[2024-01-25 17:44:35,783] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:35,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:35,785] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb80e28a-d893-406c-94d0-f6c235c7942d/dqc_reference
[2024-01-25 17:44:36,926] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:36,926] [INFO] Task started: Prodigal
[2024-01-25 17:44:36,927] [INFO] Running command: gunzip -c /var/lib/cwl/stgd70fd06b-e63c-412c-93db-3962c2f82b3b/GCF_000975115.1_ASM97511v1_genomic.fna.gz | prodigal -d GCF_000975115.1_ASM97511v1_genomic.fna/cds.fna -a GCF_000975115.1_ASM97511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:45,213] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:45,213] [INFO] Task started: HMMsearch
[2024-01-25 17:44:45,214] [INFO] Running command: hmmsearch --tblout GCF_000975115.1_ASM97511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb80e28a-d893-406c-94d0-f6c235c7942d/dqc_reference/reference_markers.hmm GCF_000975115.1_ASM97511v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:45,393] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:45,394] [INFO] Found 6/6 markers.
[2024-01-25 17:44:45,424] [INFO] Query marker FASTA was written to GCF_000975115.1_ASM97511v1_genomic.fna/markers.fasta
[2024-01-25 17:44:45,424] [INFO] Task started: Blastn
[2024-01-25 17:44:45,424] [INFO] Running command: blastn -query GCF_000975115.1_ASM97511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb80e28a-d893-406c-94d0-f6c235c7942d/dqc_reference/reference_markers.fasta -out GCF_000975115.1_ASM97511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:46,347] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:46,350] [INFO] Selected 17 target genomes.
[2024-01-25 17:44:46,350] [INFO] Target genome list was writen to GCF_000975115.1_ASM97511v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:46,362] [INFO] Task started: fastANI
[2024-01-25 17:44:46,362] [INFO] Running command: fastANI --query /var/lib/cwl/stgd70fd06b-e63c-412c-93db-3962c2f82b3b/GCF_000975115.1_ASM97511v1_genomic.fna.gz --refList GCF_000975115.1_ASM97511v1_genomic.fna/target_genomes.txt --output GCF_000975115.1_ASM97511v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:55,622] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:55,622] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb80e28a-d893-406c-94d0-f6c235c7942d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:55,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb80e28a-d893-406c-94d0-f6c235c7942d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:55,633] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:44:55,633] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:55,633] [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
Demequina oxidasica	strain=NBRC 106264	GCA_000975115.1	676199	676199	type	True	100.0	870	871	95	conclusive
Demequina aurantiaca	strain=NBRC 106265	GCA_000975135.1	676200	676200	type	True	87.269	745	871	95	below_threshold
Demequina activiva	strain=NBRC 110675	GCA_016862815.1	1582364	1582364	type	True	78.942	281	871	95	below_threshold
Demequina maris	strain=NBRC 109392	GCA_000971155.1	1638982	1638982	type	True	78.8302	320	871	95	below_threshold
Demequina iriomotensis	strain=NBRC 109399	GCA_000971395.1	1536641	1536641	type	True	78.8034	290	871	95	below_threshold
Demequina silvatica	strain=NBRC 109395	GCA_000971215.1	1638988	1638988	type	True	78.7863	301	871	95	below_threshold
Demequina rhizosphaerae	strain=NBRC 109397	GCA_000971255.1	1638985	1638985	type	True	78.7548	307	871	95	below_threshold
Demequina mangrovi	strain=DSM 24868	GCA_900109245.1	1043493	1043493	type	True	78.6998	301	871	95	below_threshold
Demequina pelophila	strain=NBRC 109393	GCA_000971175.1	1638984	1638984	type	True	78.6923	282	871	95	below_threshold
Demequina gelatinilytica	strain=NBRC 109390	GCA_000971115.1	1638980	1638980	type	True	78.692	301	871	95	below_threshold
Demequina mangrovi	strain=NBRC 105856	GCA_000759715.1	1043493	1043493	type	True	78.6793	306	871	95	below_threshold
Demequina phytophila	strain=NBRC 109391	GCA_000971135.1	1638981	1638981	type	True	78.6562	303	871	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.3732	141	871	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	76.9984	110	871	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	76.7132	92	871	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	76.5091	84	871	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	76.4641	71	871	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:55,635] [INFO] DFAST Taxonomy check result was written to GCF_000975115.1_ASM97511v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:55,635] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:55,636] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:55,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb80e28a-d893-406c-94d0-f6c235c7942d/dqc_reference/checkm_data
[2024-01-25 17:44:55,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:55,664] [INFO] Task started: CheckM
[2024-01-25 17:44:55,664] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000975115.1_ASM97511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000975115.1_ASM97511v1_genomic.fna/checkm_input GCF_000975115.1_ASM97511v1_genomic.fna/checkm_result
[2024-01-25 17:45:23,347] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:23,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:23,367] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:23,368] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:23,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000975115.1_ASM97511v1_genomic.fna/markers.fasta)
[2024-01-25 17:45:23,368] [INFO] Task started: Blastn
[2024-01-25 17:45:23,368] [INFO] Running command: blastn -query GCF_000975115.1_ASM97511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb80e28a-d893-406c-94d0-f6c235c7942d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000975115.1_ASM97511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:24,839] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:24,842] [INFO] Selected 17 target genomes.
[2024-01-25 17:45:24,842] [INFO] Target genome list was writen to GCF_000975115.1_ASM97511v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:24,865] [INFO] Task started: fastANI
[2024-01-25 17:45:24,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgd70fd06b-e63c-412c-93db-3962c2f82b3b/GCF_000975115.1_ASM97511v1_genomic.fna.gz --refList GCF_000975115.1_ASM97511v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000975115.1_ASM97511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:34,298] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:34,308] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:34,309] [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_000975115.1	s__Demequina oxidasica	100.0	870	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000975135.1	s__Demequina aurantiaca	87.269	745	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862815.1	s__Demequina activiva	78.942	281	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090175.1	s__Demequina sp002090175	78.93	278	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971195.1	s__Demequina soli	78.8291	294	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971395.1	s__Demequina iriomotensis	78.8186	289	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971215.1	s__Demequina silvatica	78.7863	301	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090135.1	s__Demequina sp002090135	78.7591	283	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090055.1	s__Demequina sp002090055	78.7237	299	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971175.1	s__Demequina pelophila	78.6851	283	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759715.1	s__Demequina mangrovi	78.6793	306	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000971135.1	s__Demequina phytophila	78.6431	304	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090155.1	s__Demequina sp002090155	78.6279	314	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090115.1	s__Demequina sp002090115	78.6107	250	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971235.1	s__Demequina subtropica	78.6096	300	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090075.1	s__Demequina sp002090075	78.5822	246	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000975095.1	s__Demequina aestuarii	78.4399	288	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:34,310] [INFO] GTDB search result was written to GCF_000975115.1_ASM97511v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:34,311] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:34,314] [INFO] DFAST_QC result json was written to GCF_000975115.1_ASM97511v1_genomic.fna/dqc_result.json
[2024-01-25 17:45:34,314] [INFO] DFAST_QC completed!
[2024-01-25 17:45:34,314] [INFO] Total running time: 0h0m59s