[2023-07-01 00:46:20,086] [INFO] DFAST_QC pipeline started.
[2023-07-01 00:46:20,091] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 00:46:20,091] [INFO] DQC Reference Directory: /var/lib/cwl/stg186a624d-97bb-43f0-9cdd-849a27c3f92b/dqc_reference
[2023-07-01 00:46:21,411] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 00:46:21,412] [INFO] Task started: Prodigal
[2023-07-01 00:46:21,412] [INFO] Running command: gunzip -c /var/lib/cwl/stge0601acf-9b4d-4ad6-b2cc-b799d86b917b/GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna.gz | prodigal -d GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/cds.fna -a GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 00:46:26,224] [INFO] Task succeeded: Prodigal
[2023-07-01 00:46:26,225] [INFO] Task started: HMMsearch
[2023-07-01 00:46:26,225] [INFO] Running command: hmmsearch --tblout GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg186a624d-97bb-43f0-9cdd-849a27c3f92b/dqc_reference/reference_markers.hmm GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/protein.faa > /dev/null
[2023-07-01 00:46:26,469] [INFO] Task succeeded: HMMsearch
[2023-07-01 00:46:26,470] [INFO] Found 6/6 markers.
[2023-07-01 00:46:26,506] [INFO] Query marker FASTA was written to GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/markers.fasta
[2023-07-01 00:46:26,507] [INFO] Task started: Blastn
[2023-07-01 00:46:26,507] [INFO] Running command: blastn -query GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg186a624d-97bb-43f0-9cdd-849a27c3f92b/dqc_reference/reference_markers.fasta -out GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 00:46:27,662] [INFO] Task succeeded: Blastn
[2023-07-01 00:46:27,666] [INFO] Selected 16 target genomes.
[2023-07-01 00:46:27,666] [INFO] Target genome list was writen to GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/target_genomes.txt
[2023-07-01 00:46:27,671] [INFO] Task started: fastANI
[2023-07-01 00:46:27,671] [INFO] Running command: fastANI --query /var/lib/cwl/stge0601acf-9b4d-4ad6-b2cc-b799d86b917b/GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna.gz --refList GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/target_genomes.txt --output GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 00:46:36,110] [INFO] Task succeeded: fastANI
[2023-07-01 00:46:36,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg186a624d-97bb-43f0-9cdd-849a27c3f92b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 00:46:36,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg186a624d-97bb-43f0-9cdd-849a27c3f92b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 00:46:36,125] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 00:46:36,126] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 00:46:36,126] [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 lacusekhoensis	strain=DSM 12544	GCA_017876395.1	150832	150832	type	True	93.6422	369	393	95	below_threshold
Nesterenkonia cremea	strain=CGMCC 1.15388	GCA_014642675.1	1882340	1882340	type	True	89.2474	362	393	95	below_threshold
Nesterenkonia xinjiangensis	strain=DSM 15475	GCA_013410745.1	225327	225327	type	True	79.8114	217	393	95	below_threshold
Nesterenkonia sandarakina	strain=DSM 15664	GCA_013410215.1	272918	272918	type	True	79.7868	213	393	95	below_threshold
Nesterenkonia lutea	strain=DSM 15666	GCA_014873955.1	272919	272919	type	True	79.5834	199	393	95	below_threshold
Nesterenkonia alkaliphila	strain=F10	GCA_009758175.1	1463631	1463631	type	True	79.5388	199	393	95	below_threshold
Nesterenkonia jeotgali	strain=DSM 19081	GCA_014138825.1	317018	317018	type	True	79.5174	216	393	95	below_threshold
Nesterenkonia alkaliphila	strain=CGMCC 1.12781	GCA_014639295.1	1463631	1463631	type	True	79.505	200	393	95	below_threshold
Nesterenkonia sedimenti	strain=MY13	GCA_012641515.1	1463632	1463632	type	True	79.3338	175	393	95	below_threshold
Nesterenkonia halotolerans	strain=DSM 15474	GCA_014874065.1	225325	225325	type	True	79.1997	204	393	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	78.7619	162	393	95	below_threshold
Nesterenkonia ebinurensis	strain=MD2	GCA_008711175.1	2608252	2608252	type	True	78.6565	181	393	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.3981	72	393	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	77.2587	63	393	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	76.25	51	393	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	76.25	51	393	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 00:46:36,128] [INFO] DFAST Taxonomy check result was written to GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/tc_result.tsv
[2023-07-01 00:46:36,129] [INFO] ===== Taxonomy check completed =====
[2023-07-01 00:46:36,129] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 00:46:36,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg186a624d-97bb-43f0-9cdd-849a27c3f92b/dqc_reference/checkm_data
[2023-07-01 00:46:36,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 00:46:36,159] [INFO] Task started: CheckM
[2023-07-01 00:46:36,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/checkm_input GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/checkm_result
[2023-07-01 00:46:57,390] [INFO] Task succeeded: CheckM
[2023-07-01 00:46:57,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.49%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 00:46:57,415] [INFO] ===== Completeness check finished =====
[2023-07-01 00:46:57,415] [INFO] ===== Start GTDB Search =====
[2023-07-01 00:46:57,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/markers.fasta)
[2023-07-01 00:46:57,416] [INFO] Task started: Blastn
[2023-07-01 00:46:57,416] [INFO] Running command: blastn -query GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg186a624d-97bb-43f0-9cdd-849a27c3f92b/dqc_reference/reference_markers_gtdb.fasta -out GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 00:46:59,349] [INFO] Task succeeded: Blastn
[2023-07-01 00:46:59,353] [INFO] Selected 15 target genomes.
[2023-07-01 00:46:59,354] [INFO] Target genome list was writen to GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 00:46:59,366] [INFO] Task started: fastANI
[2023-07-01 00:46:59,367] [INFO] Running command: fastANI --query /var/lib/cwl/stge0601acf-9b4d-4ad6-b2cc-b799d86b917b/GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna.gz --refList GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 00:47:07,383] [INFO] Task succeeded: fastANI
[2023-07-01 00:47:07,408] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 00:47:07,409] [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_017876395.1	s__Nesterenkonia lacusekhoensis	93.6422	369	393	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	89.2474	362	393	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	79.9426	223	393	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	79.9049	244	393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220985.1	s__Nesterenkonia sp000220985	79.859	220	393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017347085.1	s__Nesterenkonia sp017347085	79.8114	219	393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013410745.1	s__Nesterenkonia xinjiangensis	79.8114	217	393	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	79.7661	216	393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_013410215.1	s__Nesterenkonia sandarakina	79.762	214	393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	97.10	97.05	0.88	0.86	3	-
GCF_014873955.1	s__Nesterenkonia lutea	79.5834	199	393	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	79.5129	200	393	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	79.3055	176	393	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	79.2225	203	393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455245.1	s__Nesterenkonia massiliensis	78.9427	173	393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008711175.1	s__Nesterenkonia sp008711175	78.6565	181	393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 00:47:07,411] [INFO] GTDB search result was written to GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/result_gtdb.tsv
[2023-07-01 00:47:07,412] [INFO] ===== GTDB Search completed =====
[2023-07-01 00:47:07,419] [INFO] DFAST_QC result json was written to GCA_946221825.1_rLcxdbAhAR_bin.25.MAG_genomic.fna/dqc_result.json
[2023-07-01 00:47:07,419] [INFO] DFAST_QC completed!
[2023-07-01 00:47:07,419] [INFO] Total running time: 0h0m47s