[2024-01-24 15:27:11,261] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:11,269] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:11,270] [INFO] DQC Reference Directory: /var/lib/cwl/stga18234b6-66c3-47d4-80dd-f267fbd5fb28/dqc_reference
[2024-01-24 15:27:12,709] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:12,710] [INFO] Task started: Prodigal
[2024-01-24 15:27:12,710] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b067d5c-387d-46e5-8b8f-3f2cfb22e361/GCF_007828845.1_ASM782884v1_genomic.fna.gz | prodigal -d GCF_007828845.1_ASM782884v1_genomic.fna/cds.fna -a GCF_007828845.1_ASM782884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:21,438] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:21,438] [INFO] Task started: HMMsearch
[2024-01-24 15:27:21,438] [INFO] Running command: hmmsearch --tblout GCF_007828845.1_ASM782884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga18234b6-66c3-47d4-80dd-f267fbd5fb28/dqc_reference/reference_markers.hmm GCF_007828845.1_ASM782884v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:21,689] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:21,690] [INFO] Found 6/6 markers.
[2024-01-24 15:27:21,719] [INFO] Query marker FASTA was written to GCF_007828845.1_ASM782884v1_genomic.fna/markers.fasta
[2024-01-24 15:27:21,719] [INFO] Task started: Blastn
[2024-01-24 15:27:21,719] [INFO] Running command: blastn -query GCF_007828845.1_ASM782884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga18234b6-66c3-47d4-80dd-f267fbd5fb28/dqc_reference/reference_markers.fasta -out GCF_007828845.1_ASM782884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:22,911] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:22,919] [INFO] Selected 10 target genomes.
[2024-01-24 15:27:22,919] [INFO] Target genome list was writen to GCF_007828845.1_ASM782884v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:23,332] [INFO] Task started: fastANI
[2024-01-24 15:27:23,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b067d5c-387d-46e5-8b8f-3f2cfb22e361/GCF_007828845.1_ASM782884v1_genomic.fna.gz --refList GCF_007828845.1_ASM782884v1_genomic.fna/target_genomes.txt --output GCF_007828845.1_ASM782884v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:30,930] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:30,931] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga18234b6-66c3-47d4-80dd-f267fbd5fb28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:30,931] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga18234b6-66c3-47d4-80dd-f267fbd5fb28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:30,941] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 15:27:30,941] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:30,941] [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_007828845.1	33887	33887	type	True	100.0	1064	1064	95	conclusive
Rathayibacter rathayi	strain=DSM 7485	GCA_004011095.1	33887	33887	type	True	99.9955	1032	1064	95	conclusive
Rathayibacter rathayi	strain=VKM Ac-1601	GCA_900215645.1	33887	33887	type	True	99.9701	1020	1064	95	conclusive
Rathayibacter rathayi	strain=VKM Ac-1601	GCA_009806975.1	33887	33887	type	True	99.9657	1016	1064	95	conclusive
Rathayibacter tritici	strain=DSM 7486	GCA_002932875.1	33888	33888	type	True	92.1153	865	1064	95	below_threshold
Rathayibacter tanaceti	strain=VKM Ac-2596	GCA_001634385.1	1671680	1671680	type	True	85.843	690	1064	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.9751	387	1064	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.7773	312	1064	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.7219	319	1064	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.2245	359	1064	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:30,943] [INFO] DFAST Taxonomy check result was written to GCF_007828845.1_ASM782884v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:30,943] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:30,943] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:30,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga18234b6-66c3-47d4-80dd-f267fbd5fb28/dqc_reference/checkm_data
[2024-01-24 15:27:30,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:30,982] [INFO] Task started: CheckM
[2024-01-24 15:27:30,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007828845.1_ASM782884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007828845.1_ASM782884v1_genomic.fna/checkm_input GCF_007828845.1_ASM782884v1_genomic.fna/checkm_result
[2024-01-24 15:28:01,958] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:01,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:02,179] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:02,179] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:02,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007828845.1_ASM782884v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:02,180] [INFO] Task started: Blastn
[2024-01-24 15:28:02,180] [INFO] Running command: blastn -query GCF_007828845.1_ASM782884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga18234b6-66c3-47d4-80dd-f267fbd5fb28/dqc_reference/reference_markers_gtdb.fasta -out GCF_007828845.1_ASM782884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:03,994] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:03,999] [INFO] Selected 13 target genomes.
[2024-01-24 15:28:03,999] [INFO] Target genome list was writen to GCF_007828845.1_ASM782884v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:04,011] [INFO] Task started: fastANI
[2024-01-24 15:28:04,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b067d5c-387d-46e5-8b8f-3f2cfb22e361/GCF_007828845.1_ASM782884v1_genomic.fna.gz --refList GCF_007828845.1_ASM782884v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007828845.1_ASM782884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:15,544] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:15,558] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:15,558] [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	99.9955	1032	1064	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	92.1343	864	1064	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	89.2181	825	1064	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	84.9621	761	1064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.89	98.89	0.92	0.92	2	-
GCF_013205055.1	s__Rathayibacter sp013205055	84.8675	759	1064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009834185.1	s__Rathayibacter sp009834185	84.7969	789	1064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834225.1	s__Rathayibacter sp009834225	84.6297	754	1064	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	84.606	774	1064	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	84.5401	742	1064	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	84.4351	696	1064	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	84.1664	694	1064	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	84.0762	733	1064	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	83.6646	687	1064	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 15:28:15,560] [INFO] GTDB search result was written to GCF_007828845.1_ASM782884v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:15,561] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:15,565] [INFO] DFAST_QC result json was written to GCF_007828845.1_ASM782884v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:15,565] [INFO] DFAST_QC completed!
[2024-01-24 15:28:15,565] [INFO] Total running time: 0h1m4s