[2024-01-24 14:14:45,784] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:45,787] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:45,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d448eb6-841e-41c1-81f6-e419ef79a05b/dqc_reference
[2024-01-24 14:14:47,097] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:47,098] [INFO] Task started: Prodigal
[2024-01-24 14:14:47,098] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d7d2161-ffa1-47bb-8ecf-2af95e6f1bc6/GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/cds.fna -a GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:56,100] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:56,100] [INFO] Task started: HMMsearch
[2024-01-24 14:14:56,100] [INFO] Running command: hmmsearch --tblout GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d448eb6-841e-41c1-81f6-e419ef79a05b/dqc_reference/reference_markers.hmm GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:56,352] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:56,354] [INFO] Found 6/6 markers.
[2024-01-24 14:14:56,384] [INFO] Query marker FASTA was written to GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:14:56,384] [INFO] Task started: Blastn
[2024-01-24 14:14:56,385] [INFO] Running command: blastn -query GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d448eb6-841e-41c1-81f6-e419ef79a05b/dqc_reference/reference_markers.fasta -out GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:57,066] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:57,069] [INFO] Selected 12 target genomes.
[2024-01-24 14:14:57,069] [INFO] Target genome list was writen to GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:14:57,085] [INFO] Task started: fastANI
[2024-01-24 14:14:57,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d7d2161-ffa1-47bb-8ecf-2af95e6f1bc6/GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna.gz --refList GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:11,786] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:11,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d448eb6-841e-41c1-81f6-e419ef79a05b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:11,788] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d448eb6-841e-41c1-81f6-e419ef79a05b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:11,801] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:15:11,801] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:11,801] [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
Alysiella filiformis	strain=DSM 16848	GCA_900230205.1	194196	194196	type	True	100.0	767	771	95	conclusive
Alysiella filiformis	strain=DSM 16848	GCA_014054525.1	194196	194196	type	True	99.9798	769	771	95	conclusive
Alysiella filiformis	strain=DSM 16848	GCA_020162295.1	194196	194196	type	True	99.9777	771	771	95	conclusive
Alysiella crassa	strain=S6	GCA_022871045.1	153491	153491	type	True	85.5348	492	771	95	below_threshold
Alysiella crassa	strain=DSM 2578	GCA_000745955.1	153491	153491	type	True	85.4897	466	771	95	below_threshold
Alysiella crassa	strain=NCTC10283	GCA_900445245.1	153491	153491	type	True	85.2681	488	771	95	below_threshold
Kingella kingae	strain=4177/66	GCA_022871005.1	504	504	type	True	79.2766	370	771	95	below_threshold
Simonsiella muelleri	strain=ATCC 29453	GCA_000163775.2	72	72	type	True	78.7592	319	771	95	below_threshold
Simonsiella muelleri	strain=ATCC 29453	GCA_002951835.1	72	72	type	True	78.7419	321	771	95	below_threshold
Vitreoscilla stercoraria	strain=SAG 1488-6	GCA_022870945.1	61	61	type	True	76.3026	71	771	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:11,803] [INFO] DFAST Taxonomy check result was written to GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:15:11,804] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:11,804] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:11,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d448eb6-841e-41c1-81f6-e419ef79a05b/dqc_reference/checkm_data
[2024-01-24 14:15:11,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:11,833] [INFO] Task started: CheckM
[2024-01-24 14:15:11,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/checkm_input GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:15:42,901] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:42,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:42,924] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:42,924] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:42,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:15:42,925] [INFO] Task started: Blastn
[2024-01-24 14:15:42,925] [INFO] Running command: blastn -query GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d448eb6-841e-41c1-81f6-e419ef79a05b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:44,085] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:44,087] [INFO] Selected 10 target genomes.
[2024-01-24 14:15:44,088] [INFO] Target genome list was writen to GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:44,111] [INFO] Task started: fastANI
[2024-01-24 14:15:44,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d7d2161-ffa1-47bb-8ecf-2af95e6f1bc6/GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna.gz --refList GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:52,043] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:52,052] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:52,053] [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_014054525.1	s__Alysiella filiformis	99.9798	769	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_000745955.1	s__Alysiella crassa	85.4696	467	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.94	99.94	0.99	0.99	2	-
GCF_900111845.1	s__Kingella kingae	79.2607	359	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	98.43	98.16	0.96	0.94	37	-
GCF_002951835.1	s__Simonsiella muelleri	78.7311	322	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Simonsiella	95.0	99.93	99.93	0.98	0.98	2	-
GCF_000751855.1	s__Kingella negevensis	78.6179	296	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	99.09	98.48	0.96	0.94	3	-
GCF_014054725.1	s__Conchiformibius steedae	78.2825	279	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Conchiformibius	95.0	98.09	96.18	0.94	0.87	3	-
GCF_014054985.1	s__Kingella_B oralis	77.9809	284	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B	95.0	98.22	96.45	0.95	0.91	3	-
GCA_017446355.1	s__RGIG3394 sp017446355	77.1877	139	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__RGIG3394	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813705.1	s__Neisseria cerebrosa	77.0157	124	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5429	97.92	97.52	0.91	0.89	5	-
GCF_000745895.1	s__Stenoxybacter acetivorans	76.4764	120	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Stenoxybacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:52,054] [INFO] GTDB search result was written to GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:52,055] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:52,058] [INFO] DFAST_QC result json was written to GCF_900230205.1_IMG-taxon_2574179727_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:15:52,058] [INFO] DFAST_QC completed!
[2024-01-24 14:15:52,058] [INFO] Total running time: 0h1m6s