[2024-01-24 12:53:55,571] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:55,574] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:55,574] [INFO] DQC Reference Directory: /var/lib/cwl/stg331cd668-3777-471d-9bba-165b3cb2f74d/dqc_reference
[2024-01-24 12:53:56,845] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:56,846] [INFO] Task started: Prodigal
[2024-01-24 12:53:56,847] [INFO] Running command: gunzip -c /var/lib/cwl/stga9cd7afa-d1d8-4e90-abe6-f8945f146ce8/GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/cds.fna -a GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:15,282] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:15,283] [INFO] Task started: HMMsearch
[2024-01-24 12:54:15,283] [INFO] Running command: hmmsearch --tblout GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg331cd668-3777-471d-9bba-165b3cb2f74d/dqc_reference/reference_markers.hmm GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:15,650] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:15,651] [INFO] Found 6/6 markers.
[2024-01-24 12:54:15,696] [INFO] Query marker FASTA was written to GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:54:15,696] [INFO] Task started: Blastn
[2024-01-24 12:54:15,696] [INFO] Running command: blastn -query GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg331cd668-3777-471d-9bba-165b3cb2f74d/dqc_reference/reference_markers.fasta -out GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:16,784] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:16,788] [INFO] Selected 12 target genomes.
[2024-01-24 12:54:16,788] [INFO] Target genome list was writen to GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:54:16,794] [INFO] Task started: fastANI
[2024-01-24 12:54:16,794] [INFO] Running command: fastANI --query /var/lib/cwl/stga9cd7afa-d1d8-4e90-abe6-f8945f146ce8/GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna.gz --refList GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:31,902] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:31,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg331cd668-3777-471d-9bba-165b3cb2f74d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:31,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg331cd668-3777-471d-9bba-165b3cb2f74d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:31,914] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:31,915] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:31,915] [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
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	100.0	1813	1821	95	conclusive
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	93.2326	1504	1821	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	93.127	1551	1821	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	92.3924	1350	1821	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	85.6981	1267	1821	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	85.6753	1195	1821	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	80.8331	813	1821	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	80.7702	863	1821	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.404	669	1821	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.3501	678	1821	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.2794	668	1821	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	80.001	744	1821	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:31,917] [INFO] DFAST Taxonomy check result was written to GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:54:31,918] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:31,918] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:31,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg331cd668-3777-471d-9bba-165b3cb2f74d/dqc_reference/checkm_data
[2024-01-24 12:54:31,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:31,974] [INFO] Task started: CheckM
[2024-01-24 12:54:31,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/checkm_input GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:55:46,456] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:46,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:46,481] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:46,482] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:46,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:55:46,482] [INFO] Task started: Blastn
[2024-01-24 12:55:46,482] [INFO] Running command: blastn -query GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg331cd668-3777-471d-9bba-165b3cb2f74d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:48,602] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:48,605] [INFO] Selected 6 target genomes.
[2024-01-24 12:55:48,606] [INFO] Target genome list was writen to GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:48,609] [INFO] Task started: fastANI
[2024-01-24 12:55:48,609] [INFO] Running command: fastANI --query /var/lib/cwl/stga9cd7afa-d1d8-4e90-abe6-f8945f146ce8/GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna.gz --refList GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:57,725] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:57,733] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:57,733] [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_900104515.1	s__Acidovorax_A cattleyae	100.0	1814	1821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.69	99.69	0.82	0.82	2	conclusive
GCF_000687165.1	s__Acidovorax_A oryzae	93.2094	1506	1821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	98.08	98.08	0.87	0.87	2	-
GCF_000176855.2	s__Acidovorax_A avenae	93.1268	1551	1821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	96.92	95.92	0.74	0.51	18	-
GCF_900100305.1	s__Acidovorax_A citrulli	92.3791	1351	1821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.47	99.27	0.97	0.96	11	-
GCA_002397315.1	s__Acidovorax_A sp002397315	88.4792	1294	1821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269065.1	s__Acidovorax_A anthurii	85.6585	1198	1821	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:57,735] [INFO] GTDB search result was written to GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:57,736] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:57,739] [INFO] DFAST_QC result json was written to GCF_900104515.1_IMG-taxon_2634166355_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:55:57,739] [INFO] DFAST_QC completed!
[2024-01-24 12:55:57,739] [INFO] Total running time: 0h2m2s