-1fdd6e5e3466/dqc_reference
[2024-01-25 18:51:36,714] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:36,715] [INFO] Task started: Prodigal
[2024-01-25 18:51:36,715] [INFO] Running command: gunzip -c /var/lib/cwl/stge0793847-5590-46d3-b09e-0fcd0832a8e0/GCF_009467795.1_ASM946779v1_genomic.fna.gz | prodigal -d GCF_009467795.1_ASM946779v1_genomic.fna/cds.fna -a GCF_009467795.1_ASM946779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:41,743] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:41,744] [INFO] Task started: HMMsearch
[2024-01-25 18:51:41,744] [INFO] Running command: hmmsearch --tblout GCF_009467795.1_ASM946779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg671f13e9-7b88-46f4-a627-1fdd6e5e3466/dqc_reference/reference_markers.hmm GCF_009467795.1_ASM946779v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:41,897] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:41,899] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge0793847-5590-46d3-b09e-0fcd0832a8e0/GCF_009467795.1_ASM946779v1_genomic.fna.gz]
[2024-01-25 18:51:41,917] [INFO] Query marker FASTA was written to GCF_009467795.1_ASM946779v1_genomic.fna/markers.fasta
[2024-01-25 18:51:41,918] [INFO] Task started: Blastn
[2024-01-25 18:51:41,918] [INFO] Running command: blastn -query GCF_009467795.1_ASM946779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg671f13e9-7b88-46f4-a627-1fdd6e5e3466/dqc_reference/reference_markers.fasta -out GCF_009467795.1_ASM946779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:42,846] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:42,849] [INFO] Selected 10 target genomes.
[2024-01-25 18:51:42,849] [INFO] Target genome list was writen to GCF_009467795.1_ASM946779v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:42,864] [INFO] Task started: fastANI
[2024-01-25 18:51:42,864] [INFO] Running command: fastANI --query /var/lib/cwl/stge0793847-5590-46d3-b09e-0fcd0832a8e0/GCF_009467795.1_ASM946779v1_genomic.fna.gz --refList GCF_009467795.1_ASM946779v1_genomic.fna/target_genomes.txt --output GCF_009467795.1_ASM946779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:48,421] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:48,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg671f13e9-7b88-46f4-a627-1fdd6e5e3466/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:48,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg671f13e9-7b88-46f4-a627-1fdd6e5e3466/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:48,429] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:51:48,430] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:51:48,430] [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
Nesterenkonia halophila	strain=DSM 16378	GCA_009467795.1	302044	302044	type	True	100.0	715	715	95	conclusive
Nesterenkonia xinjiangensis	strain=DSM 15475	GCA_013410745.1	225327	225327	type	True	80.9178	491	715	95	below_threshold
Nesterenkonia jeotgali	strain=DSM 19081	GCA_014138825.1	317018	317018	type	True	80.1558	343	715	95	below_threshold
Nesterenkonia cremea	strain=CGMCC 1.15388	GCA_014642675.1	1882340	1882340	type	True	80.1257	366	715	95	below_threshold
Nesterenkonia lacusekhoensis	strain=DSM 12544	GCA_017876395.1	150832	150832	type	True	80.0612	339	715	95	below_threshold
Nesterenkonia sandarakina	strain=DSM 15664	GCA_013410215.1	272918	272918	type	True	79.9934	357	715	95	below_threshold
Nesterenkonia aurantiaca	strain=DSM 27373	GCA_004364585.1	1436010	1436010	type	True	79.7698	364	715	95	below_threshold
Nesterenkonia lutea	strain=DSM 15666	GCA_014873955.1	272919	272919	type	True	79.5903	329	715	95	below_threshold
Nesterenkonia halotolerans	strain=DSM 15474	GCA_014874065.1	225325	225325	type	True	79.5507	338	715	95	below_threshold
Nesterenkonia populi	strain=DSM 27959	GCA_007994735.1	1591087	1591087	type	True	79.273	262	715	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:48,431] [INFO] DFAST Taxonomy check result was written to GCF_009467795.1_ASM946779v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:48,433] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:48,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:48,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg671f13e9-7b88-46f4-a627-1fdd6e5e3466/dqc_reference/checkm_data
[2024-01-25 18:51:48,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:48,461] [INFO] Task started: CheckM
[2024-01-25 18:51:48,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009467795.1_ASM946779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009467795.1_ASM946779v1_genomic.fna/checkm_input GCF_009467795.1_ASM946779v1_genomic.fna/checkm_result
[2024-01-25 18:52:16,376] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:16,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:16,395] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:16,395] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:16,396] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009467795.1_ASM946779v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:16,397] [INFO] Task started: Blastn
[2024-01-25 18:52:16,397] [INFO] Running command: blastn -query GCF_009467795.1_ASM946779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg671f13e9-7b88-46f4-a627-1fdd6e5e3466/dqc_reference/reference_markers_gtdb.fasta -out GCF_009467795.1_ASM946779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:17,774] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:17,777] [INFO] Selected 10 target genomes.
[2024-01-25 18:52:17,777] [INFO] Target genome list was writen to GCF_009467795.1_ASM946779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:17,783] [INFO] Task started: fastANI
[2024-01-25 18:52:17,783] [INFO] Running command: fastANI --query /var/lib/cwl/stge0793847-5590-46d3-b09e-0fcd0832a8e0/GCF_009467795.1_ASM946779v1_genomic.fna.gz --refList GCF_009467795.1_ASM946779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009467795.1_ASM946779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:23,798] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:23,806] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:23,806] [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_009467795.1	s__Nesterenkonia halophila	100.0	715	715	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_000220985.1	s__Nesterenkonia sp000220985	92.6002	559	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758425.2	s__Nesterenkonia sp001758425	81.1318	462	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410745.1	s__Nesterenkonia xinjiangensis	80.9315	490	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642675.1	s__Nesterenkonia cremea	80.1414	365	715	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	80.0603	339	715	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	79.7699	364	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_014873955.1	s__Nesterenkonia lutea	79.5747	330	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874065.1	s__Nesterenkonia halotolerans	79.5353	339	715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003600155.1	s__Nesterenkonia muleiensis	78.6811	257	715	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 18:52:23,808] [INFO] GTDB search result was written to GCF_009467795.1_ASM946779v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:23,808] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:23,811] [INFO] DFAST_QC result json was written to GCF_009467795.1_ASM946779v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:23,811] [INFO] DFAST_QC completed!
[2024-01-25 18:52:23,811] [INFO] Total running time: 0h0m48s