[2024-01-24 14:22:04,570] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:04,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:04,572] [INFO] DQC Reference Directory: /var/lib/cwl/stg080d5f98-c4a6-4746-a70e-3b15775bcab6/dqc_reference
[2024-01-24 14:22:05,993] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,994] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,994] [INFO] Running command: gunzip -c /var/lib/cwl/stg985f1552-d211-448c-9610-affcbd721fef/GCF_014642675.1_ASM1464267v1_genomic.fna.gz | prodigal -d GCF_014642675.1_ASM1464267v1_genomic.fna/cds.fna -a GCF_014642675.1_ASM1464267v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:15,164] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:15,165] [INFO] Task started: HMMsearch
[2024-01-24 14:22:15,165] [INFO] Running command: hmmsearch --tblout GCF_014642675.1_ASM1464267v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg080d5f98-c4a6-4746-a70e-3b15775bcab6/dqc_reference/reference_markers.hmm GCF_014642675.1_ASM1464267v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:15,485] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:15,486] [INFO] Found 6/6 markers.
[2024-01-24 14:22:15,523] [INFO] Query marker FASTA was written to GCF_014642675.1_ASM1464267v1_genomic.fna/markers.fasta
[2024-01-24 14:22:15,523] [INFO] Task started: Blastn
[2024-01-24 14:22:15,523] [INFO] Running command: blastn -query GCF_014642675.1_ASM1464267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg080d5f98-c4a6-4746-a70e-3b15775bcab6/dqc_reference/reference_markers.fasta -out GCF_014642675.1_ASM1464267v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:16,678] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:16,681] [INFO] Selected 14 target genomes.
[2024-01-24 14:22:16,682] [INFO] Target genome list was writen to GCF_014642675.1_ASM1464267v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:16,686] [INFO] Task started: fastANI
[2024-01-24 14:22:16,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg985f1552-d211-448c-9610-affcbd721fef/GCF_014642675.1_ASM1464267v1_genomic.fna.gz --refList GCF_014642675.1_ASM1464267v1_genomic.fna/target_genomes.txt --output GCF_014642675.1_ASM1464267v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:26,112] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:26,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg080d5f98-c4a6-4746-a70e-3b15775bcab6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:26,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg080d5f98-c4a6-4746-a70e-3b15775bcab6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:26,129] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:26,130] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:26,130] [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 cremea	strain=CGMCC 1.15388	GCA_014642675.1	1882340	1882340	type	True	100.0	1009	1010	95	conclusive
Nesterenkonia lacusekhoensis	strain=DSM 12544	GCA_017876395.1	150832	150832	type	True	89.111	754	1010	95	below_threshold
Nesterenkonia sandarakina	strain=DSM 15664	GCA_013410215.1	272918	272918	type	True	80.2726	470	1010	95	below_threshold
Nesterenkonia jeotgali	strain=DSM 19081	GCA_014138825.1	317018	317018	type	True	80.1954	474	1010	95	below_threshold
Nesterenkonia sedimenti	strain=MY13	GCA_012641515.1	1463632	1463632	type	True	80.1231	400	1010	95	below_threshold
Nesterenkonia halophila	strain=DSM 16378	GCA_009467795.1	302044	302044	type	True	80.0716	383	1010	95	below_threshold
Nesterenkonia populi	strain=DSM 27959	GCA_007994735.1	1591087	1591087	type	True	80.0041	429	1010	95	below_threshold
Nesterenkonia xinjiangensis	strain=DSM 15475	GCA_013410745.1	225327	225327	type	True	79.931	516	1010	95	below_threshold
Nesterenkonia halotolerans	strain=DSM 15474	GCA_014874065.1	225325	225325	type	True	79.8926	465	1010	95	below_threshold
Nesterenkonia ebinurensis	strain=MD2	GCA_008711175.1	2608252	2608252	type	True	79.6192	370	1010	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	79.1865	316	1010	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.9534	255	1010	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.5114	200	1010	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.4064	212	1010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:26,140] [INFO] DFAST Taxonomy check result was written to GCF_014642675.1_ASM1464267v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:26,141] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:26,141] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:26,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg080d5f98-c4a6-4746-a70e-3b15775bcab6/dqc_reference/checkm_data
[2024-01-24 14:22:26,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:26,185] [INFO] Task started: CheckM
[2024-01-24 14:22:26,185] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014642675.1_ASM1464267v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014642675.1_ASM1464267v1_genomic.fna/checkm_input GCF_014642675.1_ASM1464267v1_genomic.fna/checkm_result
[2024-01-24 14:22:59,441] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:59,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:59,503] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:59,503] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:59,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014642675.1_ASM1464267v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:59,504] [INFO] Task started: Blastn
[2024-01-24 14:22:59,504] [INFO] Running command: blastn -query GCF_014642675.1_ASM1464267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg080d5f98-c4a6-4746-a70e-3b15775bcab6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014642675.1_ASM1464267v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:01,151] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:01,155] [INFO] Selected 13 target genomes.
[2024-01-24 14:23:01,156] [INFO] Target genome list was writen to GCF_014642675.1_ASM1464267v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:01,168] [INFO] Task started: fastANI
[2024-01-24 14:23:01,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg985f1552-d211-448c-9610-affcbd721fef/GCF_014642675.1_ASM1464267v1_genomic.fna.gz --refList GCF_014642675.1_ASM1464267v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014642675.1_ASM1464267v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:09,913] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:09,932] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:09,933] [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_014642675.1	s__Nesterenkonia cremea	100.0	1009	1010	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_017876395.1	s__Nesterenkonia lacusekhoensis	89.12	754	1010	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	80.64	533	1010	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	80.4738	476	1010	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	80.3781	494	1010	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	80.2731	470	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	97.10	97.05	0.88	0.86	3	-
GCF_003003175.1	s__Nesterenkonia sandarakina_A	80.211	487	1010	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	80.0657	383	1010	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	80.0117	428	1010	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	79.9766	483	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_013410745.1	s__Nesterenkonia xinjiangensis	79.9181	517	1010	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	79.9044	464	1010	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	79.6323	369	1010	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 14:23:09,934] [INFO] GTDB search result was written to GCF_014642675.1_ASM1464267v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:09,935] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:09,939] [INFO] DFAST_QC result json was written to GCF_014642675.1_ASM1464267v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:09,939] [INFO] DFAST_QC completed!
[2024-01-24 14:23:09,939] [INFO] Total running time: 0h1m5s