[2024-01-24 14:28:17,980] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:17,984] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:17,985] [INFO] DQC Reference Directory: /var/lib/cwl/stg465ab8f7-fd39-4824-a16a-3ee10a74b246/dqc_reference
[2024-01-24 14:28:20,483] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,484] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,485] [INFO] Running command: gunzip -c /var/lib/cwl/stg95eb6bea-7270-481d-af0d-18b36d4e2115/GCF_004340625.1_ASM434062v1_genomic.fna.gz | prodigal -d GCF_004340625.1_ASM434062v1_genomic.fna/cds.fna -a GCF_004340625.1_ASM434062v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:29,087] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:29,088] [INFO] Task started: HMMsearch
[2024-01-24 14:28:29,088] [INFO] Running command: hmmsearch --tblout GCF_004340625.1_ASM434062v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg465ab8f7-fd39-4824-a16a-3ee10a74b246/dqc_reference/reference_markers.hmm GCF_004340625.1_ASM434062v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:29,395] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:29,397] [INFO] Found 6/6 markers.
[2024-01-24 14:28:29,432] [INFO] Query marker FASTA was written to GCF_004340625.1_ASM434062v1_genomic.fna/markers.fasta
[2024-01-24 14:28:29,434] [INFO] Task started: Blastn
[2024-01-24 14:28:29,435] [INFO] Running command: blastn -query GCF_004340625.1_ASM434062v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg465ab8f7-fd39-4824-a16a-3ee10a74b246/dqc_reference/reference_markers.fasta -out GCF_004340625.1_ASM434062v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:30,847] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:30,851] [INFO] Selected 13 target genomes.
[2024-01-24 14:28:30,852] [INFO] Target genome list was writen to GCF_004340625.1_ASM434062v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:30,871] [INFO] Task started: fastANI
[2024-01-24 14:28:30,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg95eb6bea-7270-481d-af0d-18b36d4e2115/GCF_004340625.1_ASM434062v1_genomic.fna.gz --refList GCF_004340625.1_ASM434062v1_genomic.fna/target_genomes.txt --output GCF_004340625.1_ASM434062v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:41,502] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:41,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg465ab8f7-fd39-4824-a16a-3ee10a74b246/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:41,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg465ab8f7-fd39-4824-a16a-3ee10a74b246/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:41,517] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:28:41,517] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:41,517] [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 tanaceti	strain=VKM Ac-2596	GCA_004340625.1	1671680	1671680	type	True	100.0	1052	1053	95	conclusive
Rathayibacter tanaceti	strain=VKM Ac-2596	GCA_001634385.1	1671680	1671680	type	True	99.8284	885	1053	95	conclusive
Rathayibacter tritici	strain=DSM 7486	GCA_002932875.1	33888	33888	type	True	86.19	776	1053	95	below_threshold
Rathayibacter rathayi	strain=VKM Ac-1601	GCA_900215645.1	33887	33887	type	True	85.841	795	1053	95	below_threshold
Rathayibacter rathayi	strain=VKM Ac-1601	GCA_009806975.1	33887	33887	type	True	85.8187	784	1053	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	85.3833	825	1053	95	below_threshold
Rathayibacter agropyri	strain=VKM Ac-2828	GCA_013249015.1	1634927	1634927	type	True	85.2381	745	1053	95	below_threshold
Rathayibacter caricis	strain=DSM 15933	GCA_003044275.1	110936	110936	type	True	85.0252	816	1053	95	below_threshold
Rathayibacter oskolensis	strain=VKM Ac-2121	GCA_900177245.1	1891671	1891671	type	True	84.9061	776	1053	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.4005	419	1053	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.3089	430	1053	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.8291	382	1053	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.8024	370	1053	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:41,519] [INFO] DFAST Taxonomy check result was written to GCF_004340625.1_ASM434062v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:41,519] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:41,519] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:41,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg465ab8f7-fd39-4824-a16a-3ee10a74b246/dqc_reference/checkm_data
[2024-01-24 14:28:41,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:41,554] [INFO] Task started: CheckM
[2024-01-24 14:28:41,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004340625.1_ASM434062v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004340625.1_ASM434062v1_genomic.fna/checkm_input GCF_004340625.1_ASM434062v1_genomic.fna/checkm_result
[2024-01-24 14:29:23,772] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:23,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:23,799] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:23,800] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:23,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004340625.1_ASM434062v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:23,801] [INFO] Task started: Blastn
[2024-01-24 14:29:23,801] [INFO] Running command: blastn -query GCF_004340625.1_ASM434062v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg465ab8f7-fd39-4824-a16a-3ee10a74b246/dqc_reference/reference_markers_gtdb.fasta -out GCF_004340625.1_ASM434062v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:25,923] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:25,927] [INFO] Selected 14 target genomes.
[2024-01-24 14:29:25,927] [INFO] Target genome list was writen to GCF_004340625.1_ASM434062v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:25,937] [INFO] Task started: fastANI
[2024-01-24 14:29:25,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg95eb6bea-7270-481d-af0d-18b36d4e2115/GCF_004340625.1_ASM434062v1_genomic.fna.gz --refList GCF_004340625.1_ASM434062v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004340625.1_ASM434062v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:40,209] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:40,224] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:40,225] [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_001634385.1	s__Rathayibacter tanaceti	99.8284	885	1053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.97	99.97	1.00	1.00	3	conclusive
GCF_009866585.1	s__Rathayibacter sp002930885	87.5257	825	1053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.23	95.98	0.89	0.85	55	-
GCF_002932875.1	s__Rathayibacter tritici	86.1657	778	1053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.66	99.47	0.96	0.94	6	-
GCF_004011095.1	s__Rathayibacter rathayi	85.7832	789	1053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.62	99.25	0.95	0.91	27	-
GCF_009807095.1	s__Rathayibacter sp009807095	85.471	812	1053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.31	99.31	0.97	0.97	2	-
GCF_009834225.1	s__Rathayibacter sp009834225	85.4509	812	1053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834185.1	s__Rathayibacter sp009834185	85.4247	820	1053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009866655.1	s__Rathayibacter sp009866655	85.4151	806	1053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.89	98.89	0.92	0.92	2	-
GCF_004011135.1	s__Rathayibacter festucae	85.3642	826	1053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	96.98	96.51	0.89	0.87	11	-
GCF_013205025.1	s__Rathayibacter sp013205025	85.3005	823	1053	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	85.2211	747	1053	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	85.1356	822	1053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001995175.1	s__Rathayibacter sp001995175	85.1275	766	1053	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	84.9214	755	1053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:40,227] [INFO] GTDB search result was written to GCF_004340625.1_ASM434062v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:40,227] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:40,231] [INFO] DFAST_QC result json was written to GCF_004340625.1_ASM434062v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:40,231] [INFO] DFAST_QC completed!
[2024-01-24 14:29:40,231] [INFO] Total running time: 0h1m22s