[2024-01-24 13:57:00,696] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:00,698] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:00,698] [INFO] DQC Reference Directory: /var/lib/cwl/stgb97bcd16-b360-4df1-bbce-b1c5b9957ff5/dqc_reference
[2024-01-24 13:57:02,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:02,178] [INFO] Task started: Prodigal
[2024-01-24 13:57:02,178] [INFO] Running command: gunzip -c /var/lib/cwl/stg88f45639-eb2c-4b85-b335-0cc3f3a555e3/GCF_003667545.1_ASM366754v1_genomic.fna.gz | prodigal -d GCF_003667545.1_ASM366754v1_genomic.fna/cds.fna -a GCF_003667545.1_ASM366754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:11,564] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:11,564] [INFO] Task started: HMMsearch
[2024-01-24 13:57:11,564] [INFO] Running command: hmmsearch --tblout GCF_003667545.1_ASM366754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb97bcd16-b360-4df1-bbce-b1c5b9957ff5/dqc_reference/reference_markers.hmm GCF_003667545.1_ASM366754v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:11,875] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:11,876] [INFO] Found 6/6 markers.
[2024-01-24 13:57:11,903] [INFO] Query marker FASTA was written to GCF_003667545.1_ASM366754v1_genomic.fna/markers.fasta
[2024-01-24 13:57:11,904] [INFO] Task started: Blastn
[2024-01-24 13:57:11,904] [INFO] Running command: blastn -query GCF_003667545.1_ASM366754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb97bcd16-b360-4df1-bbce-b1c5b9957ff5/dqc_reference/reference_markers.fasta -out GCF_003667545.1_ASM366754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:13,061] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:13,068] [INFO] Selected 14 target genomes.
[2024-01-24 13:57:13,069] [INFO] Target genome list was writen to GCF_003667545.1_ASM366754v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:13,077] [INFO] Task started: fastANI
[2024-01-24 13:57:13,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg88f45639-eb2c-4b85-b335-0cc3f3a555e3/GCF_003667545.1_ASM366754v1_genomic.fna.gz --refList GCF_003667545.1_ASM366754v1_genomic.fna/target_genomes.txt --output GCF_003667545.1_ASM366754v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:22,975] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:22,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb97bcd16-b360-4df1-bbce-b1c5b9957ff5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:22,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb97bcd16-b360-4df1-bbce-b1c5b9957ff5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:22,990] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:22,990] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:22,990] [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
Mycetocola manganoxydans	strain=CCTCC AB209002	GCA_003667545.1	699879	699879	type	True	100.0	1006	1008	95	conclusive
Mycetocola manganoxydans	strain=KCTC 19753	GCA_014651755.1	699879	699879	type	True	99.9961	1006	1008	95	conclusive
Mycetocola miduiensis	strain=CGMCC 1.11101	GCA_900115155.1	995034	995034	type	True	81.9421	631	1008	95	below_threshold
Mycetocola zhujimingii	strain=449 = CGMCC 1.16372	GCA_003065425.1	2079792	2079792	type	True	80.5955	533	1008	95	below_threshold
Mycetocola zhadangensis	strain=ZD1-4	GCA_003668565.1	1164595	1164595	type	True	80.1439	493	1008	95	below_threshold
Mycetocola zhadangensis	strain=CGMCC 1.12042	GCA_014636455.1	1164595	1164595	type	True	80.1291	503	1008	95	below_threshold
Microterricola gilva	strain=DSM 18319	GCA_004217495.1	393267	393267	type	True	78.6981	333	1008	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	78.2735	218	1008	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	78.1992	345	1008	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	78.1393	259	1008	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.1052	273	1008	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.0988	328	1008	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.0976	338	1008	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	77.679	256	1008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:22,992] [INFO] DFAST Taxonomy check result was written to GCF_003667545.1_ASM366754v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:22,993] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:22,993] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:22,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb97bcd16-b360-4df1-bbce-b1c5b9957ff5/dqc_reference/checkm_data
[2024-01-24 13:57:22,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:23,031] [INFO] Task started: CheckM
[2024-01-24 13:57:23,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003667545.1_ASM366754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003667545.1_ASM366754v1_genomic.fna/checkm_input GCF_003667545.1_ASM366754v1_genomic.fna/checkm_result
[2024-01-24 13:58:06,640] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:06,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:06,662] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:06,662] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:06,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003667545.1_ASM366754v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:06,663] [INFO] Task started: Blastn
[2024-01-24 13:58:06,663] [INFO] Running command: blastn -query GCF_003667545.1_ASM366754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb97bcd16-b360-4df1-bbce-b1c5b9957ff5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003667545.1_ASM366754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:08,352] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:08,357] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:08,358] [INFO] Target genome list was writen to GCF_003667545.1_ASM366754v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:08,370] [INFO] Task started: fastANI
[2024-01-24 13:58:08,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg88f45639-eb2c-4b85-b335-0cc3f3a555e3/GCF_003667545.1_ASM366754v1_genomic.fna.gz --refList GCF_003667545.1_ASM366754v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003667545.1_ASM366754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:15,925] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:15,935] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:15,935] [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_003667545.1	s__Mycetocola_A manganoxydans	100.0	1006	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900115155.1	s__Mycetocola_A miduiensis	81.9461	631	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752285.1	s__Mycetocola_A sp015752285	81.6885	650	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003065425.1	s__Mycetocola_A zhujimingii	80.6072	532	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	98.22	98.22	0.95	0.95	2	-
GCF_003668565.1	s__Mycetocola_A zhadangensis	80.1372	494	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004801905.1	s__Leifsonia_A flavus	78.3821	281	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142065.1	s__Agromyces cerinus	78.2228	332	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003067705.1	s__Planctomonas deserti	78.2042	311	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Planctomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749405.1	s__Agromyces lapidis	78.185	347	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216665.1	s__Agromyces ramosus	78.1757	328	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:15,937] [INFO] GTDB search result was written to GCF_003667545.1_ASM366754v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:15,937] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:15,941] [INFO] DFAST_QC result json was written to GCF_003667545.1_ASM366754v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:15,941] [INFO] DFAST_QC completed!
[2024-01-24 13:58:15,941] [INFO] Total running time: 0h1m15s