[2024-01-24 11:35:08,386] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:08,389] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:08,389] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c656ff5-17b4-4c82-9af7-d81c44ef7593/dqc_reference
[2024-01-24 11:35:09,596] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:09,597] [INFO] Task started: Prodigal
[2024-01-24 11:35:09,597] [INFO] Running command: gunzip -c /var/lib/cwl/stgeafe26c3-ddd7-440a-986c-bd930d61260f/GCF_004011095.1_ASM401109v1_genomic.fna.gz | prodigal -d GCF_004011095.1_ASM401109v1_genomic.fna/cds.fna -a GCF_004011095.1_ASM401109v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:18,034] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:18,035] [INFO] Task started: HMMsearch
[2024-01-24 11:35:18,035] [INFO] Running command: hmmsearch --tblout GCF_004011095.1_ASM401109v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c656ff5-17b4-4c82-9af7-d81c44ef7593/dqc_reference/reference_markers.hmm GCF_004011095.1_ASM401109v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:18,274] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:18,276] [INFO] Found 6/6 markers.
[2024-01-24 11:35:18,303] [INFO] Query marker FASTA was written to GCF_004011095.1_ASM401109v1_genomic.fna/markers.fasta
[2024-01-24 11:35:18,304] [INFO] Task started: Blastn
[2024-01-24 11:35:18,304] [INFO] Running command: blastn -query GCF_004011095.1_ASM401109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c656ff5-17b4-4c82-9af7-d81c44ef7593/dqc_reference/reference_markers.fasta -out GCF_004011095.1_ASM401109v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:19,425] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:19,428] [INFO] Selected 10 target genomes.
[2024-01-24 11:35:19,428] [INFO] Target genome list was writen to GCF_004011095.1_ASM401109v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:19,446] [INFO] Task started: fastANI
[2024-01-24 11:35:19,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgeafe26c3-ddd7-440a-986c-bd930d61260f/GCF_004011095.1_ASM401109v1_genomic.fna.gz --refList GCF_004011095.1_ASM401109v1_genomic.fna/target_genomes.txt --output GCF_004011095.1_ASM401109v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:27,191] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:27,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c656ff5-17b4-4c82-9af7-d81c44ef7593/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:27,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c656ff5-17b4-4c82-9af7-d81c44ef7593/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:27,205] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:35:27,205] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:27,205] [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
Rathayibacter rathayi	strain=DSM 7485	GCA_004011095.1	33887	33887	type	True	100.0	1033	1034	95	conclusive
Rathayibacter rathayi	strain=DSM 7485	GCA_007828845.1	33887	33887	type	True	99.9959	1031	1034	95	conclusive
Rathayibacter rathayi	strain=VKM Ac-1601	GCA_900215645.1	33887	33887	type	True	99.9756	1005	1034	95	conclusive
Rathayibacter rathayi	strain=VKM Ac-1601	GCA_009806975.1	33887	33887	type	True	99.9722	994	1034	95	conclusive
Rathayibacter tritici	strain=DSM 7486	GCA_002932875.1	33888	33888	type	True	92.0853	853	1034	95	below_threshold
Rathayibacter tanaceti	strain=VKM Ac-2596	GCA_001634385.1	1671680	1671680	type	True	85.9333	690	1034	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.9633	390	1034	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.6953	310	1034	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.4516	334	1034	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.234	350	1034	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:27,207] [INFO] DFAST Taxonomy check result was written to GCF_004011095.1_ASM401109v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:27,207] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:27,208] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:27,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c656ff5-17b4-4c82-9af7-d81c44ef7593/dqc_reference/checkm_data
[2024-01-24 11:35:27,209] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:27,241] [INFO] Task started: CheckM
[2024-01-24 11:35:27,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004011095.1_ASM401109v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004011095.1_ASM401109v1_genomic.fna/checkm_input GCF_004011095.1_ASM401109v1_genomic.fna/checkm_result
[2024-01-24 11:35:56,129] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:56,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:56,152] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:56,152] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:56,152] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004011095.1_ASM401109v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:56,153] [INFO] Task started: Blastn
[2024-01-24 11:35:56,153] [INFO] Running command: blastn -query GCF_004011095.1_ASM401109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c656ff5-17b4-4c82-9af7-d81c44ef7593/dqc_reference/reference_markers_gtdb.fasta -out GCF_004011095.1_ASM401109v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:57,963] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:57,966] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:57,966] [INFO] Target genome list was writen to GCF_004011095.1_ASM401109v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:57,976] [INFO] Task started: fastANI
[2024-01-24 11:35:57,976] [INFO] Running command: fastANI --query /var/lib/cwl/stgeafe26c3-ddd7-440a-986c-bd930d61260f/GCF_004011095.1_ASM401109v1_genomic.fna.gz --refList GCF_004011095.1_ASM401109v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004011095.1_ASM401109v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:09,167] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:09,179] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:09,179] [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_004011095.1	s__Rathayibacter rathayi	100.0	1033	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.62	99.25	0.95	0.91	27	conclusive
GCF_002932875.1	s__Rathayibacter tritici	92.0928	853	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.66	99.47	0.96	0.94	6	-
GCF_009866585.1	s__Rathayibacter sp002930885	89.2035	829	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.23	95.98	0.89	0.85	55	-
GCF_009866655.1	s__Rathayibacter sp009866655	84.9647	757	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.89	98.89	0.92	0.92	2	-
GCF_009834185.1	s__Rathayibacter sp009834185	84.8666	777	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013205055.1	s__Rathayibacter sp013205055	84.7134	766	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009834225.1	s__Rathayibacter sp009834225	84.6625	755	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249015.1	s__Rathayibacter agropyri	84.5339	791	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807095.1	s__Rathayibacter sp009807095	84.4845	735	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.31	99.31	0.97	0.97	2	-
GCF_001995175.1	s__Rathayibacter sp001995175	84.3877	706	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355185.1	s__Rathayibacter sp017355185	84.1877	688	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177245.1	s__Rathayibacter oskolensis	83.9559	746	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351245.1	s__Rathayibacter sp015351245	83.8015	683	1034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:09,182] [INFO] GTDB search result was written to GCF_004011095.1_ASM401109v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:09,183] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:09,187] [INFO] DFAST_QC result json was written to GCF_004011095.1_ASM401109v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:09,187] [INFO] DFAST_QC completed!
[2024-01-24 11:36:09,187] [INFO] Total running time: 0h1m1s