[2024-01-24 15:02:24,195] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:24,197] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:24,197] [INFO] DQC Reference Directory: /var/lib/cwl/stgff136ca5-3dfa-4b84-8812-738439522649/dqc_reference
[2024-01-24 15:02:26,425] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:26,426] [INFO] Task started: Prodigal
[2024-01-24 15:02:26,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg08a26add-755d-4c87-bd2d-5b806ad15502/GCF_030161575.1_ASM3016157v1_genomic.fna.gz | prodigal -d GCF_030161575.1_ASM3016157v1_genomic.fna/cds.fna -a GCF_030161575.1_ASM3016157v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:36,102] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:36,103] [INFO] Task started: HMMsearch
[2024-01-24 15:02:36,103] [INFO] Running command: hmmsearch --tblout GCF_030161575.1_ASM3016157v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff136ca5-3dfa-4b84-8812-738439522649/dqc_reference/reference_markers.hmm GCF_030161575.1_ASM3016157v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:36,403] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:36,405] [INFO] Found 6/6 markers.
[2024-01-24 15:02:36,439] [INFO] Query marker FASTA was written to GCF_030161575.1_ASM3016157v1_genomic.fna/markers.fasta
[2024-01-24 15:02:36,440] [INFO] Task started: Blastn
[2024-01-24 15:02:36,440] [INFO] Running command: blastn -query GCF_030161575.1_ASM3016157v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff136ca5-3dfa-4b84-8812-738439522649/dqc_reference/reference_markers.fasta -out GCF_030161575.1_ASM3016157v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:37,854] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:37,858] [INFO] Selected 25 target genomes.
[2024-01-24 15:02:37,858] [INFO] Target genome list was writen to GCF_030161575.1_ASM3016157v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:37,890] [INFO] Task started: fastANI
[2024-01-24 15:02:37,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg08a26add-755d-4c87-bd2d-5b806ad15502/GCF_030161575.1_ASM3016157v1_genomic.fna.gz --refList GCF_030161575.1_ASM3016157v1_genomic.fna/target_genomes.txt --output GCF_030161575.1_ASM3016157v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:56,294] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:56,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff136ca5-3dfa-4b84-8812-738439522649/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:56,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff136ca5-3dfa-4b84-8812-738439522649/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:56,314] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:02:56,314] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:02:56,314] [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
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.9651	453	1080	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	79.6071	522	1080	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	79.5826	391	1080	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	79.3736	455	1080	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	79.3043	437	1080	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	79.3031	443	1080	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.2806	452	1080	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	79.2733	415	1080	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	79.2606	434	1080	95	below_threshold
Rathayibacter caricis	strain=DSM 15933	GCA_003044275.1	110936	110936	type	True	79.24	477	1080	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.2393	452	1080	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	79.2172	471	1080	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.1851	477	1080	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	79.1839	362	1080	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.1722	458	1080	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	79.1176	432	1080	95	below_threshold
Frigoribacterium faeni	strain=DSM 10309	GCA_014137965.1	145483	145483	type	True	79.0621	439	1080	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	79.0413	460	1080	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	79.0176	438	1080	95	below_threshold
Microbacterium lemovicicum	strain=Viu22	GCA_003991875.1	1072463	1072463	type	True	78.7512	394	1080	95	below_threshold
Agrococcus jejuensis	strain=DSM 22002	GCA_900099705.1	399736	399736	type	True	78.7359	466	1080	95	below_threshold
Agrococcus terreus	strain=CGMCC 1.6960	GCA_014645235.1	574649	574649	type	True	78.6485	445	1080	95	below_threshold
Labedella gwakjiensis	strain=KSW2-17	GCA_003990035.1	390269	390269	type	True	78.3525	379	1080	95	below_threshold
Labedella gwakjiensis	strain=DSM 21548	GCA_003014675.1	390269	390269	type	True	78.3192	386	1080	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	78.2074	385	1080	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:56,316] [INFO] DFAST Taxonomy check result was written to GCF_030161575.1_ASM3016157v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:56,318] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:56,318] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:56,318] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff136ca5-3dfa-4b84-8812-738439522649/dqc_reference/checkm_data
[2024-01-24 15:02:56,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:56,371] [INFO] Task started: CheckM
[2024-01-24 15:02:56,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161575.1_ASM3016157v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161575.1_ASM3016157v1_genomic.fna/checkm_input GCF_030161575.1_ASM3016157v1_genomic.fna/checkm_result
[2024-01-24 15:03:48,667] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:48,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:48,685] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:48,685] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:48,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161575.1_ASM3016157v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:48,686] [INFO] Task started: Blastn
[2024-01-24 15:03:48,686] [INFO] Running command: blastn -query GCF_030161575.1_ASM3016157v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff136ca5-3dfa-4b84-8812-738439522649/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161575.1_ASM3016157v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:51,006] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:51,010] [INFO] Selected 29 target genomes.
[2024-01-24 15:03:51,010] [INFO] Target genome list was writen to GCF_030161575.1_ASM3016157v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:51,035] [INFO] Task started: fastANI
[2024-01-24 15:03:51,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg08a26add-755d-4c87-bd2d-5b806ad15502/GCF_030161575.1_ASM3016157v1_genomic.fna.gz --refList GCF_030161575.1_ASM3016157v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161575.1_ASM3016157v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:15,858] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:15,890] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:04:15,890] [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
GCA_012530535.1	s__Yonghaparkia sp012530535	80.0527	462	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	80.0182	446	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003627075.1	s__Protaetiibacter intestinalis	79.894	459	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517535.1	s__Schumannella sp006517535	79.7802	491	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408685.1	s__Schumannella luteola	79.7761	519	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797715.1	s__Diaminobutyricimonas aerilata	79.7434	445	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502445.1	s__Yonghaparkia sp005502445	79.6465	375	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464255.1	s__Chryseoglobus sp001464255	79.6332	283	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011135.1	s__Rathayibacter festucae	79.5412	529	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	96.98	96.51	0.89	0.87	11	-
GCF_003576185.1	s__Clavibacter phaseoli	79.4843	354	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.97	95.69	0.87	0.85	4	-
GCF_006517435.1	s__Schumannella sp006517435	79.4804	511	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014483895.1	s__Protaetiibacter sp014483895	79.4419	465	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751785.1	s__Frigoribacterium sp003751785	79.4159	496	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834185.1	s__Rathayibacter sp009834185	79.384	523	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761235.1	s__Frigoribacterium faeni_A	79.3528	479	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014775655.1	s__Clavibacter zhangzhiyongii	79.3111	447	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.40	98.40	0.96	0.96	2	-
GCF_016907355.1	s__Agromyces aurantiacus	79.2591	467	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000355695.1	s__Clavibacter nebraskensis	79.2416	438	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.1408	99.97	99.95	1.00	1.00	6	-
GCF_001647635.1	s__Leifsonia xyli_A	79.2321	409	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308515.1	s__Pseudolysinimonas sp017308515	79.2129	416	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013205055.1	s__Rathayibacter sp013205055	79.2123	526	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013414345.1	s__Marinisubtilis indicus	79.1885	358	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	96.33	95.90	0.85	0.83	6	-
GCF_014204935.1	s__Conyzicola lurida	79.0927	455	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217625.1	s__Leifsonia shinshuensis_A	79.0633	431	1080	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	79.0165	463	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351075.1	s__Clavibacter sp015351075	78.9458	460	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384855.1	s__Agromyces sp003384855	78.8976	491	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002150995.1	s__Clavibacter michiganensis_K	78.8844	476	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.44	98.42	0.92	0.92	3	-
GCF_003234565.1	s__Curtobacterium sp003234565	78.4108	354	1080	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.63	98.46	0.93	0.92	8	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:15,895] [INFO] GTDB search result was written to GCF_030161575.1_ASM3016157v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:15,896] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:15,904] [INFO] DFAST_QC result json was written to GCF_030161575.1_ASM3016157v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:15,904] [INFO] DFAST_QC completed!
[2024-01-24 15:04:15,904] [INFO] Total running time: 0h1m52s