[2024-01-24 13:13:23,628] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:23,631] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:23,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg94e75047-de79-4274-80e0-55f71b12630b/dqc_reference
[2024-01-24 13:13:24,910] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:24,910] [INFO] Task started: Prodigal
[2024-01-24 13:13:24,911] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf150559-ff24-4223-a57a-ae9d791af8fb/GCF_005771525.1_ASM577152v1_genomic.fna.gz | prodigal -d GCF_005771525.1_ASM577152v1_genomic.fna/cds.fna -a GCF_005771525.1_ASM577152v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:34,799] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:34,800] [INFO] Task started: HMMsearch
[2024-01-24 13:13:34,800] [INFO] Running command: hmmsearch --tblout GCF_005771525.1_ASM577152v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94e75047-de79-4274-80e0-55f71b12630b/dqc_reference/reference_markers.hmm GCF_005771525.1_ASM577152v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:35,091] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:35,092] [INFO] Found 6/6 markers.
[2024-01-24 13:13:35,143] [INFO] Query marker FASTA was written to GCF_005771525.1_ASM577152v1_genomic.fna/markers.fasta
[2024-01-24 13:13:35,143] [INFO] Task started: Blastn
[2024-01-24 13:13:35,143] [INFO] Running command: blastn -query GCF_005771525.1_ASM577152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94e75047-de79-4274-80e0-55f71b12630b/dqc_reference/reference_markers.fasta -out GCF_005771525.1_ASM577152v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:35,999] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:36,005] [INFO] Selected 17 target genomes.
[2024-01-24 13:13:36,006] [INFO] Target genome list was writen to GCF_005771525.1_ASM577152v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:36,123] [INFO] Task started: fastANI
[2024-01-24 13:13:36,124] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf150559-ff24-4223-a57a-ae9d791af8fb/GCF_005771525.1_ASM577152v1_genomic.fna.gz --refList GCF_005771525.1_ASM577152v1_genomic.fna/target_genomes.txt --output GCF_005771525.1_ASM577152v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:48,308] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:48,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94e75047-de79-4274-80e0-55f71b12630b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:48,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94e75047-de79-4274-80e0-55f71b12630b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:48,322] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:48,322] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:48,322] [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 salmonea	strain=GY074	GCA_005771525.1	1804987	1804987	type	True	100.0	1028	1036	95	conclusive
Nesterenkonia haasae	strain=Hz 6-5	GCA_010119385.1	2587813	2587813	type	True	83.7947	693	1036	95	below_threshold
Nesterenkonia sphaerica	strain=GY239	GCA_005771565.1	1804988	1804988	type	True	80.1664	439	1036	95	below_threshold
Nesterenkonia natronophila	strain=M8	GCA_003595215.1	2174932	2174932	type	True	80.0223	461	1036	95	below_threshold
Nesterenkonia alkaliphila	strain=CGMCC 1.12781	GCA_014639295.1	1463631	1463631	type	True	79.9124	349	1036	95	below_threshold
Nesterenkonia alkaliphila	strain=F10	GCA_009758175.1	1463631	1463631	type	True	79.7657	344	1036	95	below_threshold
Nesterenkonia sedimenti	strain=MY13	GCA_012641515.1	1463632	1463632	type	True	79.0856	307	1036	95	below_threshold
Nesterenkonia ebinurensis	strain=MD2	GCA_008711175.1	2608252	2608252	type	True	78.3555	326	1036	95	below_threshold
Nesterenkonia muleiensis	strain=RB2	GCA_003600155.1	2282648	2282648	type	True	78.2666	365	1036	95	below_threshold
Nesterenkonia lacusekhoensis	strain=DSM 12544	GCA_017876395.1	150832	150832	type	True	78.1081	214	1036	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	77.7308	193	1036	95	below_threshold
Nesterenkonia aurantiaca	strain=DSM 27373	GCA_004364585.1	1436010	1436010	type	True	77.6634	196	1036	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	76.6038	65	1036	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	76.0552	55	1036	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:48,324] [INFO] DFAST Taxonomy check result was written to GCF_005771525.1_ASM577152v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:48,325] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:48,326] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:48,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94e75047-de79-4274-80e0-55f71b12630b/dqc_reference/checkm_data
[2024-01-24 13:13:48,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:48,363] [INFO] Task started: CheckM
[2024-01-24 13:13:48,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005771525.1_ASM577152v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005771525.1_ASM577152v1_genomic.fna/checkm_input GCF_005771525.1_ASM577152v1_genomic.fna/checkm_result
[2024-01-24 13:14:22,201] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:22,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:22,221] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:22,222] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:22,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005771525.1_ASM577152v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:22,222] [INFO] Task started: Blastn
[2024-01-24 13:14:22,223] [INFO] Running command: blastn -query GCF_005771525.1_ASM577152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94e75047-de79-4274-80e0-55f71b12630b/dqc_reference/reference_markers_gtdb.fasta -out GCF_005771525.1_ASM577152v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:23,401] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:23,404] [INFO] Selected 12 target genomes.
[2024-01-24 13:14:23,404] [INFO] Target genome list was writen to GCF_005771525.1_ASM577152v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:23,485] [INFO] Task started: fastANI
[2024-01-24 13:14:23,486] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf150559-ff24-4223-a57a-ae9d791af8fb/GCF_005771525.1_ASM577152v1_genomic.fna.gz --refList GCF_005771525.1_ASM577152v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005771525.1_ASM577152v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:30,966] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:30,977] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:30,977] [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_005771525.1	s__Nesterenkonia salmonea	100.0	1028	1036	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_010119385.1	s__Nesterenkonia haasae	83.8081	691	1036	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	98.27	98.27	0.87	0.87	2	-
GCF_005771565.1	s__Nesterenkonia sphaerica	80.1664	439	1036	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	80.0223	461	1036	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	79.7752	342	1036	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012641515.1	s__Nesterenkonia sp012641515	79.087	306	1036	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	78.3555	326	1036	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	78.2873	363	1036	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	78.1251	213	1036	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	77.7308	193	1036	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	77.6634	196	1036	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_000421745.1	s__Nesterenkonia alba	77.6244	176	1036	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 13:14:30,979] [INFO] GTDB search result was written to GCF_005771525.1_ASM577152v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:30,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:30,983] [INFO] DFAST_QC result json was written to GCF_005771525.1_ASM577152v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:30,983] [INFO] DFAST_QC completed!
[2024-01-24 13:14:30,983] [INFO] Total running time: 0h1m7s