[2024-01-24 14:31:15,065] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:15,068] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:15,068] [INFO] DQC Reference Directory: /var/lib/cwl/stgebbb1b85-e603-4dc0-81d9-e7cf89a4b4d6/dqc_reference
[2024-01-24 14:31:16,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:16,637] [INFO] Task started: Prodigal
[2024-01-24 14:31:16,637] [INFO] Running command: gunzip -c /var/lib/cwl/stg88a613c9-e4cf-4fe6-a0fb-3f3b87ec39d1/GCF_013410525.1_ASM1341052v1_genomic.fna.gz | prodigal -d GCF_013410525.1_ASM1341052v1_genomic.fna/cds.fna -a GCF_013410525.1_ASM1341052v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:26,079] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:26,080] [INFO] Task started: HMMsearch
[2024-01-24 14:31:26,080] [INFO] Running command: hmmsearch --tblout GCF_013410525.1_ASM1341052v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebbb1b85-e603-4dc0-81d9-e7cf89a4b4d6/dqc_reference/reference_markers.hmm GCF_013410525.1_ASM1341052v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:26,350] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:26,351] [INFO] Found 6/6 markers.
[2024-01-24 14:31:26,384] [INFO] Query marker FASTA was written to GCF_013410525.1_ASM1341052v1_genomic.fna/markers.fasta
[2024-01-24 14:31:26,385] [INFO] Task started: Blastn
[2024-01-24 14:31:26,385] [INFO] Running command: blastn -query GCF_013410525.1_ASM1341052v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebbb1b85-e603-4dc0-81d9-e7cf89a4b4d6/dqc_reference/reference_markers.fasta -out GCF_013410525.1_ASM1341052v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:27,542] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:27,545] [INFO] Selected 20 target genomes.
[2024-01-24 14:31:27,545] [INFO] Target genome list was writen to GCF_013410525.1_ASM1341052v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:27,564] [INFO] Task started: fastANI
[2024-01-24 14:31:27,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg88a613c9-e4cf-4fe6-a0fb-3f3b87ec39d1/GCF_013410525.1_ASM1341052v1_genomic.fna.gz --refList GCF_013410525.1_ASM1341052v1_genomic.fna/target_genomes.txt --output GCF_013410525.1_ASM1341052v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:41,878] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:41,879] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebbb1b85-e603-4dc0-81d9-e7cf89a4b4d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:41,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebbb1b85-e603-4dc0-81d9-e7cf89a4b4d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:41,896] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:41,896] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:41,897] [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
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	100.0	1014	1014	95	conclusive
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	99.9906	1011	1014	95	conclusive
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.623	415	1014	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	79.6126	459	1014	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	79.3481	426	1014	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	79.1049	388	1014	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	79.097	297	1014	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	78.9839	371	1014	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	78.9578	316	1014	95	below_threshold
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	78.9467	277	1014	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	78.8698	417	1014	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.8555	387	1014	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	78.7891	377	1014	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	78.7126	422	1014	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	78.6418	379	1014	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.6047	417	1014	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	78.5307	380	1014	95	below_threshold
Herbiconiux ginsengi	strain=CGMCC 4.3491	GCA_900107435.1	381665	381665	type	True	78.4777	404	1014	95	below_threshold
Glaciihabitans tibetensis	strain=CGMCC 1.12484	GCA_003003265.1	1266600	1266600	type	True	78.4257	330	1014	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.2963	373	1014	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:41,898] [INFO] DFAST Taxonomy check result was written to GCF_013410525.1_ASM1341052v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:41,899] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:41,899] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:41,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebbb1b85-e603-4dc0-81d9-e7cf89a4b4d6/dqc_reference/checkm_data
[2024-01-24 14:31:41,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:41,941] [INFO] Task started: CheckM
[2024-01-24 14:31:41,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013410525.1_ASM1341052v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013410525.1_ASM1341052v1_genomic.fna/checkm_input GCF_013410525.1_ASM1341052v1_genomic.fna/checkm_result
[2024-01-24 14:32:29,643] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:29,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:29,661] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:29,662] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:29,662] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013410525.1_ASM1341052v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:29,662] [INFO] Task started: Blastn
[2024-01-24 14:32:29,663] [INFO] Running command: blastn -query GCF_013410525.1_ASM1341052v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebbb1b85-e603-4dc0-81d9-e7cf89a4b4d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_013410525.1_ASM1341052v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:31,393] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:31,397] [INFO] Selected 18 target genomes.
[2024-01-24 14:32:31,397] [INFO] Target genome list was writen to GCF_013410525.1_ASM1341052v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:31,411] [INFO] Task started: fastANI
[2024-01-24 14:32:31,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg88a613c9-e4cf-4fe6-a0fb-3f3b87ec39d1/GCF_013410525.1_ASM1341052v1_genomic.fna.gz --refList GCF_013410525.1_ASM1341052v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013410525.1_ASM1341052v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:43,301] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:43,317] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:43,318] [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_010686725.1	s__Galbitalea soli	99.9906	1011	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Galbitalea	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_001725325.1	s__Rhodoglobus sp001725325	80.0177	459	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCA_903920435.1	s__Rhodoglobus sp903920435	79.7154	416	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	98.49	97.73	0.85	0.78	4	-
GCF_014204935.1	s__Conyzicola lurida	79.6126	458	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797715.1	s__Diaminobutyricimonas aerilata	79.384	425	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797855.1	s__Compostimonas suwonensis	79.3139	401	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Compostimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310685.1	s__Conyzicola arctica	79.1865	416	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008001035.1	s__Homoserinimonas sp008001035	79.054	319	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Homoserinimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018449675.1	s__Glaciihabitans sp018449675	79.0225	401	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Glaciihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003067705.1	s__Planctomonas deserti	78.9827	391	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Planctomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716125.1	s__Homoserinimonas aerilata	78.9403	327	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Homoserinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907085.1	s__Clavibacter michiganensis_O	78.778	392	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013414345.1	s__Marinisubtilis indicus	78.676	342	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	96.33	95.90	0.85	0.83	6	-
GCF_004216665.1	s__Agromyces ramosus	78.5499	378	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003265.1	s__Glaciihabitans tibetensis	78.4018	332	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Glaciihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428255.1	s__Agromyces sp001428255	78.3582	395	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801905.1	s__Leifsonia_A flavus	78.3261	314	1014	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_003384855.1	s__Agromyces sp003384855	78.3245	392	1014	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 14:32:43,319] [INFO] GTDB search result was written to GCF_013410525.1_ASM1341052v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:43,320] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:43,325] [INFO] DFAST_QC result json was written to GCF_013410525.1_ASM1341052v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:43,325] [INFO] DFAST_QC completed!
[2024-01-24 14:32:43,326] [INFO] Total running time: 0h1m28s