[2024-01-24 13:40:34,952] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,957] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,957] [INFO] DQC Reference Directory: /var/lib/cwl/stg48153986-3f5f-495e-82ec-1f038c4fa695/dqc_reference
[2024-01-24 13:40:36,347] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,355] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,355] [INFO] Running command: gunzip -c /var/lib/cwl/stgce4f7d2e-8f58-4add-b0d0-ed75723f9769/GCF_000419445.1_ASM41944v1_genomic.fna.gz | prodigal -d GCF_000419445.1_ASM41944v1_genomic.fna/cds.fna -a GCF_000419445.1_ASM41944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:44,646] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:44,646] [INFO] Task started: HMMsearch
[2024-01-24 13:40:44,647] [INFO] Running command: hmmsearch --tblout GCF_000419445.1_ASM41944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48153986-3f5f-495e-82ec-1f038c4fa695/dqc_reference/reference_markers.hmm GCF_000419445.1_ASM41944v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:44,926] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:44,927] [INFO] Found 6/6 markers.
[2024-01-24 13:40:44,968] [INFO] Query marker FASTA was written to GCF_000419445.1_ASM41944v1_genomic.fna/markers.fasta
[2024-01-24 13:40:44,969] [INFO] Task started: Blastn
[2024-01-24 13:40:44,969] [INFO] Running command: blastn -query GCF_000419445.1_ASM41944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48153986-3f5f-495e-82ec-1f038c4fa695/dqc_reference/reference_markers.fasta -out GCF_000419445.1_ASM41944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:46,336] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:46,339] [INFO] Selected 22 target genomes.
[2024-01-24 13:40:46,339] [INFO] Target genome list was writen to GCF_000419445.1_ASM41944v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:46,348] [INFO] Task started: fastANI
[2024-01-24 13:40:46,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgce4f7d2e-8f58-4add-b0d0-ed75723f9769/GCF_000419445.1_ASM41944v1_genomic.fna.gz --refList GCF_000419445.1_ASM41944v1_genomic.fna/target_genomes.txt --output GCF_000419445.1_ASM41944v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:01,507] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:01,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48153986-3f5f-495e-82ec-1f038c4fa695/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:01,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48153986-3f5f-495e-82ec-1f038c4fa695/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:01,526] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:01,526] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:01,526] [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
Gryllotalpicola ginsengisoli	strain=DSM 22003	GCA_000419445.1	444608	444608	type	True	100.0	970	970	95	conclusive
Gryllotalpicola protaetiae	strain=2DFW10M-5	GCA_003627055.1	2419771	2419771	type	True	82.3439	639	970	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	79.6036	361	970	95	below_threshold
Leifsonia soli	strain=DSM 23871	GCA_013408745.1	582665	582665	type	True	79.5702	437	970	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	79.5421	475	970	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	79.4211	467	970	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.2887	476	970	95	below_threshold
Agromyces binzhouensis	strain=CGMCC 4.7180	GCA_004135055.1	1817495	1817495	type	True	79.259	327	970	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	79.2305	436	970	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	79.1837	446	970	95	below_threshold
Agromyces terreus	strain=JCM 14581	GCA_009749465.1	424795	424795	type	True	79.0604	443	970	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.9802	410	970	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.8387	418	970	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.7896	412	970	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.784	404	970	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	78.7089	411	970	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.682	395	970	95	below_threshold
Amnibacterium setariae	strain=DD4a	GCA_003581425.1	2306585	2306585	type	True	78.5955	405	970	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.5953	386	970	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	78.5789	372	970	95	below_threshold
Frigoribacterium faeni	strain=DSM 10309	GCA_014137965.1	145483	145483	type	True	78.48	377	970	95	below_threshold
Labedella populi	strain=8H24J-4-2	GCA_004078655.1	2498850	2498850	type	True	78.0401	301	970	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:01,528] [INFO] DFAST Taxonomy check result was written to GCF_000419445.1_ASM41944v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:01,529] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:01,529] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:01,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48153986-3f5f-495e-82ec-1f038c4fa695/dqc_reference/checkm_data
[2024-01-24 13:41:01,530] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:01,560] [INFO] Task started: CheckM
[2024-01-24 13:41:01,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000419445.1_ASM41944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000419445.1_ASM41944v1_genomic.fna/checkm_input GCF_000419445.1_ASM41944v1_genomic.fna/checkm_result
[2024-01-24 13:41:44,082] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:44,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:44,102] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:44,103] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:44,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000419445.1_ASM41944v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:44,104] [INFO] Task started: Blastn
[2024-01-24 13:41:44,104] [INFO] Running command: blastn -query GCF_000419445.1_ASM41944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48153986-3f5f-495e-82ec-1f038c4fa695/dqc_reference/reference_markers_gtdb.fasta -out GCF_000419445.1_ASM41944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:46,294] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:46,306] [INFO] Selected 18 target genomes.
[2024-01-24 13:41:46,306] [INFO] Target genome list was writen to GCF_000419445.1_ASM41944v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:46,332] [INFO] Task started: fastANI
[2024-01-24 13:41:46,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgce4f7d2e-8f58-4add-b0d0-ed75723f9769/GCF_000419445.1_ASM41944v1_genomic.fna.gz --refList GCF_000419445.1_ASM41944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000419445.1_ASM41944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:00,388] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:00,403] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:00,403] [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_000419445.1	s__Gryllotalpicola ginsengisoli	100.0	970	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gryllotalpicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003627055.1	s__Gryllotalpicola protaetiae	82.4393	631	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gryllotalpicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009780695.1	s__Gryllotalpicola sp009780695	82.2818	547	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gryllotalpicola	95.0	99.84	99.84	0.94	0.94	2	-
GCF_003664105.1	s__Leifsonia sp003664105	79.807	455	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003367665.1	s__Leifsonia sp003367665	79.7718	482	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410375.1	s__Leifsonia shinshuensis	79.528	478	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217625.1	s__Leifsonia shinshuensis_A	79.4996	496	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633535.1	s__Leifsonia aquatica_A	79.3868	437	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789225.1	s__WSTA01 sp009789225	79.2719	427	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__WSTA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729855.1	s__Agromyces luteolus	79.231	441	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749465.1	s__Agromyces terreus	79.1052	439	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959775.1	s__Agromyces sp004959775	79.1041	440	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012985205.1	s__Humibacter sp012985205	78.9571	417	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Humibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761235.1	s__Frigoribacterium faeni_A	78.8594	414	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364285.1	s__Frigoribacterium sp004364285	78.6581	411	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	96.77	95.63	0.92	0.87	5	-
GCA_013204985.1	s__Rathayibacter sp013204985	78.3915	390	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004078655.1	s__Labedella populi	78.0492	300	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719255.1	s__Gulosibacter sp012719255	77.6817	303	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:00,405] [INFO] GTDB search result was written to GCF_000419445.1_ASM41944v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:00,405] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:00,410] [INFO] DFAST_QC result json was written to GCF_000419445.1_ASM41944v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:00,410] [INFO] DFAST_QC completed!
[2024-01-24 13:42:00,410] [INFO] Total running time: 0h1m25s