[2023-06-13 14:45:07,006] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:45:07,009] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:45:07,009] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a3a3ed5-4d08-47bf-8461-67ae8c430966/dqc_reference
[2023-06-13 14:45:08,338] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:45:08,339] [INFO] Task started: Prodigal
[2023-06-13 14:45:08,339] [INFO] Running command: gunzip -c /var/lib/cwl/stg460743b3-256c-41f1-9bbf-0937fb2380b0/GCA_022448455.1_ASM2244845v1_genomic.fna.gz | prodigal -d GCA_022448455.1_ASM2244845v1_genomic.fna/cds.fna -a GCA_022448455.1_ASM2244845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:45:11,734] [INFO] Task succeeded: Prodigal
[2023-06-13 14:45:11,734] [INFO] Task started: HMMsearch
[2023-06-13 14:45:11,734] [INFO] Running command: hmmsearch --tblout GCA_022448455.1_ASM2244845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a3a3ed5-4d08-47bf-8461-67ae8c430966/dqc_reference/reference_markers.hmm GCA_022448455.1_ASM2244845v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:45:11,930] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:45:11,931] [INFO] Found 6/6 markers.
[2023-06-13 14:45:11,958] [INFO] Query marker FASTA was written to GCA_022448455.1_ASM2244845v1_genomic.fna/markers.fasta
[2023-06-13 14:45:11,959] [INFO] Task started: Blastn
[2023-06-13 14:45:11,959] [INFO] Running command: blastn -query GCA_022448455.1_ASM2244845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a3a3ed5-4d08-47bf-8461-67ae8c430966/dqc_reference/reference_markers.fasta -out GCA_022448455.1_ASM2244845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:45:12,552] [INFO] Task succeeded: Blastn
[2023-06-13 14:45:12,556] [INFO] Selected 24 target genomes.
[2023-06-13 14:45:12,556] [INFO] Target genome list was writen to GCA_022448455.1_ASM2244845v1_genomic.fna/target_genomes.txt
[2023-06-13 14:45:12,575] [INFO] Task started: fastANI
[2023-06-13 14:45:12,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg460743b3-256c-41f1-9bbf-0937fb2380b0/GCA_022448455.1_ASM2244845v1_genomic.fna.gz --refList GCA_022448455.1_ASM2244845v1_genomic.fna/target_genomes.txt --output GCA_022448455.1_ASM2244845v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:45:24,469] [INFO] Task succeeded: fastANI
[2023-06-13 14:45:24,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a3a3ed5-4d08-47bf-8461-67ae8c430966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:45:24,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a3a3ed5-4d08-47bf-8461-67ae8c430966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:45:24,474] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:45:24,475] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:45:24,475] [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
Candidatus Pseudothioglobus singularis	strain=PS1	GCA_001281385.1	1427364	1427364	type	True	77.3521	108	533	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:45:24,477] [INFO] DFAST Taxonomy check result was written to GCA_022448455.1_ASM2244845v1_genomic.fna/tc_result.tsv
[2023-06-13 14:45:24,478] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:45:24,478] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:45:24,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a3a3ed5-4d08-47bf-8461-67ae8c430966/dqc_reference/checkm_data
[2023-06-13 14:45:24,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:45:24,499] [INFO] Task started: CheckM
[2023-06-13 14:45:24,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022448455.1_ASM2244845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022448455.1_ASM2244845v1_genomic.fna/checkm_input GCA_022448455.1_ASM2244845v1_genomic.fna/checkm_result
[2023-06-13 14:45:41,886] [INFO] Task succeeded: CheckM
[2023-06-13 14:45:41,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:45:41,905] [INFO] ===== Completeness check finished =====
[2023-06-13 14:45:41,905] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:45:41,906] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022448455.1_ASM2244845v1_genomic.fna/markers.fasta)
[2023-06-13 14:45:41,906] [INFO] Task started: Blastn
[2023-06-13 14:45:41,906] [INFO] Running command: blastn -query GCA_022448455.1_ASM2244845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a3a3ed5-4d08-47bf-8461-67ae8c430966/dqc_reference/reference_markers_gtdb.fasta -out GCA_022448455.1_ASM2244845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:45:42,819] [INFO] Task succeeded: Blastn
[2023-06-13 14:45:42,823] [INFO] Selected 15 target genomes.
[2023-06-13 14:45:42,823] [INFO] Target genome list was writen to GCA_022448455.1_ASM2244845v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:45:42,869] [INFO] Task started: fastANI
[2023-06-13 14:45:42,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg460743b3-256c-41f1-9bbf-0937fb2380b0/GCA_022448455.1_ASM2244845v1_genomic.fna.gz --refList GCA_022448455.1_ASM2244845v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022448455.1_ASM2244845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:45:47,312] [INFO] Task succeeded: fastANI
[2023-06-13 14:45:47,321] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 14:45:47,321] [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
GCA_000213395.2	s__Pseudothioglobus sp000213395	91.1959	251	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000372785.1	s__Pseudothioglobus sp000372785	90.185	304	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.69	95.69	0.64	0.64	2	-
GCA_902606745.1	s__Pseudothioglobus sp902606745	89.6717	324	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698045.1	s__Pseudothioglobus sp002698045	78.6939	108	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.47	95.47	0.68	0.68	2	-
GCA_905620445.1	s__Pseudothioglobus sp905620445	77.7358	83	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384565.1	s__Pseudothioglobus aerophilus	77.5799	118	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	99.14	98.97	0.83	0.77	11	-
GCF_003326015.1	s__Pseudothioglobus singularis_A	77.5529	142	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281385.1	s__Pseudothioglobus singularis	77.3255	109	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.68	95.87	0.84	0.66	7	-
GCA_902509905.1	s__Pseudothioglobus sp902509905	77.2993	82	533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.83	95.81	0.73	0.73	3	-
--------------------------------------------------------------------------------
[2023-06-13 14:45:47,323] [INFO] GTDB search result was written to GCA_022448455.1_ASM2244845v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:45:47,324] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:45:47,327] [INFO] DFAST_QC result json was written to GCA_022448455.1_ASM2244845v1_genomic.fna/dqc_result.json
[2023-06-13 14:45:47,327] [INFO] DFAST_QC completed!
[2023-06-13 14:45:47,327] [INFO] Total running time: 0h0m40s