[2023-06-27 16:55:29,490] [INFO] DFAST_QC pipeline started.
[2023-06-27 16:55:29,497] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 16:55:29,497] [INFO] DQC Reference Directory: /var/lib/cwl/stgccc192bc-4d15-44f3-ac02-45c41d4a8b82/dqc_reference
[2023-06-27 16:55:32,788] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 16:55:32,789] [INFO] Task started: Prodigal
[2023-06-27 16:55:32,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg5607ac82-a07c-4cd6-9f85-15edf69c3acf/GCA_027352875.1_ASM2735287v1_genomic.fna.gz | prodigal -d GCA_027352875.1_ASM2735287v1_genomic.fna/cds.fna -a GCA_027352875.1_ASM2735287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 16:55:37,708] [INFO] Task succeeded: Prodigal
[2023-06-27 16:55:37,709] [INFO] Task started: HMMsearch
[2023-06-27 16:55:37,709] [INFO] Running command: hmmsearch --tblout GCA_027352875.1_ASM2735287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccc192bc-4d15-44f3-ac02-45c41d4a8b82/dqc_reference/reference_markers.hmm GCA_027352875.1_ASM2735287v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 16:55:37,958] [INFO] Task succeeded: HMMsearch
[2023-06-27 16:55:37,960] [INFO] Found 6/6 markers.
[2023-06-27 16:55:37,984] [INFO] Query marker FASTA was written to GCA_027352875.1_ASM2735287v1_genomic.fna/markers.fasta
[2023-06-27 16:55:37,984] [INFO] Task started: Blastn
[2023-06-27 16:55:37,985] [INFO] Running command: blastn -query GCA_027352875.1_ASM2735287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccc192bc-4d15-44f3-ac02-45c41d4a8b82/dqc_reference/reference_markers.fasta -out GCA_027352875.1_ASM2735287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 16:55:39,108] [INFO] Task succeeded: Blastn
[2023-06-27 16:55:39,113] [INFO] Selected 26 target genomes.
[2023-06-27 16:55:39,113] [INFO] Target genome list was writen to GCA_027352875.1_ASM2735287v1_genomic.fna/target_genomes.txt
[2023-06-27 16:55:39,120] [INFO] Task started: fastANI
[2023-06-27 16:55:39,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg5607ac82-a07c-4cd6-9f85-15edf69c3acf/GCA_027352875.1_ASM2735287v1_genomic.fna.gz --refList GCA_027352875.1_ASM2735287v1_genomic.fna/target_genomes.txt --output GCA_027352875.1_ASM2735287v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 16:55:56,016] [INFO] Task succeeded: fastANI
[2023-06-27 16:55:56,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccc192bc-4d15-44f3-ac02-45c41d4a8b82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 16:55:56,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccc192bc-4d15-44f3-ac02-45c41d4a8b82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 16:55:56,043] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 16:55:56,043] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 16:55:56,043] [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	80.3251	349	603	95	below_threshold
Gryllotalpicola protaetiae	strain=2DFW10M-5	GCA_003627055.1	2419771	2419771	type	True	80.0674	354	603	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	79.2505	308	603	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	79.2336	239	603	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	79.1061	273	603	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	79.0605	299	603	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	79.0373	300	603	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.0159	306	603	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	79.0159	303	603	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	78.9784	303	603	95	below_threshold
Agromyces subbeticus	strain=DSM 16689	GCA_000421565.1	293890	293890	type	True	78.8272	278	603	95	below_threshold
Agromyces salentinus	strain=JCM 14323	GCA_009749395.1	269421	269421	type	True	78.8076	271	603	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.7971	282	603	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	78.728	281	603	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.6871	279	603	95	below_threshold
Agrococcus lahaulensis	strain=DSM 17612	GCA_000425105.1	341722	341722	type	True	78.6365	265	603	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	78.6053	245	603	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	78.5104	273	603	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	78.4978	266	603	95	below_threshold
Frigoribacterium faeni	strain=DSM 10309	GCA_014137965.1	145483	145483	type	True	78.3997	236	603	95	below_threshold
Labedella populi	strain=8H24J-4-2	GCA_004078655.1	2498850	2498850	type	True	78.3761	202	603	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	78.3194	243	603	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	78.3172	245	603	95	below_threshold
Labedella phragmitis	strain=11W25H-1	GCA_004078635.1	2498849	2498849	type	True	78.2679	222	603	95	below_threshold
Labedella endophytica	strain=EGI 6500705	GCA_003990045.1	1523160	1523160	type	True	78.2141	226	603	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	78.1863	239	603	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 16:55:56,048] [INFO] DFAST Taxonomy check result was written to GCA_027352875.1_ASM2735287v1_genomic.fna/tc_result.tsv
[2023-06-27 16:55:56,050] [INFO] ===== Taxonomy check completed =====
[2023-06-27 16:55:56,050] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 16:55:56,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccc192bc-4d15-44f3-ac02-45c41d4a8b82/dqc_reference/checkm_data
[2023-06-27 16:55:56,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 16:55:56,093] [INFO] Task started: CheckM
[2023-06-27 16:55:56,093] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027352875.1_ASM2735287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027352875.1_ASM2735287v1_genomic.fna/checkm_input GCA_027352875.1_ASM2735287v1_genomic.fna/checkm_result
[2023-06-27 16:56:17,698] [INFO] Task succeeded: CheckM
[2023-06-27 16:56:17,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 16:56:17,720] [INFO] ===== Completeness check finished =====
[2023-06-27 16:56:17,720] [INFO] ===== Start GTDB Search =====
[2023-06-27 16:56:17,721] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027352875.1_ASM2735287v1_genomic.fna/markers.fasta)
[2023-06-27 16:56:17,721] [INFO] Task started: Blastn
[2023-06-27 16:56:17,721] [INFO] Running command: blastn -query GCA_027352875.1_ASM2735287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccc192bc-4d15-44f3-ac02-45c41d4a8b82/dqc_reference/reference_markers_gtdb.fasta -out GCA_027352875.1_ASM2735287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 16:56:19,489] [INFO] Task succeeded: Blastn
[2023-06-27 16:56:19,494] [INFO] Selected 27 target genomes.
[2023-06-27 16:56:19,494] [INFO] Target genome list was writen to GCA_027352875.1_ASM2735287v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 16:56:19,508] [INFO] Task started: fastANI
[2023-06-27 16:56:19,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg5607ac82-a07c-4cd6-9f85-15edf69c3acf/GCA_027352875.1_ASM2735287v1_genomic.fna.gz --refList GCA_027352875.1_ASM2735287v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027352875.1_ASM2735287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 16:56:35,998] [INFO] Task succeeded: fastANI
[2023-06-27 16:56:36,023] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 16:56:36,024] [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	80.3424	348	603	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	80.2731	308	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gryllotalpicola	95.0	99.84	99.84	0.94	0.94	2	-
GCF_003627055.1	s__Gryllotalpicola protaetiae	80.0986	352	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gryllotalpicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789225.1	s__WSTA01 sp009789225	79.4603	286	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__WSTA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627075.1	s__Protaetiibacter intestinalis	79.3625	295	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003852775.1	s__Protaetiibacter sp003852775	79.317	274	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648575.1	s__Agromyces mediolanus	79.2347	309	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620055.1	s__Agromyces sp001620055	79.1816	278	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634985.1	s__Agromyces sp003634985	79.0863	281	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709675.1	s__Agromyces bracchium	79.0602	300	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729855.1	s__Agromyces luteolus	79.0535	299	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013205055.1	s__Rathayibacter sp013205055	79.0235	294	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002797855.1	s__Compostimonas suwonensis	79.009	284	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Compostimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898805.1	s__Leifsonia sp001898805	78.9913	291	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190775.1	s__Leifsonia aquatica	78.8957	308	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.62	97.25	0.95	0.90	3	-
GCF_004006235.1	s__Agromyces sp004006235	78.8804	290	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751785.1	s__Frigoribacterium sp003751785	78.83	277	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280205.1	s__Clavibacter capsici	78.8228	270	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.16	95.31	0.96	0.91	6	-
GCF_004216665.1	s__Agromyces ramosus	78.7206	282	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351075.1	s__Clavibacter sp015351075	78.6976	264	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000069225.1	s__Clavibacter sepedonicus	78.6615	254	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.98	99.98	0.98	0.96	4	-
GCF_016907085.1	s__Clavibacter michiganensis_O	78.6481	271	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010686705.1	s__Diaminobutyricibacter tongyongensis	78.5635	232	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078385.1	s__Microbacterium sp900078385	78.4391	230	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097495.1	s__Naasia flavum	78.4106	227	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Naasia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004078655.1	s__Labedella populi	78.35	204	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423905.1	s__Frigoribacterium sp001423905	78.3157	249	603	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	96.23	96.23	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-27 16:56:36,026] [INFO] GTDB search result was written to GCA_027352875.1_ASM2735287v1_genomic.fna/result_gtdb.tsv
[2023-06-27 16:56:36,026] [INFO] ===== GTDB Search completed =====
[2023-06-27 16:56:36,031] [INFO] DFAST_QC result json was written to GCA_027352875.1_ASM2735287v1_genomic.fna/dqc_result.json
[2023-06-27 16:56:36,032] [INFO] DFAST_QC completed!
[2023-06-27 16:56:36,032] [INFO] Total running time: 0h1m7s