[2024-01-24 13:31:34,126] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:34,128] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:34,129] [INFO] DQC Reference Directory: /var/lib/cwl/stg6da76597-8f8f-4690-908a-59536b868710/dqc_reference
[2024-01-24 13:31:35,397] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:35,398] [INFO] Task started: Prodigal
[2024-01-24 13:31:35,398] [INFO] Running command: gunzip -c /var/lib/cwl/stg28639756-fe8f-48dc-9ff6-bfd4ee72c034/GCF_014138825.1_ASM1413882v1_genomic.fna.gz | prodigal -d GCF_014138825.1_ASM1413882v1_genomic.fna/cds.fna -a GCF_014138825.1_ASM1413882v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:44,749] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:44,749] [INFO] Task started: HMMsearch
[2024-01-24 13:31:44,749] [INFO] Running command: hmmsearch --tblout GCF_014138825.1_ASM1413882v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6da76597-8f8f-4690-908a-59536b868710/dqc_reference/reference_markers.hmm GCF_014138825.1_ASM1413882v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:45,029] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:45,030] [INFO] Found 6/6 markers.
[2024-01-24 13:31:45,064] [INFO] Query marker FASTA was written to GCF_014138825.1_ASM1413882v1_genomic.fna/markers.fasta
[2024-01-24 13:31:45,065] [INFO] Task started: Blastn
[2024-01-24 13:31:45,065] [INFO] Running command: blastn -query GCF_014138825.1_ASM1413882v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6da76597-8f8f-4690-908a-59536b868710/dqc_reference/reference_markers.fasta -out GCF_014138825.1_ASM1413882v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:46,223] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:46,226] [INFO] Selected 11 target genomes.
[2024-01-24 13:31:46,226] [INFO] Target genome list was writen to GCF_014138825.1_ASM1413882v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:46,231] [INFO] Task started: fastANI
[2024-01-24 13:31:46,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg28639756-fe8f-48dc-9ff6-bfd4ee72c034/GCF_014138825.1_ASM1413882v1_genomic.fna.gz --refList GCF_014138825.1_ASM1413882v1_genomic.fna/target_genomes.txt --output GCF_014138825.1_ASM1413882v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:54,016] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:54,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6da76597-8f8f-4690-908a-59536b868710/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:54,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6da76597-8f8f-4690-908a-59536b868710/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:54,027] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:31:54,028] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:31:54,028] [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 jeotgali	strain=DSM 19081	GCA_014138825.1	317018	317018	type	True	100.0	1000	1000	95	inconclusive
Nesterenkonia sandarakina	strain=DSM 15664	GCA_013410215.1	272918	272918	type	True	97.1427	862	1000	95	inconclusive
Nesterenkonia aurantiaca	strain=DSM 27373	GCA_004364585.1	1436010	1436010	type	True	87.5012	802	1000	95	below_threshold
Nesterenkonia lutea	strain=DSM 15666	GCA_014873955.1	272919	272919	type	True	83.7493	683	1000	95	below_threshold
Nesterenkonia halotolerans	strain=DSM 15474	GCA_014874065.1	225325	225325	type	True	83.7322	709	1000	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	79.2252	307	1000	95	below_threshold
Nesterenkonia ebinurensis	strain=MD2	GCA_008711175.1	2608252	2608252	type	True	78.9628	365	1000	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	77.6869	180	1000	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	77.2881	136	1000	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	77.1187	159	1000	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:54,029] [INFO] DFAST Taxonomy check result was written to GCF_014138825.1_ASM1413882v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:54,030] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:54,030] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:54,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6da76597-8f8f-4690-908a-59536b868710/dqc_reference/checkm_data
[2024-01-24 13:31:54,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:54,065] [INFO] Task started: CheckM
[2024-01-24 13:31:54,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014138825.1_ASM1413882v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014138825.1_ASM1413882v1_genomic.fna/checkm_input GCF_014138825.1_ASM1413882v1_genomic.fna/checkm_result
[2024-01-24 13:32:29,847] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:29,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:29,866] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:29,866] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:29,867] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014138825.1_ASM1413882v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:29,867] [INFO] Task started: Blastn
[2024-01-24 13:32:29,867] [INFO] Running command: blastn -query GCF_014138825.1_ASM1413882v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6da76597-8f8f-4690-908a-59536b868710/dqc_reference/reference_markers_gtdb.fasta -out GCF_014138825.1_ASM1413882v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:31,620] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:31,624] [INFO] Selected 9 target genomes.
[2024-01-24 13:32:31,624] [INFO] Target genome list was writen to GCF_014138825.1_ASM1413882v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:31,638] [INFO] Task started: fastANI
[2024-01-24 13:32:31,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg28639756-fe8f-48dc-9ff6-bfd4ee72c034/GCF_014138825.1_ASM1413882v1_genomic.fna.gz --refList GCF_014138825.1_ASM1413882v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014138825.1_ASM1413882v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:37,888] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:37,895] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:37,895] [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_013410215.1	s__Nesterenkonia sandarakina	97.1427	862	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	97.10	97.05	0.88	0.86	3	conclusive
GCF_003003175.1	s__Nesterenkonia sandarakina_A	87.9087	836	1000	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	87.8008	835	1000	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	87.4902	803	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_014873955.1	s__Nesterenkonia lutea	83.7493	683	1000	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	83.7022	709	1000	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	83.3907	690	1000	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 13:32:37,899] [INFO] GTDB search result was written to GCF_014138825.1_ASM1413882v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:37,899] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:37,903] [INFO] DFAST_QC result json was written to GCF_014138825.1_ASM1413882v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:37,903] [INFO] DFAST_QC completed!
[2024-01-24 13:32:37,903] [INFO] Total running time: 0h1m4s