[2024-01-24 13:37:05,048] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,050] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,050] [INFO] DQC Reference Directory: /var/lib/cwl/stg51b57635-0bbd-48b7-a716-28b083955ed0/dqc_reference
[2024-01-24 13:37:06,501] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,502] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg65033d4a-700d-45af-bdcf-20f4b3013100/GCF_014639295.1_ASM1463929v1_genomic.fna.gz | prodigal -d GCF_014639295.1_ASM1463929v1_genomic.fna/cds.fna -a GCF_014639295.1_ASM1463929v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:16,424] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:16,425] [INFO] Task started: HMMsearch
[2024-01-24 13:37:16,425] [INFO] Running command: hmmsearch --tblout GCF_014639295.1_ASM1463929v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51b57635-0bbd-48b7-a716-28b083955ed0/dqc_reference/reference_markers.hmm GCF_014639295.1_ASM1463929v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:16,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:16,768] [INFO] Found 6/6 markers.
[2024-01-24 13:37:16,798] [INFO] Query marker FASTA was written to GCF_014639295.1_ASM1463929v1_genomic.fna/markers.fasta
[2024-01-24 13:37:16,799] [INFO] Task started: Blastn
[2024-01-24 13:37:16,799] [INFO] Running command: blastn -query GCF_014639295.1_ASM1463929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51b57635-0bbd-48b7-a716-28b083955ed0/dqc_reference/reference_markers.fasta -out GCF_014639295.1_ASM1463929v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:17,793] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:17,803] [INFO] Selected 12 target genomes.
[2024-01-24 13:37:17,803] [INFO] Target genome list was writen to GCF_014639295.1_ASM1463929v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:17,810] [INFO] Task started: fastANI
[2024-01-24 13:37:17,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg65033d4a-700d-45af-bdcf-20f4b3013100/GCF_014639295.1_ASM1463929v1_genomic.fna.gz --refList GCF_014639295.1_ASM1463929v1_genomic.fna/target_genomes.txt --output GCF_014639295.1_ASM1463929v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:26,569] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:26,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51b57635-0bbd-48b7-a716-28b083955ed0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:26,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51b57635-0bbd-48b7-a716-28b083955ed0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:26,580] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:26,581] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:26,581] [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 alkaliphila	strain=CGMCC 1.12781	GCA_014639295.1	1463631	1463631	type	True	100.0	1086	1088	95	conclusive
Nesterenkonia alkaliphila	strain=F10	GCA_009758175.1	1463631	1463631	type	True	99.943	1041	1088	95	conclusive
Nesterenkonia ebinurensis	strain=MD2	GCA_008711175.1	2608252	2608252	type	True	83.9927	672	1088	95	below_threshold
Nesterenkonia sedimenti	strain=MY13	GCA_012641515.1	1463632	1463632	type	True	81.0826	507	1088	95	below_threshold
Nesterenkonia muleiensis	strain=RB2	GCA_003600155.1	2282648	2282648	type	True	80.7244	522	1088	95	below_threshold
Nesterenkonia sphaerica	strain=GY239	GCA_005771565.1	1804988	1804988	type	True	80.085	412	1088	95	below_threshold
Nesterenkonia lacusekhoensis	strain=DSM 12544	GCA_017876395.1	150832	150832	type	True	79.7428	388	1088	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	79.6201	339	1088	95	below_threshold
Nesterenkonia xinjiangensis	strain=DSM 15475	GCA_013410745.1	225327	225327	type	True	78.9749	321	1088	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	76.6917	132	1088	95	below_threshold
Humibacter ginsenosidimutans	strain=WJ7-1	GCA_007859675.1	2599293	2599293	type	True	76.6464	75	1088	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	76.5766	90	1088	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:26,583] [INFO] DFAST Taxonomy check result was written to GCF_014639295.1_ASM1463929v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:26,583] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:26,583] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:26,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51b57635-0bbd-48b7-a716-28b083955ed0/dqc_reference/checkm_data
[2024-01-24 13:37:26,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:26,619] [INFO] Task started: CheckM
[2024-01-24 13:37:26,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014639295.1_ASM1463929v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014639295.1_ASM1463929v1_genomic.fna/checkm_input GCF_014639295.1_ASM1463929v1_genomic.fna/checkm_result
[2024-01-24 13:38:00,679] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:00,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:00,697] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:00,697] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:00,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014639295.1_ASM1463929v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:00,698] [INFO] Task started: Blastn
[2024-01-24 13:38:00,698] [INFO] Running command: blastn -query GCF_014639295.1_ASM1463929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51b57635-0bbd-48b7-a716-28b083955ed0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014639295.1_ASM1463929v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:02,294] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:02,297] [INFO] Selected 12 target genomes.
[2024-01-24 13:38:02,298] [INFO] Target genome list was writen to GCF_014639295.1_ASM1463929v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:02,317] [INFO] Task started: fastANI
[2024-01-24 13:38:02,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg65033d4a-700d-45af-bdcf-20f4b3013100/GCF_014639295.1_ASM1463929v1_genomic.fna.gz --refList GCF_014639295.1_ASM1463929v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014639295.1_ASM1463929v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:10,145] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:10,156] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:10,157] [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_009758175.1	s__Nesterenkonia alkaliphila	99.943	1041	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_008711175.1	s__Nesterenkonia sp008711175	83.9904	672	1088	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	81.0578	510	1088	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	80.7493	520	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771565.1	s__Nesterenkonia sphaerica	80.085	412	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994735.1	s__Nesterenkonia populi	79.795	357	1088	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	79.7427	388	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195445.1	s__Nesterenkonia koreensis	79.6141	339	1088	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	79.4672	423	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421745.1	s__Nesterenkonia alba	79.0952	301	1088	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	78.9749	321	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003595215.1	s__Nesterenkonia natronophila	78.4384	293	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:10,159] [INFO] GTDB search result was written to GCF_014639295.1_ASM1463929v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:10,159] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:10,162] [INFO] DFAST_QC result json was written to GCF_014639295.1_ASM1463929v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:10,162] [INFO] DFAST_QC completed!
[2024-01-24 13:38:10,163] [INFO] Total running time: 0h1m5s