[2024-01-25 18:46:05,700] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:05,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:05,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg4834498e-a9d5-41e7-949a-842ede10ac9a/dqc_reference
[2024-01-25 18:46:06,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:06,875] [INFO] Task started: Prodigal
[2024-01-25 18:46:06,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg09f9f4d9-4d98-41da-adb5-f00ccc563670/GCF_009758175.1_ASM975817v1_genomic.fna.gz | prodigal -d GCF_009758175.1_ASM975817v1_genomic.fna/cds.fna -a GCF_009758175.1_ASM975817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:15,212] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:15,213] [INFO] Task started: HMMsearch
[2024-01-25 18:46:15,213] [INFO] Running command: hmmsearch --tblout GCF_009758175.1_ASM975817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4834498e-a9d5-41e7-949a-842ede10ac9a/dqc_reference/reference_markers.hmm GCF_009758175.1_ASM975817v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:15,430] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:15,431] [INFO] Found 6/6 markers.
[2024-01-25 18:46:15,459] [INFO] Query marker FASTA was written to GCF_009758175.1_ASM975817v1_genomic.fna/markers.fasta
[2024-01-25 18:46:15,460] [INFO] Task started: Blastn
[2024-01-25 18:46:15,460] [INFO] Running command: blastn -query GCF_009758175.1_ASM975817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4834498e-a9d5-41e7-949a-842ede10ac9a/dqc_reference/reference_markers.fasta -out GCF_009758175.1_ASM975817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:16,383] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:16,385] [INFO] Selected 12 target genomes.
[2024-01-25 18:46:16,386] [INFO] Target genome list was writen to GCF_009758175.1_ASM975817v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:16,389] [INFO] Task started: fastANI
[2024-01-25 18:46:16,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg09f9f4d9-4d98-41da-adb5-f00ccc563670/GCF_009758175.1_ASM975817v1_genomic.fna.gz --refList GCF_009758175.1_ASM975817v1_genomic.fna/target_genomes.txt --output GCF_009758175.1_ASM975817v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:24,346] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:24,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4834498e-a9d5-41e7-949a-842ede10ac9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:24,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4834498e-a9d5-41e7-949a-842ede10ac9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:24,355] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:46:24,355] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:46:24,356] [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=F10	GCA_009758175.1	1463631	1463631	type	True	100.0	1048	1059	95	conclusive
Nesterenkonia alkaliphila	strain=CGMCC 1.12781	GCA_014639295.1	1463631	1463631	type	True	99.9995	1057	1059	95	conclusive
Nesterenkonia ebinurensis	strain=MD2	GCA_008711175.1	2608252	2608252	type	True	83.9739	663	1059	95	below_threshold
Nesterenkonia sedimenti	strain=MY13	GCA_012641515.1	1463632	1463632	type	True	80.9843	493	1059	95	below_threshold
Nesterenkonia muleiensis	strain=RB2	GCA_003600155.1	2282648	2282648	type	True	80.8156	508	1059	95	below_threshold
Nesterenkonia sphaerica	strain=GY239	GCA_005771565.1	1804988	1804988	type	True	80.1823	402	1059	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	79.702	328	1059	95	below_threshold
Nesterenkonia lacusekhoensis	strain=DSM 12544	GCA_017876395.1	150832	150832	type	True	79.5025	378	1059	95	below_threshold
Nesterenkonia xinjiangensis	strain=DSM 15475	GCA_013410745.1	225327	225327	type	True	78.7011	324	1059	95	below_threshold
Humibacter ginsenosidimutans	strain=WJ7-1	GCA_007859675.1	2599293	2599293	type	True	76.6572	76	1059	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	76.6153	127	1059	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	76.5081	83	1059	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:24,357] [INFO] DFAST Taxonomy check result was written to GCF_009758175.1_ASM975817v1_genomic.fna/tc_result.tsv
[2024-01-25 18:46:24,357] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:24,357] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:24,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4834498e-a9d5-41e7-949a-842ede10ac9a/dqc_reference/checkm_data
[2024-01-25 18:46:24,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:24,395] [INFO] Task started: CheckM
[2024-01-25 18:46:24,395] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009758175.1_ASM975817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009758175.1_ASM975817v1_genomic.fna/checkm_input GCF_009758175.1_ASM975817v1_genomic.fna/checkm_result
[2024-01-25 18:46:52,427] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:52,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:52,444] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:52,444] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:52,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009758175.1_ASM975817v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:52,444] [INFO] Task started: Blastn
[2024-01-25 18:46:52,445] [INFO] Running command: blastn -query GCF_009758175.1_ASM975817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4834498e-a9d5-41e7-949a-842ede10ac9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009758175.1_ASM975817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:53,887] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:53,891] [INFO] Selected 12 target genomes.
[2024-01-25 18:46:53,891] [INFO] Target genome list was writen to GCF_009758175.1_ASM975817v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:53,902] [INFO] Task started: fastANI
[2024-01-25 18:46:53,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg09f9f4d9-4d98-41da-adb5-f00ccc563670/GCF_009758175.1_ASM975817v1_genomic.fna.gz --refList GCF_009758175.1_ASM975817v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009758175.1_ASM975817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:01,384] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:01,392] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:01,392] [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	100.0	1048	1059	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	83.9698	663	1059	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	81.0102	491	1059	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	80.8431	506	1059	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	80.1954	403	1059	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	79.7537	350	1059	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	79.686	329	1059	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	79.5154	377	1059	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	79.3726	407	1059	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	79.099	304	1059	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	78.6945	325	1059	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	78.6441	281	1059	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 18:47:01,394] [INFO] GTDB search result was written to GCF_009758175.1_ASM975817v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:01,395] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:01,409] [INFO] DFAST_QC result json was written to GCF_009758175.1_ASM975817v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:01,410] [INFO] DFAST_QC completed!
[2024-01-25 18:47:01,410] [INFO] Total running time: 0h0m56s