[2024-01-24 12:51:05,443] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:05,445] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:05,445] [INFO] DQC Reference Directory: /var/lib/cwl/stg5631da6a-61ec-4cc4-b4d1-e99eb5a6a700/dqc_reference
[2024-01-24 12:51:06,664] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:06,664] [INFO] Task started: Prodigal
[2024-01-24 12:51:06,665] [INFO] Running command: gunzip -c /var/lib/cwl/stg21d0397a-7dc7-4ea0-b616-8bf87e580470/GCF_019575955.1_ASM1957595v1_genomic.fna.gz | prodigal -d GCF_019575955.1_ASM1957595v1_genomic.fna/cds.fna -a GCF_019575955.1_ASM1957595v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:14,708] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:14,708] [INFO] Task started: HMMsearch
[2024-01-24 12:51:14,708] [INFO] Running command: hmmsearch --tblout GCF_019575955.1_ASM1957595v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5631da6a-61ec-4cc4-b4d1-e99eb5a6a700/dqc_reference/reference_markers.hmm GCF_019575955.1_ASM1957595v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:14,923] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:14,925] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg21d0397a-7dc7-4ea0-b616-8bf87e580470/GCF_019575955.1_ASM1957595v1_genomic.fna.gz]
[2024-01-24 12:51:14,956] [INFO] Query marker FASTA was written to GCF_019575955.1_ASM1957595v1_genomic.fna/markers.fasta
[2024-01-24 12:51:14,956] [INFO] Task started: Blastn
[2024-01-24 12:51:14,956] [INFO] Running command: blastn -query GCF_019575955.1_ASM1957595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5631da6a-61ec-4cc4-b4d1-e99eb5a6a700/dqc_reference/reference_markers.fasta -out GCF_019575955.1_ASM1957595v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:15,943] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:15,947] [INFO] Selected 18 target genomes.
[2024-01-24 12:51:15,948] [INFO] Target genome list was writen to GCF_019575955.1_ASM1957595v1_genomic.fna/target_genomes.txt
[2024-01-24 12:51:15,964] [INFO] Task started: fastANI
[2024-01-24 12:51:15,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg21d0397a-7dc7-4ea0-b616-8bf87e580470/GCF_019575955.1_ASM1957595v1_genomic.fna.gz --refList GCF_019575955.1_ASM1957595v1_genomic.fna/target_genomes.txt --output GCF_019575955.1_ASM1957595v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:51:25,605] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:25,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5631da6a-61ec-4cc4-b4d1-e99eb5a6a700/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:51:25,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5631da6a-61ec-4cc4-b4d1-e99eb5a6a700/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:51:25,623] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:51:25,623] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:51:25,623] [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 pannonica	strain=DSM 29786	GCA_019575955.1	1548602	1548602	type	True	100.0	899	899	95	conclusive
Nesterenkonia populi	strain=DSM 27959	GCA_007994735.1	1591087	1591087	type	True	81.6998	541	899	95	below_threshold
Nesterenkonia lacusekhoensis	strain=DSM 12544	GCA_017876395.1	150832	150832	type	True	78.784	291	899	95	below_threshold
Nesterenkonia cremea	strain=CGMCC 1.15388	GCA_014642675.1	1882340	1882340	type	True	78.7018	339	899	95	below_threshold
Nesterenkonia sandarakina	strain=DSM 15664	GCA_013410215.1	272918	272918	type	True	78.5208	284	899	95	below_threshold
Nesterenkonia lutea	strain=DSM 15666	GCA_014873955.1	272919	272919	type	True	78.4675	269	899	95	below_threshold
Nesterenkonia jeotgali	strain=DSM 19081	GCA_014138825.1	317018	317018	type	True	78.4032	293	899	95	below_threshold
Nesterenkonia xinjiangensis	strain=DSM 15475	GCA_013410745.1	225327	225327	type	True	78.3647	296	899	95	below_threshold
Nesterenkonia aurantiaca	strain=DSM 27373	GCA_004364585.1	1436010	1436010	type	True	78.3624	297	899	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	78.3065	217	899	95	below_threshold
Nesterenkonia alkaliphila	strain=CGMCC 1.12781	GCA_014639295.1	1463631	1463631	type	True	78.1633	254	899	95	below_threshold
Nesterenkonia alkaliphila	strain=F10	GCA_009758175.1	1463631	1463631	type	True	78.1469	247	899	95	below_threshold
Nesterenkonia sedimenti	strain=MY13	GCA_012641515.1	1463632	1463632	type	True	78.0049	226	899	95	below_threshold
Nesterenkonia muleiensis	strain=RB2	GCA_003600155.1	2282648	2282648	type	True	77.8251	264	899	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	77.5209	159	899	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.1666	103	899	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	77.0976	102	899	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	76.8161	82	899	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:51:25,625] [INFO] DFAST Taxonomy check result was written to GCF_019575955.1_ASM1957595v1_genomic.fna/tc_result.tsv
[2024-01-24 12:51:25,625] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:51:25,626] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:51:25,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5631da6a-61ec-4cc4-b4d1-e99eb5a6a700/dqc_reference/checkm_data
[2024-01-24 12:51:25,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:51:25,659] [INFO] Task started: CheckM
[2024-01-24 12:51:25,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019575955.1_ASM1957595v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019575955.1_ASM1957595v1_genomic.fna/checkm_input GCF_019575955.1_ASM1957595v1_genomic.fna/checkm_result
[2024-01-24 12:51:53,270] [INFO] Task succeeded: CheckM
[2024-01-24 12:51:53,272] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:51:53,298] [INFO] ===== Completeness check finished =====
[2024-01-24 12:51:53,298] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:51:53,299] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019575955.1_ASM1957595v1_genomic.fna/markers.fasta)
[2024-01-24 12:51:53,299] [INFO] Task started: Blastn
[2024-01-24 12:51:53,299] [INFO] Running command: blastn -query GCF_019575955.1_ASM1957595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5631da6a-61ec-4cc4-b4d1-e99eb5a6a700/dqc_reference/reference_markers_gtdb.fasta -out GCF_019575955.1_ASM1957595v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:54,753] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:54,757] [INFO] Selected 13 target genomes.
[2024-01-24 12:51:54,757] [INFO] Target genome list was writen to GCF_019575955.1_ASM1957595v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:51:54,777] [INFO] Task started: fastANI
[2024-01-24 12:51:54,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg21d0397a-7dc7-4ea0-b616-8bf87e580470/GCF_019575955.1_ASM1957595v1_genomic.fna.gz --refList GCF_019575955.1_ASM1957595v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019575955.1_ASM1957595v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:52:01,763] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:01,778] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:52:01,779] [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_007922635.1	s__Nesterenkonia sp007922635	97.667	821	899	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_007994735.1	s__Nesterenkonia populi	81.7031	541	899	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	78.733	336	899	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	78.7043	296	899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410215.1	s__Nesterenkonia sandarakina	78.5581	285	899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	97.10	97.05	0.88	0.86	3	-
GCF_017347085.1	s__Nesterenkonia sp017347085	78.4184	294	899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004364585.1	s__Nesterenkonia aurantiaca	78.3757	296	899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_014195445.1	s__Nesterenkonia koreensis	78.3416	217	899	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	78.3255	294	899	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	78.1469	247	899	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	78.0367	224	899	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	77.8251	264	899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114115.1	s__Nesterenkonia stercoripullorum	77.1982	149	899	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 12:52:01,780] [INFO] GTDB search result was written to GCF_019575955.1_ASM1957595v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:52:01,781] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:52:01,784] [INFO] DFAST_QC result json was written to GCF_019575955.1_ASM1957595v1_genomic.fna/dqc_result.json
[2024-01-24 12:52:01,784] [INFO] DFAST_QC completed!
[2024-01-24 12:52:01,784] [INFO] Total running time: 0h0m56s