[2024-01-24 12:47:49,743] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:49,745] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:49,745] [INFO] DQC Reference Directory: /var/lib/cwl/stge2ab858b-c35d-4ff8-86f0-d82ed26be859/dqc_reference
[2024-01-24 12:47:50,953] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:50,954] [INFO] Task started: Prodigal
[2024-01-24 12:47:50,955] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf530f26-9296-4afb-9ec8-06c6c84c5e89/GCF_003667525.1_ASM366752v1_genomic.fna.gz | prodigal -d GCF_003667525.1_ASM366752v1_genomic.fna/cds.fna -a GCF_003667525.1_ASM366752v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:59,137] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:59,137] [INFO] Task started: HMMsearch
[2024-01-24 12:47:59,137] [INFO] Running command: hmmsearch --tblout GCF_003667525.1_ASM366752v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2ab858b-c35d-4ff8-86f0-d82ed26be859/dqc_reference/reference_markers.hmm GCF_003667525.1_ASM366752v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:59,373] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:59,375] [INFO] Found 6/6 markers.
[2024-01-24 12:47:59,402] [INFO] Query marker FASTA was written to GCF_003667525.1_ASM366752v1_genomic.fna/markers.fasta
[2024-01-24 12:47:59,403] [INFO] Task started: Blastn
[2024-01-24 12:47:59,403] [INFO] Running command: blastn -query GCF_003667525.1_ASM366752v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2ab858b-c35d-4ff8-86f0-d82ed26be859/dqc_reference/reference_markers.fasta -out GCF_003667525.1_ASM366752v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:00,565] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:00,570] [INFO] Selected 26 target genomes.
[2024-01-24 12:48:00,571] [INFO] Target genome list was writen to GCF_003667525.1_ASM366752v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:00,646] [INFO] Task started: fastANI
[2024-01-24 12:48:00,647] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf530f26-9296-4afb-9ec8-06c6c84c5e89/GCF_003667525.1_ASM366752v1_genomic.fna.gz --refList GCF_003667525.1_ASM366752v1_genomic.fna/target_genomes.txt --output GCF_003667525.1_ASM366752v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:15,806] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:15,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2ab858b-c35d-4ff8-86f0-d82ed26be859/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:15,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2ab858b-c35d-4ff8-86f0-d82ed26be859/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:15,830] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:48:15,831] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:48:15,831] [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
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	79.0623	292	1001	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	78.7937	281	1001	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	78.7486	386	1001	95	below_threshold
Plantibacter flavus	strain=VKM Ac-2504	GCA_900177615.1	150123	150123	type	True	78.7084	335	1001	95	below_threshold
Plantibacter flavus	strain=DSM 14012	GCA_003755125.1	150123	150123	type	True	78.6723	340	1001	95	below_threshold
Rathayibacter caricis	strain=DSM 15933	GCA_003044275.1	110936	110936	type	True	78.6463	359	1001	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.6174	352	1001	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	78.6054	366	1001	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	78.5655	354	1001	95	below_threshold
Labedella phragmitis	strain=11W25H-1	GCA_004078635.1	2498849	2498849	type	True	78.5482	321	1001	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	78.5359	357	1001	95	below_threshold
Labedella populi	strain=8H24J-4-2	GCA_004078655.1	2498850	2498850	type	True	78.5215	280	1001	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	78.4866	301	1001	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	78.457	283	1001	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	78.4553	289	1001	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.454	310	1001	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	78.4527	303	1001	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	78.4279	294	1001	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	78.4095	315	1001	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	78.3941	361	1001	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	78.355	324	1001	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.354	338	1001	95	below_threshold
Microbacterium marinum	strain=DSM 24947	GCA_014204835.1	421115	421115	type	True	78.35	263	1001	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	78.3444	322	1001	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.3088	332	1001	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	78.2892	301	1001	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:15,833] [INFO] DFAST Taxonomy check result was written to GCF_003667525.1_ASM366752v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:15,833] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:15,833] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:15,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2ab858b-c35d-4ff8-86f0-d82ed26be859/dqc_reference/checkm_data
[2024-01-24 12:48:15,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:15,865] [INFO] Task started: CheckM
[2024-01-24 12:48:15,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003667525.1_ASM366752v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003667525.1_ASM366752v1_genomic.fna/checkm_input GCF_003667525.1_ASM366752v1_genomic.fna/checkm_result
[2024-01-24 12:48:48,467] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:48,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:48,495] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:48,496] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:48,497] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003667525.1_ASM366752v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:48,497] [INFO] Task started: Blastn
[2024-01-24 12:48:48,497] [INFO] Running command: blastn -query GCF_003667525.1_ASM366752v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2ab858b-c35d-4ff8-86f0-d82ed26be859/dqc_reference/reference_markers_gtdb.fasta -out GCF_003667525.1_ASM366752v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:50,337] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:50,342] [INFO] Selected 28 target genomes.
[2024-01-24 12:48:50,342] [INFO] Target genome list was writen to GCF_003667525.1_ASM366752v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:50,371] [INFO] Task started: fastANI
[2024-01-24 12:48:50,371] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf530f26-9296-4afb-9ec8-06c6c84c5e89/GCF_003667525.1_ASM366752v1_genomic.fna.gz --refList GCF_003667525.1_ASM366752v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003667525.1_ASM366752v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:08,185] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:08,212] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:08,212] [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_900163835.1	s__Mycetocola_B reblochoni	99.9332	915	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_B	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_002936985.1	s__Microterricola pindariensis	78.9902	337	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	96.4039	N/A	N/A	N/A	N/A	1	-
GCF_900104895.1	s__Microterricola viridarii	78.817	351	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	96.4039	N/A	N/A	N/A	N/A	1	-
GCF_003576405.1	s__Clavibacter sp003576405	78.7136	276	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.88	99.88	0.93	0.93	2	-
GCF_004011135.1	s__Rathayibacter festucae	78.7068	390	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	96.98	96.51	0.89	0.87	11	-
GCF_002024505.1	s__Plantibacter flavus_A	78.6856	338	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Plantibacter	95.1912	97.90	97.77	0.92	0.88	5	-
GCF_003856975.1	s__Plantibacter cousiniae	78.6646	361	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Plantibacter	95.9127	96.92	96.01	0.91	0.89	11	-
GCF_009834225.1	s__Rathayibacter sp009834225	78.6496	365	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122505.1	s__Agromyces sp008122505	78.6283	351	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177795.1	s__Plantibacter sp900177795	78.6046	366	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Plantibacter	95.9127	N/A	N/A	N/A	N/A	1	-
GCF_003751785.1	s__Frigoribacterium sp003751785	78.6032	345	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013205025.1	s__Rathayibacter sp013205025	78.5771	381	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410375.1	s__Leifsonia shinshuensis	78.5655	367	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078385.1	s__Microbacterium sp900078385	78.5594	276	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735645.1	s__Microbacterium oryzae	78.5536	296	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190775.1	s__Leifsonia aquatica	78.5481	356	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.62	97.25	0.95	0.90	3	-
GCF_012317045.1	s__Leifsonia sp002105485	78.488	323	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.03	98.03	0.91	0.91	2	-
GCF_018588945.1	s__Microbacterium flavescens	78.4717	282	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003067705.1	s__Planctomonas deserti	78.4544	322	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Planctomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009866585.1	s__Rathayibacter sp002930885	78.4541	349	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.23	95.98	0.89	0.85	55	-
GCA_001898805.1	s__Leifsonia sp001898805	78.4492	360	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907085.1	s__Clavibacter michiganensis_O	78.4372	331	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797715.1	s__Diaminobutyricimonas aerilata	78.4335	311	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280205.1	s__Clavibacter capsici	78.4112	342	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.16	95.31	0.96	0.91	6	-
GCA_001725325.1	s__Rhodoglobus sp001725325	78.3948	299	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCA_002325245.1	s__Pseudolysinimonas sp002325245	78.3884	272	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	99.78	99.17	0.96	0.89	14	-
GCF_000633535.1	s__Leifsonia aquatica_A	78.1431	345	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618005.1	s__Clavibacter tessellarius_A	78.1377	337	1001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:08,214] [INFO] GTDB search result was written to GCF_003667525.1_ASM366752v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:08,215] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:08,220] [INFO] DFAST_QC result json was written to GCF_003667525.1_ASM366752v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:08,220] [INFO] DFAST_QC completed!
[2024-01-24 12:49:08,220] [INFO] Total running time: 0h1m18s