[2024-01-24 15:09:55,280] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:09:55,283] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:09:55,284] [INFO] DQC Reference Directory: /var/lib/cwl/stgc36993e8-dc71-4fab-8457-03b4d7a520ca/dqc_reference
[2024-01-24 15:09:58,166] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:09:58,169] [INFO] Task started: Prodigal
[2024-01-24 15:09:58,169] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c579373-0362-42d8-93b9-5a38e981a0ed/GCF_008711175.1_ASM871117v1_genomic.fna.gz | prodigal -d GCF_008711175.1_ASM871117v1_genomic.fna/cds.fna -a GCF_008711175.1_ASM871117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:10,070] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:10,071] [INFO] Task started: HMMsearch
[2024-01-24 15:10:10,071] [INFO] Running command: hmmsearch --tblout GCF_008711175.1_ASM871117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc36993e8-dc71-4fab-8457-03b4d7a520ca/dqc_reference/reference_markers.hmm GCF_008711175.1_ASM871117v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:10,458] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:10,460] [INFO] Found 6/6 markers.
[2024-01-24 15:10:10,508] [INFO] Query marker FASTA was written to GCF_008711175.1_ASM871117v1_genomic.fna/markers.fasta
[2024-01-24 15:10:10,509] [INFO] Task started: Blastn
[2024-01-24 15:10:10,509] [INFO] Running command: blastn -query GCF_008711175.1_ASM871117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc36993e8-dc71-4fab-8457-03b4d7a520ca/dqc_reference/reference_markers.fasta -out GCF_008711175.1_ASM871117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:11,601] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:11,605] [INFO] Selected 15 target genomes.
[2024-01-24 15:10:11,606] [INFO] Target genome list was writen to GCF_008711175.1_ASM871117v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:11,612] [INFO] Task started: fastANI
[2024-01-24 15:10:11,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c579373-0362-42d8-93b9-5a38e981a0ed/GCF_008711175.1_ASM871117v1_genomic.fna.gz --refList GCF_008711175.1_ASM871117v1_genomic.fna/target_genomes.txt --output GCF_008711175.1_ASM871117v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:21,269] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:21,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc36993e8-dc71-4fab-8457-03b4d7a520ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:21,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc36993e8-dc71-4fab-8457-03b4d7a520ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:21,282] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:21,282] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:21,283] [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 ebinurensis	strain=MD2	GCA_008711175.1	2608252	2608252	type	True	100.0	1226	1226	95	conclusive
Nesterenkonia alkaliphila	strain=F10	GCA_009758175.1	1463631	1463631	type	True	84.0193	662	1226	95	below_threshold
Nesterenkonia alkaliphila	strain=CGMCC 1.12781	GCA_014639295.1	1463631	1463631	type	True	83.9865	670	1226	95	below_threshold
Nesterenkonia muleiensis	strain=RB2	GCA_003600155.1	2282648	2282648	type	True	81.7923	551	1226	95	below_threshold
Nesterenkonia sedimenti	strain=MY13	GCA_012641515.1	1463632	1463632	type	True	80.1672	460	1226	95	below_threshold
Nesterenkonia cremea	strain=CGMCC 1.15388	GCA_014642675.1	1882340	1882340	type	True	79.5788	386	1226	95	below_threshold
Nesterenkonia sphaerica	strain=GY239	GCA_005771565.1	1804988	1804988	type	True	79.4137	379	1226	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	79.1807	330	1226	95	below_threshold
Nesterenkonia jeotgali	strain=DSM 19081	GCA_014138825.1	317018	317018	type	True	79.0674	357	1226	95	below_threshold
Nesterenkonia massiliensis	strain=NP1	GCA_000455245.1	1232429	1232429	type	True	79.063	331	1226	95	below_threshold
Nesterenkonia alba	strain=DSM 19423	GCA_000421745.1	515814	515814	type	True	78.6558	310	1226	95	below_threshold
Nesterenkonia halotolerans	strain=DSM 15474	GCA_014874065.1	225325	225325	type	True	78.6411	313	1226	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	77.3544	88	1226	95	below_threshold
Arthrobacter terrae	strain=Z1-20	GCA_015708085.1	2935737	2935737	type	True	77.1295	57	1226	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	76.9408	122	1226	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:21,285] [INFO] DFAST Taxonomy check result was written to GCF_008711175.1_ASM871117v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:21,286] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:21,286] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:21,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc36993e8-dc71-4fab-8457-03b4d7a520ca/dqc_reference/checkm_data
[2024-01-24 15:10:21,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:21,330] [INFO] Task started: CheckM
[2024-01-24 15:10:21,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008711175.1_ASM871117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008711175.1_ASM871117v1_genomic.fna/checkm_input GCF_008711175.1_ASM871117v1_genomic.fna/checkm_result
[2024-01-24 15:10:58,087] [INFO] Task succeeded: CheckM
[2024-01-24 15:10:58,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:10:58,108] [INFO] ===== Completeness check finished =====
[2024-01-24 15:10:58,109] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:10:58,109] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008711175.1_ASM871117v1_genomic.fna/markers.fasta)
[2024-01-24 15:10:58,110] [INFO] Task started: Blastn
[2024-01-24 15:10:58,110] [INFO] Running command: blastn -query GCF_008711175.1_ASM871117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc36993e8-dc71-4fab-8457-03b4d7a520ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_008711175.1_ASM871117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:59,523] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:59,527] [INFO] Selected 13 target genomes.
[2024-01-24 15:10:59,528] [INFO] Target genome list was writen to GCF_008711175.1_ASM871117v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:10:59,539] [INFO] Task started: fastANI
[2024-01-24 15:10:59,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c579373-0362-42d8-93b9-5a38e981a0ed/GCF_008711175.1_ASM871117v1_genomic.fna.gz --refList GCF_008711175.1_ASM871117v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008711175.1_ASM871117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:08,089] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:08,107] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:08,107] [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_008711175.1	s__Nesterenkonia sp008711175	100.0	1226	1226	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_009758175.1	s__Nesterenkonia alkaliphila	84.0231	662	1226	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003600155.1	s__Nesterenkonia muleiensis	81.7788	552	1226	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641515.1	s__Nesterenkonia sp012641515	80.1548	461	1226	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	79.5923	385	1226	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771565.1	s__Nesterenkonia sphaerica	79.3937	381	1226	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	79.1807	330	1226	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	79.134	379	1226	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	79.0501	332	1226	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000421745.1	s__Nesterenkonia alba	78.6643	311	1226	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	78.6278	314	1226	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019173455.1	s__Nesterenkonia sp019173455	78.5421	303	1226	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771525.1	s__Nesterenkonia salmonea	78.4228	316	1226	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 15:11:08,109] [INFO] GTDB search result was written to GCF_008711175.1_ASM871117v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:08,109] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:08,113] [INFO] DFAST_QC result json was written to GCF_008711175.1_ASM871117v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:08,114] [INFO] DFAST_QC completed!
[2024-01-24 15:11:08,114] [INFO] Total running time: 0h1m13s