[2024-01-24 11:35:11,743] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,749] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg7763917b-7e37-4387-b3ca-fe2a62540efe/dqc_reference
[2024-01-24 11:35:13,064] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:13,065] [INFO] Task started: Prodigal
[2024-01-24 11:35:13,065] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b907d3b-fe78-43fb-a772-1e08001b02ae/GCF_014645015.1_ASM1464501v1_genomic.fna.gz | prodigal -d GCF_014645015.1_ASM1464501v1_genomic.fna/cds.fna -a GCF_014645015.1_ASM1464501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:22,544] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:22,545] [INFO] Task started: HMMsearch
[2024-01-24 11:35:22,545] [INFO] Running command: hmmsearch --tblout GCF_014645015.1_ASM1464501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7763917b-7e37-4387-b3ca-fe2a62540efe/dqc_reference/reference_markers.hmm GCF_014645015.1_ASM1464501v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:22,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:22,807] [INFO] Found 6/6 markers.
[2024-01-24 11:35:22,835] [INFO] Query marker FASTA was written to GCF_014645015.1_ASM1464501v1_genomic.fna/markers.fasta
[2024-01-24 11:35:22,835] [INFO] Task started: Blastn
[2024-01-24 11:35:22,836] [INFO] Running command: blastn -query GCF_014645015.1_ASM1464501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7763917b-7e37-4387-b3ca-fe2a62540efe/dqc_reference/reference_markers.fasta -out GCF_014645015.1_ASM1464501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:23,692] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:23,700] [INFO] Selected 19 target genomes.
[2024-01-24 11:35:23,700] [INFO] Target genome list was writen to GCF_014645015.1_ASM1464501v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:23,708] [INFO] Task started: fastANI
[2024-01-24 11:35:23,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b907d3b-fe78-43fb-a772-1e08001b02ae/GCF_014645015.1_ASM1464501v1_genomic.fna.gz --refList GCF_014645015.1_ASM1464501v1_genomic.fna/target_genomes.txt --output GCF_014645015.1_ASM1464501v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:35,262] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:35,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7763917b-7e37-4387-b3ca-fe2a62540efe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:35,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7763917b-7e37-4387-b3ca-fe2a62540efe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:35,279] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:35,279] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:35,280] [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
Salinibacterium xinjiangense	strain=CGMCC 1.5381	GCA_014645015.1	386302	386302	type	True	100.0	1003	1004	95	conclusive
Salinibacterium xinjiangense	strain=CGMCC 1.05381	GCA_900230175.1	386302	386302	type	True	99.9992	1002	1004	95	conclusive
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	78.2726	345	1004	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	78.1755	290	1004	95	below_threshold
Lacisediminihabitans profunda	strain=CHu50b-6-2	GCA_008040105.1	2594790	2594790	type	True	78.0011	303	1004	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	78.001	279	1004	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	77.9902	286	1004	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	77.9851	187	1004	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=LMG 3663	GCA_002240565.1	33014	28447	type	True	77.9458	217	1004	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	77.9451	218	1004	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	77.8901	188	1004	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	77.872	217	1004	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	77.811	213	1004	95	below_threshold
Lacisediminihabitans changchengi	strain=G11-30	GCA_016634425.1	2787634	2787634	type	True	77.796	261	1004	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	77.6687	245	1004	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	77.6575	215	1004	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	77.5848	238	1004	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.4648	223	1004	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	77.2226	226	1004	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:35,289] [INFO] DFAST Taxonomy check result was written to GCF_014645015.1_ASM1464501v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:35,290] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:35,291] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:35,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7763917b-7e37-4387-b3ca-fe2a62540efe/dqc_reference/checkm_data
[2024-01-24 11:35:35,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:35,329] [INFO] Task started: CheckM
[2024-01-24 11:35:35,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645015.1_ASM1464501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645015.1_ASM1464501v1_genomic.fna/checkm_input GCF_014645015.1_ASM1464501v1_genomic.fna/checkm_result
[2024-01-24 11:36:07,644] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:07,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:07,666] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:07,667] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:07,668] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645015.1_ASM1464501v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:07,668] [INFO] Task started: Blastn
[2024-01-24 11:36:07,668] [INFO] Running command: blastn -query GCF_014645015.1_ASM1464501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7763917b-7e37-4387-b3ca-fe2a62540efe/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645015.1_ASM1464501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:08,901] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:08,904] [INFO] Selected 9 target genomes.
[2024-01-24 11:36:08,905] [INFO] Target genome list was writen to GCF_014645015.1_ASM1464501v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:08,912] [INFO] Task started: fastANI
[2024-01-24 11:36:08,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b907d3b-fe78-43fb-a772-1e08001b02ae/GCF_014645015.1_ASM1464501v1_genomic.fna.gz --refList GCF_014645015.1_ASM1464501v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645015.1_ASM1464501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:14,758] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:14,772] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:14,773] [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_014645015.1	s__Rhodoglobus xinjiangensis	100.0	1003	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_015752305.1	s__Rhodoglobus sp015752305	85.5537	730	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725325.1	s__Rhodoglobus sp001725325	79.2878	411	1004	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	79.0416	405	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	98.49	97.73	0.85	0.78	4	-
GCF_004310685.1	s__Conyzicola arctica	78.9093	332	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410945.1	s__Rhodoglobus sp013410945	78.3097	314	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449675.1	s__Glaciihabitans sp018449675	77.9342	250	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Glaciihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428745.1	s__Leifsonia sp001428745	77.6184	249	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003852775.1	s__Protaetiibacter sp003852775	77.3805	218	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:14,774] [INFO] GTDB search result was written to GCF_014645015.1_ASM1464501v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:14,775] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:14,778] [INFO] DFAST_QC result json was written to GCF_014645015.1_ASM1464501v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:14,778] [INFO] DFAST_QC completed!
[2024-01-24 11:36:14,779] [INFO] Total running time: 0h1m3s