[2024-01-24 14:28:07,844] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:07,846] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:07,846] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a03be10-5949-4976-8824-6a61f5c79a66/dqc_reference
[2024-01-24 14:28:10,422] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,423] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,424] [INFO] Running command: gunzip -c /var/lib/cwl/stg7afcb18c-c475-411a-b5be-355bd5b107d9/GCF_008710705.1_ASM871070v1_genomic.fna.gz | prodigal -d GCF_008710705.1_ASM871070v1_genomic.fna/cds.fna -a GCF_008710705.1_ASM871070v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:19,616] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:19,617] [INFO] Task started: HMMsearch
[2024-01-24 14:28:19,617] [INFO] Running command: hmmsearch --tblout GCF_008710705.1_ASM871070v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a03be10-5949-4976-8824-6a61f5c79a66/dqc_reference/reference_markers.hmm GCF_008710705.1_ASM871070v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:19,928] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:19,930] [INFO] Found 6/6 markers.
[2024-01-24 14:28:19,973] [INFO] Query marker FASTA was written to GCF_008710705.1_ASM871070v1_genomic.fna/markers.fasta
[2024-01-24 14:28:19,974] [INFO] Task started: Blastn
[2024-01-24 14:28:19,974] [INFO] Running command: blastn -query GCF_008710705.1_ASM871070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a03be10-5949-4976-8824-6a61f5c79a66/dqc_reference/reference_markers.fasta -out GCF_008710705.1_ASM871070v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:21,399] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:21,403] [INFO] Selected 21 target genomes.
[2024-01-24 14:28:21,403] [INFO] Target genome list was writen to GCF_008710705.1_ASM871070v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:21,427] [INFO] Task started: fastANI
[2024-01-24 14:28:21,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg7afcb18c-c475-411a-b5be-355bd5b107d9/GCF_008710705.1_ASM871070v1_genomic.fna.gz --refList GCF_008710705.1_ASM871070v1_genomic.fna/target_genomes.txt --output GCF_008710705.1_ASM871070v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:37,522] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:37,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a03be10-5949-4976-8824-6a61f5c79a66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:37,523] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a03be10-5949-4976-8824-6a61f5c79a66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:37,539] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:37,539] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:37,540] [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
Microbacterium radiodurans	strain=DSM 25564	GCA_008710705.1	661398	661398	type	True	100.0	1056	1056	95	conclusive
Microbacterium imperiale	strain=DSM 20530	GCA_017876655.1	33884	33884	type	True	84.2462	736	1056	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.6103	563	1056	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	81.4279	543	1056	95	below_threshold
Microbacterium lacticum	strain=JCM 1379	GCA_014646835.1	33885	33885	type	True	81.3686	522	1056	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	81.3629	546	1056	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	81.3238	544	1056	95	below_threshold
Microbacterium lacticum	strain=NBRC 14135	GCA_006539445.1	33885	33885	type	True	81.2904	530	1056	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	81.2764	542	1056	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	81.18	539	1056	95	below_threshold
Microbacterium marinum	strain=DSM 24947	GCA_014204835.1	421115	421115	type	True	81.055	511	1056	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	80.9249	532	1056	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	80.7277	560	1056	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.7217	559	1056	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_001456955.1	993073	993073	type	True	80.7169	512	1056	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	80.6846	553	1056	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_900096885.1	993073	993073	type	True	80.67	516	1056	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.6562	531	1056	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.6298	528	1056	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.3229	552	1056	95	below_threshold
Microbacterium timonense	strain=Marseille-P5731	GCA_900292075.1	2086576	2086576	type	True	80.0728	500	1056	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:37,541] [INFO] DFAST Taxonomy check result was written to GCF_008710705.1_ASM871070v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:37,542] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:37,542] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:37,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a03be10-5949-4976-8824-6a61f5c79a66/dqc_reference/checkm_data
[2024-01-24 14:28:37,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:37,581] [INFO] Task started: CheckM
[2024-01-24 14:28:37,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008710705.1_ASM871070v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008710705.1_ASM871070v1_genomic.fna/checkm_input GCF_008710705.1_ASM871070v1_genomic.fna/checkm_result
[2024-01-24 14:29:23,674] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:23,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:23,693] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:23,693] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:23,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008710705.1_ASM871070v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:23,694] [INFO] Task started: Blastn
[2024-01-24 14:29:23,694] [INFO] Running command: blastn -query GCF_008710705.1_ASM871070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a03be10-5949-4976-8824-6a61f5c79a66/dqc_reference/reference_markers_gtdb.fasta -out GCF_008710705.1_ASM871070v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:25,773] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:25,777] [INFO] Selected 9 target genomes.
[2024-01-24 14:29:25,777] [INFO] Target genome list was writen to GCF_008710705.1_ASM871070v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:25,797] [INFO] Task started: fastANI
[2024-01-24 14:29:25,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg7afcb18c-c475-411a-b5be-355bd5b107d9/GCF_008710705.1_ASM871070v1_genomic.fna.gz --refList GCF_008710705.1_ASM871070v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008710705.1_ASM871070v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:33,585] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:33,593] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:33,594] [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_008710705.1	s__Microbacterium radiodurans	100.0	1056	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017876655.1	s__Microbacterium imperiale	84.2525	735	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245215.1	s__Microbacterium sp002245215	84.2118	747	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339645.1	s__Microbacterium arborescens	84.0784	752	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	98.95	0.97	0.96	7	-
GCF_013389665.1	s__Microbacterium oleivorans_C	84.0597	764	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289625.1	s__Microbacterium sp003289625	84.0418	737	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.69	98.69	0.93	0.93	2	-
GCF_003610405.1	s__Microbacterium sp003610405	83.9588	735	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102175.1	s__Microbacterium sp900102175	83.7703	762	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651225.1	s__Microbacterium telephonicum	81.6097	563	1056	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 14:29:33,595] [INFO] GTDB search result was written to GCF_008710705.1_ASM871070v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:33,596] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:33,600] [INFO] DFAST_QC result json was written to GCF_008710705.1_ASM871070v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:33,600] [INFO] DFAST_QC completed!
[2024-01-24 14:29:33,600] [INFO] Total running time: 0h1m26s