[2024-01-24 12:47:22,098] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:22,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:22,100] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4f64945-2487-4b38-9ffb-ca21e6c20b04/dqc_reference
[2024-01-24 12:47:23,297] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:23,298] [INFO] Task started: Prodigal
[2024-01-24 12:47:23,298] [INFO] Running command: gunzip -c /var/lib/cwl/stgdba51095-ce7a-4d3e-acef-68906d140cc0/GCF_008040105.1_ASM804010v1_genomic.fna.gz | prodigal -d GCF_008040105.1_ASM804010v1_genomic.fna/cds.fna -a GCF_008040105.1_ASM804010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:35,351] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:35,351] [INFO] Task started: HMMsearch
[2024-01-24 12:47:35,351] [INFO] Running command: hmmsearch --tblout GCF_008040105.1_ASM804010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4f64945-2487-4b38-9ffb-ca21e6c20b04/dqc_reference/reference_markers.hmm GCF_008040105.1_ASM804010v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:35,652] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:35,654] [INFO] Found 6/6 markers.
[2024-01-24 12:47:35,698] [INFO] Query marker FASTA was written to GCF_008040105.1_ASM804010v1_genomic.fna/markers.fasta
[2024-01-24 12:47:35,699] [INFO] Task started: Blastn
[2024-01-24 12:47:35,699] [INFO] Running command: blastn -query GCF_008040105.1_ASM804010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4f64945-2487-4b38-9ffb-ca21e6c20b04/dqc_reference/reference_markers.fasta -out GCF_008040105.1_ASM804010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:36,852] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:36,857] [INFO] Selected 22 target genomes.
[2024-01-24 12:47:36,857] [INFO] Target genome list was writen to GCF_008040105.1_ASM804010v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:36,868] [INFO] Task started: fastANI
[2024-01-24 12:47:36,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgdba51095-ce7a-4d3e-acef-68906d140cc0/GCF_008040105.1_ASM804010v1_genomic.fna.gz --refList GCF_008040105.1_ASM804010v1_genomic.fna/target_genomes.txt --output GCF_008040105.1_ASM804010v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:52,441] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:52,442] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4f64945-2487-4b38-9ffb-ca21e6c20b04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:52,442] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4f64945-2487-4b38-9ffb-ca21e6c20b04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:52,461] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:52,461] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:52,462] [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
Lacisediminihabitans profunda	strain=CHu50b-6-2	GCA_008040105.1	2594790	2594790	type	True	100.0	1309	1311	95	conclusive
Lacisediminihabitans changchengi	strain=G11-30	GCA_016634425.1	2787634	2787634	type	True	79.9359	459	1311	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	79.7519	472	1311	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	79.5879	467	1311	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	79.5045	412	1311	95	below_threshold
Marisediminicola antarctica	strain=ZS314	GCA_009930795.1	674079	674079	type	True	79.3675	455	1311	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	79.2036	296	1311	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	79.0834	325	1311	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	79.0353	333	1311	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	78.8821	430	1311	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	78.8453	376	1311	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.8164	369	1311	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.807	358	1311	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	78.8013	376	1311	95	below_threshold
Terrimesophilobacter mesophilus	strain=DSM 19267	GCA_014200375.1	433647	433647	type	True	78.7595	310	1311	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.6936	347	1311	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	78.6917	409	1311	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.6101	401	1311	95	below_threshold
Microterricola gilva	strain=DSM 18319	GCA_004217495.1	393267	393267	type	True	78.5835	383	1311	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	78.4619	431	1311	95	below_threshold
Subtercola boreus	strain=K300	GCA_003399685.1	120213	120213	suspected-type	True	78.3816	366	1311	95	below_threshold
Subtercola boreus	strain=DSM 13056	GCA_006716115.1	120213	120213	suspected-type	True	78.3678	368	1311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:52,464] [INFO] DFAST Taxonomy check result was written to GCF_008040105.1_ASM804010v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:52,464] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:52,465] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:52,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4f64945-2487-4b38-9ffb-ca21e6c20b04/dqc_reference/checkm_data
[2024-01-24 12:47:52,467] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:52,508] [INFO] Task started: CheckM
[2024-01-24 12:47:52,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008040105.1_ASM804010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008040105.1_ASM804010v1_genomic.fna/checkm_input GCF_008040105.1_ASM804010v1_genomic.fna/checkm_result
[2024-01-24 12:48:31,064] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:31,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:31,088] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:31,088] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:31,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008040105.1_ASM804010v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:31,089] [INFO] Task started: Blastn
[2024-01-24 12:48:31,089] [INFO] Running command: blastn -query GCF_008040105.1_ASM804010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4f64945-2487-4b38-9ffb-ca21e6c20b04/dqc_reference/reference_markers_gtdb.fasta -out GCF_008040105.1_ASM804010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:32,957] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:32,963] [INFO] Selected 17 target genomes.
[2024-01-24 12:48:32,963] [INFO] Target genome list was writen to GCF_008040105.1_ASM804010v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:32,977] [INFO] Task started: fastANI
[2024-01-24 12:48:32,978] [INFO] Running command: fastANI --query /var/lib/cwl/stgdba51095-ce7a-4d3e-acef-68906d140cc0/GCF_008040105.1_ASM804010v1_genomic.fna.gz --refList GCF_008040105.1_ASM804010v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008040105.1_ASM804010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:44,497] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:44,517] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:44,518] [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_008040105.1	s__Lacisediminihabitans profunda	100.0	1309	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003454135.1	s__Lacisediminihabitans sp003454135	84.1973	607	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217685.1	s__Lacisediminihabitans sp014217685	80.7382	572	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016634425.1	s__Lacisediminihabitans sp016634425	79.9471	458	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639655.1	s__Conyzicola nivalis	79.5988	466	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057645.1	s__Marisediminicola senii	79.505	412	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marisediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378715.1	s__Marisediminicola sp014378715	79.4874	419	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marisediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725325.1	s__Rhodoglobus sp001725325	79.4651	465	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_009930795.1	s__Marisediminicola antarctica	79.3667	455	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marisediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751965.1	s__Lacisediminihabitans sp015751965	79.1747	390	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903920435.1	s__Rhodoglobus sp903920435	79.1435	428	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	98.49	97.73	0.85	0.78	4	-
GCF_001618005.1	s__Clavibacter tessellarius_A	79.0002	349	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716125.1	s__Homoserinimonas aerilata	78.8485	345	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Homoserinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408685.1	s__Schumannella luteola	78.7705	409	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907085.1	s__Clavibacter michiganensis_O	78.7703	369	1311	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	78.6906	362	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.98	99.98	0.98	0.96	4	-
GCF_006716115.1	s__Subtercola boreus	78.3576	369	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:44,520] [INFO] GTDB search result was written to GCF_008040105.1_ASM804010v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:44,520] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:44,525] [INFO] DFAST_QC result json was written to GCF_008040105.1_ASM804010v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:44,525] [INFO] DFAST_QC completed!
[2024-01-24 12:48:44,525] [INFO] Total running time: 0h1m22s