[2024-01-24 12:34:20,431] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:34:20,433] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:34:20,433] [INFO] DQC Reference Directory: /var/lib/cwl/stg44d539da-63cb-448d-9eb9-e34c3a7268ba/dqc_reference
[2024-01-24 12:34:21,671] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:34:21,672] [INFO] Task started: Prodigal
[2024-01-24 12:34:21,672] [INFO] Running command: gunzip -c /var/lib/cwl/stg26021cc5-c654-4dfa-bf3c-9ea917f9f6a3/GCF_009806975.1_ASM980697v1_genomic.fna.gz | prodigal -d GCF_009806975.1_ASM980697v1_genomic.fna/cds.fna -a GCF_009806975.1_ASM980697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:34:29,913] [INFO] Task succeeded: Prodigal
[2024-01-24 12:34:29,913] [INFO] Task started: HMMsearch
[2024-01-24 12:34:29,914] [INFO] Running command: hmmsearch --tblout GCF_009806975.1_ASM980697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44d539da-63cb-448d-9eb9-e34c3a7268ba/dqc_reference/reference_markers.hmm GCF_009806975.1_ASM980697v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:34:30,146] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:34:30,148] [INFO] Found 6/6 markers.
[2024-01-24 12:34:30,176] [INFO] Query marker FASTA was written to GCF_009806975.1_ASM980697v1_genomic.fna/markers.fasta
[2024-01-24 12:34:30,177] [INFO] Task started: Blastn
[2024-01-24 12:34:30,177] [INFO] Running command: blastn -query GCF_009806975.1_ASM980697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44d539da-63cb-448d-9eb9-e34c3a7268ba/dqc_reference/reference_markers.fasta -out GCF_009806975.1_ASM980697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:31,248] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:31,251] [INFO] Selected 10 target genomes.
[2024-01-24 12:34:31,252] [INFO] Target genome list was writen to GCF_009806975.1_ASM980697v1_genomic.fna/target_genomes.txt
[2024-01-24 12:34:31,257] [INFO] Task started: fastANI
[2024-01-24 12:34:31,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg26021cc5-c654-4dfa-bf3c-9ea917f9f6a3/GCF_009806975.1_ASM980697v1_genomic.fna.gz --refList GCF_009806975.1_ASM980697v1_genomic.fna/target_genomes.txt --output GCF_009806975.1_ASM980697v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:34:38,684] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:38,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44d539da-63cb-448d-9eb9-e34c3a7268ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:34:38,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44d539da-63cb-448d-9eb9-e34c3a7268ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:34:38,698] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:34:38,698] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:34:38,698] [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=VKM Ac-1601	GCA_009806975.1	33887	33887	type	True	100.0	1039	1041	95	conclusive
Rathayibacter rathayi	strain=VKM Ac-1601	GCA_900215645.1	33887	33887	type	True	99.9969	1039	1041	95	conclusive
Rathayibacter rathayi	strain=DSM 7485	GCA_007828845.1	33887	33887	type	True	99.9419	1019	1041	95	conclusive
Rathayibacter rathayi	strain=DSM 7485	GCA_004011095.1	33887	33887	type	True	99.9286	999	1041	95	conclusive
Rathayibacter tritici	strain=DSM 7486	GCA_002932875.1	33888	33888	type	True	92.0594	861	1041	95	below_threshold
Rathayibacter tanaceti	strain=VKM Ac-2596	GCA_001634385.1	1671680	1671680	type	True	85.9329	681	1041	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.8673	393	1041	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.5469	308	1041	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.4859	324	1041	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.1911	356	1041	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:34:38,700] [INFO] DFAST Taxonomy check result was written to GCF_009806975.1_ASM980697v1_genomic.fna/tc_result.tsv
[2024-01-24 12:34:38,700] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:34:38,701] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:34:38,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44d539da-63cb-448d-9eb9-e34c3a7268ba/dqc_reference/checkm_data
[2024-01-24 12:34:38,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:34:38,737] [INFO] Task started: CheckM
[2024-01-24 12:34:38,737] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009806975.1_ASM980697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009806975.1_ASM980697v1_genomic.fna/checkm_input GCF_009806975.1_ASM980697v1_genomic.fna/checkm_result
[2024-01-24 12:35:06,681] [INFO] Task succeeded: CheckM
[2024-01-24 12:35:06,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:35:06,701] [INFO] ===== Completeness check finished =====
[2024-01-24 12:35:06,702] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:35:06,703] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009806975.1_ASM980697v1_genomic.fna/markers.fasta)
[2024-01-24 12:35:06,703] [INFO] Task started: Blastn
[2024-01-24 12:35:06,703] [INFO] Running command: blastn -query GCF_009806975.1_ASM980697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44d539da-63cb-448d-9eb9-e34c3a7268ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_009806975.1_ASM980697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:35:08,454] [INFO] Task succeeded: Blastn
[2024-01-24 12:35:08,459] [INFO] Selected 13 target genomes.
[2024-01-24 12:35:08,460] [INFO] Target genome list was writen to GCF_009806975.1_ASM980697v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:35:08,471] [INFO] Task started: fastANI
[2024-01-24 12:35:08,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg26021cc5-c654-4dfa-bf3c-9ea917f9f6a3/GCF_009806975.1_ASM980697v1_genomic.fna.gz --refList GCF_009806975.1_ASM980697v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009806975.1_ASM980697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:35:19,070] [INFO] Task succeeded: fastANI
[2024-01-24 12:35:19,087] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:35:19,087] [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	99.9286	999	1041	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	92.0594	861	1041	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	89.1626	832	1041	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	84.813	756	1041	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	84.8033	754	1041	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	84.793	773	1041	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	84.6527	763	1041	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	84.5849	746	1041	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	84.5503	736	1041	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	84.3999	695	1041	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	84.0959	744	1041	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	84.0256	699	1041	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	83.6698	672	1041	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 12:35:19,089] [INFO] GTDB search result was written to GCF_009806975.1_ASM980697v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:35:19,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:35:19,092] [INFO] DFAST_QC result json was written to GCF_009806975.1_ASM980697v1_genomic.fna/dqc_result.json
[2024-01-24 12:35:19,092] [INFO] DFAST_QC completed!
[2024-01-24 12:35:19,092] [INFO] Total running time: 0h0m59s