[2024-01-24 14:10:15,314] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:10:15,316] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:10:15,316] [INFO] DQC Reference Directory: /var/lib/cwl/stg90d87591-e539-4f78-a636-f32f5ee7fcc1/dqc_reference
[2024-01-24 14:10:16,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:10:16,690] [INFO] Task started: Prodigal
[2024-01-24 14:10:16,691] [INFO] Running command: gunzip -c /var/lib/cwl/stgd31dea78-b3c0-4df5-9873-16fd74309ccc/GCF_009930795.1_ASM993079v1_genomic.fna.gz | prodigal -d GCF_009930795.1_ASM993079v1_genomic.fna/cds.fna -a GCF_009930795.1_ASM993079v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:10:26,830] [INFO] Task succeeded: Prodigal
[2024-01-24 14:10:26,830] [INFO] Task started: HMMsearch
[2024-01-24 14:10:26,830] [INFO] Running command: hmmsearch --tblout GCF_009930795.1_ASM993079v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90d87591-e539-4f78-a636-f32f5ee7fcc1/dqc_reference/reference_markers.hmm GCF_009930795.1_ASM993079v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:10:27,110] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:10:27,111] [INFO] Found 6/6 markers.
[2024-01-24 14:10:27,141] [INFO] Query marker FASTA was written to GCF_009930795.1_ASM993079v1_genomic.fna/markers.fasta
[2024-01-24 14:10:27,141] [INFO] Task started: Blastn
[2024-01-24 14:10:27,142] [INFO] Running command: blastn -query GCF_009930795.1_ASM993079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90d87591-e539-4f78-a636-f32f5ee7fcc1/dqc_reference/reference_markers.fasta -out GCF_009930795.1_ASM993079v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:28,382] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:28,389] [INFO] Selected 21 target genomes.
[2024-01-24 14:10:28,390] [INFO] Target genome list was writen to GCF_009930795.1_ASM993079v1_genomic.fna/target_genomes.txt
[2024-01-24 14:10:28,398] [INFO] Task started: fastANI
[2024-01-24 14:10:28,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgd31dea78-b3c0-4df5-9873-16fd74309ccc/GCF_009930795.1_ASM993079v1_genomic.fna.gz --refList GCF_009930795.1_ASM993079v1_genomic.fna/target_genomes.txt --output GCF_009930795.1_ASM993079v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:10:41,390] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:41,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90d87591-e539-4f78-a636-f32f5ee7fcc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:10:41,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90d87591-e539-4f78-a636-f32f5ee7fcc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:10:41,408] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:10:41,408] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:10:41,409] [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
Marisediminicola antarctica	strain=ZS314	GCA_009930795.1	674079	674079	type	True	100.0	1116	1117	95	conclusive
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	80.4933	464	1117	95	below_threshold
Lacisediminihabitans profunda	strain=CHu50b-6-2	GCA_008040105.1	2594790	2594790	type	True	79.3881	464	1117	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	79.2818	420	1117	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	79.2458	461	1117	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	79.2097	317	1117	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	79.1373	296	1117	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.0298	369	1117	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	79.0201	364	1117	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	78.9377	378	1117	95	below_threshold
Lacisediminihabitans changchengi	strain=G11-30	GCA_016634425.1	2787634	2787634	type	True	78.9061	340	1117	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.8892	361	1117	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	78.8442	385	1117	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.8068	366	1117	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	78.7445	371	1117	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	78.7206	365	1117	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	78.6775	383	1117	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	78.5878	361	1117	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.4585	395	1117	95	below_threshold
Subtercola frigoramans	strain=DSM 13057	GCA_016907385.1	120298	120298	type	True	78.141	255	1117	95	below_threshold
Microbacterium gubbeenense	strain=DSM 15944	GCA_000422745.1	159896	159896	type	True	77.5949	224	1117	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:10:41,415] [INFO] DFAST Taxonomy check result was written to GCF_009930795.1_ASM993079v1_genomic.fna/tc_result.tsv
[2024-01-24 14:10:41,416] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:10:41,416] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:10:41,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90d87591-e539-4f78-a636-f32f5ee7fcc1/dqc_reference/checkm_data
[2024-01-24 14:10:41,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:10:41,454] [INFO] Task started: CheckM
[2024-01-24 14:10:41,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009930795.1_ASM993079v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009930795.1_ASM993079v1_genomic.fna/checkm_input GCF_009930795.1_ASM993079v1_genomic.fna/checkm_result
[2024-01-24 14:11:15,677] [INFO] Task succeeded: CheckM
[2024-01-24 14:11:15,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:11:15,697] [INFO] ===== Completeness check finished =====
[2024-01-24 14:11:15,697] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:11:15,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009930795.1_ASM993079v1_genomic.fna/markers.fasta)
[2024-01-24 14:11:15,698] [INFO] Task started: Blastn
[2024-01-24 14:11:15,698] [INFO] Running command: blastn -query GCF_009930795.1_ASM993079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90d87591-e539-4f78-a636-f32f5ee7fcc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_009930795.1_ASM993079v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:11:17,482] [INFO] Task succeeded: Blastn
[2024-01-24 14:11:17,488] [INFO] Selected 16 target genomes.
[2024-01-24 14:11:17,489] [INFO] Target genome list was writen to GCF_009930795.1_ASM993079v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:11:17,549] [INFO] Task started: fastANI
[2024-01-24 14:11:17,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgd31dea78-b3c0-4df5-9873-16fd74309ccc/GCF_009930795.1_ASM993079v1_genomic.fna.gz --refList GCF_009930795.1_ASM993079v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009930795.1_ASM993079v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:11:28,119] [INFO] Task succeeded: fastANI
[2024-01-24 14:11:28,137] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:11:28,137] [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_009930795.1	s__Marisediminicola antarctica	100.0	1116	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marisediminicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014378715.1	s__Marisediminicola sp014378715	81.026	489	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marisediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057645.1	s__Marisediminicola senii	80.5188	462	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marisediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040105.1	s__Lacisediminihabitans profunda	79.3773	465	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725325.1	s__Rhodoglobus sp001725325	79.3514	402	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014639655.1	s__Conyzicola nivalis	79.3031	419	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204935.1	s__Conyzicola lurida	79.2824	462	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217685.1	s__Lacisediminihabitans sp014217685	79.0054	380	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280205.1	s__Clavibacter capsici	78.9047	357	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.16	95.31	0.96	0.91	6	-
GCF_002931235.1	s__Subtercola sp002931235	78.7106	311	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898805.1	s__Leifsonia sp001898805	78.6708	358	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648575.1	s__Agromyces mediolanus	78.61	359	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012317045.1	s__Leifsonia sp002105485	78.5896	359	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.03	98.03	0.91	0.91	2	-
GCF_004216665.1	s__Agromyces ramosus	78.4792	384	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297555.1	s__Rhodoglobus sp004297555	78.373	190	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155915.1	s__Microbacterium sp900155915	77.8129	277	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:11:28,139] [INFO] GTDB search result was written to GCF_009930795.1_ASM993079v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:11:28,139] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:11:28,144] [INFO] DFAST_QC result json was written to GCF_009930795.1_ASM993079v1_genomic.fna/dqc_result.json
[2024-01-24 14:11:28,145] [INFO] DFAST_QC completed!
[2024-01-24 14:11:28,145] [INFO] Total running time: 0h1m13s