[2024-01-24 12:06:23,766] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:23,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:23,768] [INFO] DQC Reference Directory: /var/lib/cwl/stgeffe3b1d-525f-44ff-99e6-9168c5e6df70/dqc_reference
[2024-01-24 12:06:25,049] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,053] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,054] [INFO] Running command: gunzip -c /var/lib/cwl/stg149cc7e9-0480-4c79-99d8-cf3cc6f1aac5/GCF_000455245.1_Nm_NP1_genomic.fna.gz | prodigal -d GCF_000455245.1_Nm_NP1_genomic.fna/cds.fna -a GCF_000455245.1_Nm_NP1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:32,855] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:32,856] [INFO] Task started: HMMsearch
[2024-01-24 12:06:32,856] [INFO] Running command: hmmsearch --tblout GCF_000455245.1_Nm_NP1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeffe3b1d-525f-44ff-99e6-9168c5e6df70/dqc_reference/reference_markers.hmm GCF_000455245.1_Nm_NP1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:33,098] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:33,100] [INFO] Found 6/6 markers.
[2024-01-24 12:06:33,126] [INFO] Query marker FASTA was written to GCF_000455245.1_Nm_NP1_genomic.fna/markers.fasta
[2024-01-24 12:06:33,126] [INFO] Task started: Blastn
[2024-01-24 12:06:33,126] [INFO] Running command: blastn -query GCF_000455245.1_Nm_NP1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeffe3b1d-525f-44ff-99e6-9168c5e6df70/dqc_reference/reference_markers.fasta -out GCF_000455245.1_Nm_NP1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:34,020] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:34,024] [INFO] Selected 20 target genomes.
[2024-01-24 12:06:34,025] [INFO] Target genome list was writen to GCF_000455245.1_Nm_NP1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:34,032] [INFO] Task started: fastANI
[2024-01-24 12:06:34,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg149cc7e9-0480-4c79-99d8-cf3cc6f1aac5/GCF_000455245.1_Nm_NP1_genomic.fna.gz --refList GCF_000455245.1_Nm_NP1_genomic.fna/target_genomes.txt --output GCF_000455245.1_Nm_NP1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:45,649] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:45,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeffe3b1d-525f-44ff-99e6-9168c5e6df70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:45,650] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeffe3b1d-525f-44ff-99e6-9168c5e6df70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:45,666] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:45,666] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:45,666] [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 massiliensis	strain=NP1	GCA_000455245.1	1232429	1232429	type	True	99.9999	874	878	95	conclusive
Nesterenkonia cremea	strain=CGMCC 1.15388	GCA_014642675.1	1882340	1882340	type	True	79.4176	364	878	95	below_threshold
Nesterenkonia alkaliphila	strain=CGMCC 1.12781	GCA_014639295.1	1463631	1463631	type	True	79.412	384	878	95	below_threshold
Nesterenkonia sedimenti	strain=MY13	GCA_012641515.1	1463632	1463632	type	True	79.3795	354	878	95	below_threshold
Nesterenkonia alkaliphila	strain=F10	GCA_009758175.1	1463631	1463631	type	True	79.3263	383	878	95	below_threshold
Nesterenkonia lacusekhoensis	strain=DSM 12544	GCA_017876395.1	150832	150832	type	True	79.2737	364	878	95	below_threshold
Nesterenkonia halotolerans	strain=DSM 15474	GCA_014874065.1	225325	225325	type	True	78.9713	296	878	95	below_threshold
Nesterenkonia ebinurensis	strain=MD2	GCA_008711175.1	2608252	2608252	type	True	78.8539	341	878	95	below_threshold
Nesterenkonia muleiensis	strain=RB2	GCA_003600155.1	2282648	2282648	type	True	78.7782	335	878	95	below_threshold
Nesterenkonia lutea	strain=DSM 15666	GCA_014873955.1	272919	272919	type	True	78.6929	309	878	95	below_threshold
Nesterenkonia populi	strain=DSM 27959	GCA_007994735.1	1591087	1591087	type	True	78.6411	298	878	95	below_threshold
Nesterenkonia aurantiaca	strain=DSM 27373	GCA_004364585.1	1436010	1436010	type	True	78.6329	328	878	95	below_threshold
Nesterenkonia halophila	strain=DSM 16378	GCA_009467795.1	302044	302044	type	True	78.6054	196	878	95	below_threshold
Nesterenkonia sandarakina	strain=DSM 15664	GCA_013410215.1	272918	272918	type	True	78.5936	330	878	95	below_threshold
Nesterenkonia jeotgali	strain=DSM 19081	GCA_014138825.1	317018	317018	type	True	78.4706	326	878	95	below_threshold
Nesterenkonia xinjiangensis	strain=DSM 15475	GCA_013410745.1	225327	225327	type	True	78.4549	308	878	95	below_threshold
Brachybacterium epidermidis	strain=Marseille-Q2903	GCA_015209585.1	2781983	2781983	type	True	77.0492	88	878	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	76.9938	104	878	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	76.862	62	878	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	76.7744	84	878	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:45,676] [INFO] DFAST Taxonomy check result was written to GCF_000455245.1_Nm_NP1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:45,676] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:45,676] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:45,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeffe3b1d-525f-44ff-99e6-9168c5e6df70/dqc_reference/checkm_data
[2024-01-24 12:06:45,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:45,706] [INFO] Task started: CheckM
[2024-01-24 12:06:45,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000455245.1_Nm_NP1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000455245.1_Nm_NP1_genomic.fna/checkm_input GCF_000455245.1_Nm_NP1_genomic.fna/checkm_result
[2024-01-24 12:07:12,696] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:12,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:12,717] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:12,717] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:12,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000455245.1_Nm_NP1_genomic.fna/markers.fasta)
[2024-01-24 12:07:12,718] [INFO] Task started: Blastn
[2024-01-24 12:07:12,718] [INFO] Running command: blastn -query GCF_000455245.1_Nm_NP1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeffe3b1d-525f-44ff-99e6-9168c5e6df70/dqc_reference/reference_markers_gtdb.fasta -out GCF_000455245.1_Nm_NP1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:13,921] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:13,925] [INFO] Selected 17 target genomes.
[2024-01-24 12:07:13,925] [INFO] Target genome list was writen to GCF_000455245.1_Nm_NP1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:13,957] [INFO] Task started: fastANI
[2024-01-24 12:07:13,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg149cc7e9-0480-4c79-99d8-cf3cc6f1aac5/GCF_000455245.1_Nm_NP1_genomic.fna.gz --refList GCF_000455245.1_Nm_NP1_genomic.fna/target_genomes_gtdb.txt --output GCF_000455245.1_Nm_NP1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:23,241] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:23,257] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:23,257] [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_000455245.1	s__Nesterenkonia massiliensis	99.9999	874	878	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_012641515.1	s__Nesterenkonia sp012641515	79.4002	355	878	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	79.3748	367	878	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	79.3209	383	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017876395.1	s__Nesterenkonia lacusekhoensis	79.2732	364	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874065.1	s__Nesterenkonia halotolerans	78.9713	296	878	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	78.8409	342	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758425.2	s__Nesterenkonia sp001758425	78.8286	301	878	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	78.7644	336	878	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	78.7065	307	878	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	78.6681	339	878	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	78.6411	298	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009467795.1	s__Nesterenkonia halophila	78.6271	195	878	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	78.6209	329	878	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	78.6163	335	878	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	78.5892	331	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	97.10	97.05	0.88	0.86	3	-
GCF_013410745.1	s__Nesterenkonia xinjiangensis	78.4641	308	878	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 12:07:23,259] [INFO] GTDB search result was written to GCF_000455245.1_Nm_NP1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:23,261] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:23,267] [INFO] DFAST_QC result json was written to GCF_000455245.1_Nm_NP1_genomic.fna/dqc_result.json
[2024-01-24 12:07:23,267] [INFO] DFAST_QC completed!
[2024-01-24 12:07:23,267] [INFO] Total running time: 0h0m60s