[2024-01-24 13:18:55,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:55,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:55,616] [INFO] DQC Reference Directory: /var/lib/cwl/stga391a76c-5667-4fd0-9c3d-d73398361f19/dqc_reference
[2024-01-24 13:18:56,907] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:56,908] [INFO] Task started: Prodigal
[2024-01-24 13:18:56,908] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbc6d39e-ae80-48c2-826b-5f2d18738a05/GCF_014874065.1_ASM1487406v1_genomic.fna.gz | prodigal -d GCF_014874065.1_ASM1487406v1_genomic.fna/cds.fna -a GCF_014874065.1_ASM1487406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:06,220] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:06,220] [INFO] Task started: HMMsearch
[2024-01-24 13:19:06,221] [INFO] Running command: hmmsearch --tblout GCF_014874065.1_ASM1487406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga391a76c-5667-4fd0-9c3d-d73398361f19/dqc_reference/reference_markers.hmm GCF_014874065.1_ASM1487406v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:06,483] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:06,484] [INFO] Found 6/6 markers.
[2024-01-24 13:19:06,513] [INFO] Query marker FASTA was written to GCF_014874065.1_ASM1487406v1_genomic.fna/markers.fasta
[2024-01-24 13:19:06,514] [INFO] Task started: Blastn
[2024-01-24 13:19:06,514] [INFO] Running command: blastn -query GCF_014874065.1_ASM1487406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga391a76c-5667-4fd0-9c3d-d73398361f19/dqc_reference/reference_markers.fasta -out GCF_014874065.1_ASM1487406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:07,580] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:07,583] [INFO] Selected 10 target genomes.
[2024-01-24 13:19:07,584] [INFO] Target genome list was writen to GCF_014874065.1_ASM1487406v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:07,592] [INFO] Task started: fastANI
[2024-01-24 13:19:07,592] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbc6d39e-ae80-48c2-826b-5f2d18738a05/GCF_014874065.1_ASM1487406v1_genomic.fna.gz --refList GCF_014874065.1_ASM1487406v1_genomic.fna/target_genomes.txt --output GCF_014874065.1_ASM1487406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:14,703] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:14,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga391a76c-5667-4fd0-9c3d-d73398361f19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:14,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga391a76c-5667-4fd0-9c3d-d73398361f19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:14,715] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:14,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:14,715] [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 halotolerans	strain=DSM 15474	GCA_014874065.1	225325	225325	type	True	100.0	987	987	95	conclusive
Nesterenkonia lutea	strain=DSM 15666	GCA_014873955.1	272919	272919	type	True	85.2059	750	987	95	below_threshold
Nesterenkonia aurantiaca	strain=DSM 27373	GCA_004364585.1	1436010	1436010	type	True	84.0651	706	987	95	below_threshold
Nesterenkonia sandarakina	strain=DSM 15664	GCA_013410215.1	272918	272918	type	True	83.8462	722	987	95	below_threshold
Nesterenkonia jeotgali	strain=DSM 19081	GCA_014138825.1	317018	317018	type	True	83.7379	698	987	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	78.5317	276	987	95	below_threshold
Arthrobacter cheniae	strain=Hz2	GCA_003602275.1	1258888	1258888	type	True	77.282	149	987	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.1382	121	987	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	76.7701	120	987	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	76.2038	171	987	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:14,717] [INFO] DFAST Taxonomy check result was written to GCF_014874065.1_ASM1487406v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:14,717] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:14,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:14,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga391a76c-5667-4fd0-9c3d-d73398361f19/dqc_reference/checkm_data
[2024-01-24 13:19:14,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:14,752] [INFO] Task started: CheckM
[2024-01-24 13:19:14,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014874065.1_ASM1487406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014874065.1_ASM1487406v1_genomic.fna/checkm_input GCF_014874065.1_ASM1487406v1_genomic.fna/checkm_result
[2024-01-24 13:19:50,243] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:50,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:50,264] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:50,265] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:50,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014874065.1_ASM1487406v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:50,266] [INFO] Task started: Blastn
[2024-01-24 13:19:50,266] [INFO] Running command: blastn -query GCF_014874065.1_ASM1487406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga391a76c-5667-4fd0-9c3d-d73398361f19/dqc_reference/reference_markers_gtdb.fasta -out GCF_014874065.1_ASM1487406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:51,950] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:51,953] [INFO] Selected 7 target genomes.
[2024-01-24 13:19:51,954] [INFO] Target genome list was writen to GCF_014874065.1_ASM1487406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:51,961] [INFO] Task started: fastANI
[2024-01-24 13:19:51,962] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbc6d39e-ae80-48c2-826b-5f2d18738a05/GCF_014874065.1_ASM1487406v1_genomic.fna.gz --refList GCF_014874065.1_ASM1487406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014874065.1_ASM1487406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:57,423] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:57,430] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:57,430] [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_014874065.1	s__Nesterenkonia halotolerans	100.0	987	987	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_019173455.1	s__Nesterenkonia sp019173455	90.8183	813	987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873955.1	s__Nesterenkonia lutea	85.2173	748	987	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	84.4253	733	987	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	84.1025	703	987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_017347085.1	s__Nesterenkonia sp017347085	84.0974	716	987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013410215.1	s__Nesterenkonia sandarakina	83.8462	722	987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	97.10	97.05	0.88	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:57,438] [INFO] GTDB search result was written to GCF_014874065.1_ASM1487406v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:57,439] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:57,444] [INFO] DFAST_QC result json was written to GCF_014874065.1_ASM1487406v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:57,444] [INFO] DFAST_QC completed!
[2024-01-24 13:19:57,445] [INFO] Total running time: 0h1m2s