[2024-01-24 13:50:26,363] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:26,365] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:26,365] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c53bbca-6d53-4539-a6bf-2e1d74fe8f8e/dqc_reference
[2024-01-24 13:50:27,700] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:27,701] [INFO] Task started: Prodigal
[2024-01-24 13:50:27,702] [INFO] Running command: gunzip -c /var/lib/cwl/stg81a32c0f-ed0a-469e-b3ef-0617ce0539ed/GCF_003065425.1_ASM306542v1_genomic.fna.gz | prodigal -d GCF_003065425.1_ASM306542v1_genomic.fna/cds.fna -a GCF_003065425.1_ASM306542v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:37,320] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:37,320] [INFO] Task started: HMMsearch
[2024-01-24 13:50:37,321] [INFO] Running command: hmmsearch --tblout GCF_003065425.1_ASM306542v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c53bbca-6d53-4539-a6bf-2e1d74fe8f8e/dqc_reference/reference_markers.hmm GCF_003065425.1_ASM306542v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:37,577] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:37,579] [INFO] Found 6/6 markers.
[2024-01-24 13:50:37,612] [INFO] Query marker FASTA was written to GCF_003065425.1_ASM306542v1_genomic.fna/markers.fasta
[2024-01-24 13:50:37,612] [INFO] Task started: Blastn
[2024-01-24 13:50:37,612] [INFO] Running command: blastn -query GCF_003065425.1_ASM306542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c53bbca-6d53-4539-a6bf-2e1d74fe8f8e/dqc_reference/reference_markers.fasta -out GCF_003065425.1_ASM306542v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:38,631] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:38,636] [INFO] Selected 11 target genomes.
[2024-01-24 13:50:38,636] [INFO] Target genome list was writen to GCF_003065425.1_ASM306542v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:38,655] [INFO] Task started: fastANI
[2024-01-24 13:50:38,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg81a32c0f-ed0a-469e-b3ef-0617ce0539ed/GCF_003065425.1_ASM306542v1_genomic.fna.gz --refList GCF_003065425.1_ASM306542v1_genomic.fna/target_genomes.txt --output GCF_003065425.1_ASM306542v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:45,473] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:45,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c53bbca-6d53-4539-a6bf-2e1d74fe8f8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:45,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c53bbca-6d53-4539-a6bf-2e1d74fe8f8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:45,485] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:45,485] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:45,485] [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
Mycetocola zhujimingii	strain=449 = CGMCC 1.16372	GCA_003065425.1	2079792	2079792	type	True	100.0	1063	1063	95	conclusive
Mycetocola zhadangensis	strain=ZD1-4	GCA_003668565.1	1164595	1164595	type	True	81.904	655	1063	95	below_threshold
Mycetocola zhadangensis	strain=CGMCC 1.12042	GCA_014636455.1	1164595	1164595	type	True	81.8652	647	1063	95	below_threshold
Mycetocola manganoxydans	strain=CCTCC AB209002	GCA_003667545.1	699879	699879	type	True	80.7881	526	1063	95	below_threshold
Mycetocola miduiensis	strain=CGMCC 1.11101	GCA_900115155.1	995034	995034	type	True	80.7773	487	1063	95	below_threshold
Mycetocola manganoxydans	strain=KCTC 19753	GCA_014651755.1	699879	699879	type	True	80.7193	534	1063	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.5102	274	1063	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.3262	274	1063	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.2855	269	1063	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.1915	324	1063	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.103	314	1063	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:45,487] [INFO] DFAST Taxonomy check result was written to GCF_003065425.1_ASM306542v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:45,488] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:45,488] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:45,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c53bbca-6d53-4539-a6bf-2e1d74fe8f8e/dqc_reference/checkm_data
[2024-01-24 13:50:45,490] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:45,523] [INFO] Task started: CheckM
[2024-01-24 13:50:45,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003065425.1_ASM306542v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003065425.1_ASM306542v1_genomic.fna/checkm_input GCF_003065425.1_ASM306542v1_genomic.fna/checkm_result
[2024-01-24 13:51:18,703] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:18,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:18,725] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:18,726] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:18,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003065425.1_ASM306542v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:18,726] [INFO] Task started: Blastn
[2024-01-24 13:51:18,727] [INFO] Running command: blastn -query GCF_003065425.1_ASM306542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c53bbca-6d53-4539-a6bf-2e1d74fe8f8e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003065425.1_ASM306542v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:20,196] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:20,200] [INFO] Selected 9 target genomes.
[2024-01-24 13:51:20,200] [INFO] Target genome list was writen to GCF_003065425.1_ASM306542v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:20,267] [INFO] Task started: fastANI
[2024-01-24 13:51:20,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg81a32c0f-ed0a-469e-b3ef-0617ce0539ed/GCF_003065425.1_ASM306542v1_genomic.fna.gz --refList GCF_003065425.1_ASM306542v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003065425.1_ASM306542v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:26,547] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:26,561] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:26,562] [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_003065425.1	s__Mycetocola_A zhujimingii	100.0	1063	1063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	98.22	98.22	0.95	0.95	2	conclusive
GCF_003668565.1	s__Mycetocola_A zhadangensis	81.9155	654	1063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003667545.1	s__Mycetocola_A manganoxydans	80.7881	526	1063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115155.1	s__Mycetocola_A miduiensis	80.772	491	1063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752285.1	s__Mycetocola_A sp015752285	80.6218	538	1063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984125.1	s__Okibacterium sp001984125	79.0864	325	1063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Okibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217495.1	s__Microterricola gilva	78.9483	323	1063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570845.1	s__Leifsonia_A flava	78.5662	347	1063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	95.29	95.29	0.90	0.90	2	-
GCF_004216665.1	s__Agromyces ramosus	78.2386	334	1063	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 13:51:26,564] [INFO] GTDB search result was written to GCF_003065425.1_ASM306542v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:26,564] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:26,568] [INFO] DFAST_QC result json was written to GCF_003065425.1_ASM306542v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:26,569] [INFO] DFAST_QC completed!
[2024-01-24 13:51:26,569] [INFO] Total running time: 0h1m0s