[2023-06-18 12:30:18,029] [INFO] DFAST_QC pipeline started.
[2023-06-18 12:30:18,036] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 12:30:18,036] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b9464d9-6aa1-4f7f-9c7c-2382c64418b6/dqc_reference
[2023-06-18 12:30:19,452] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 12:30:19,453] [INFO] Task started: Prodigal
[2023-06-18 12:30:19,453] [INFO] Running command: gunzip -c /var/lib/cwl/stg921b8e50-541e-4bfd-96dd-53bb78afdca7/GCA_018969185.1_ASM1896918v1_genomic.fna.gz | prodigal -d GCA_018969185.1_ASM1896918v1_genomic.fna/cds.fna -a GCA_018969185.1_ASM1896918v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 12:30:24,810] [INFO] Task succeeded: Prodigal
[2023-06-18 12:30:24,810] [INFO] Task started: HMMsearch
[2023-06-18 12:30:24,810] [INFO] Running command: hmmsearch --tblout GCA_018969185.1_ASM1896918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b9464d9-6aa1-4f7f-9c7c-2382c64418b6/dqc_reference/reference_markers.hmm GCA_018969185.1_ASM1896918v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 12:30:25,021] [INFO] Task succeeded: HMMsearch
[2023-06-18 12:30:25,022] [INFO] Found 6/6 markers.
[2023-06-18 12:30:25,058] [INFO] Query marker FASTA was written to GCA_018969185.1_ASM1896918v1_genomic.fna/markers.fasta
[2023-06-18 12:30:25,058] [INFO] Task started: Blastn
[2023-06-18 12:30:25,059] [INFO] Running command: blastn -query GCA_018969185.1_ASM1896918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b9464d9-6aa1-4f7f-9c7c-2382c64418b6/dqc_reference/reference_markers.fasta -out GCA_018969185.1_ASM1896918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:30:25,736] [INFO] Task succeeded: Blastn
[2023-06-18 12:30:25,744] [INFO] Selected 21 target genomes.
[2023-06-18 12:30:25,745] [INFO] Target genome list was writen to GCA_018969185.1_ASM1896918v1_genomic.fna/target_genomes.txt
[2023-06-18 12:30:25,752] [INFO] Task started: fastANI
[2023-06-18 12:30:25,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg921b8e50-541e-4bfd-96dd-53bb78afdca7/GCA_018969185.1_ASM1896918v1_genomic.fna.gz --refList GCA_018969185.1_ASM1896918v1_genomic.fna/target_genomes.txt --output GCA_018969185.1_ASM1896918v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 12:30:33,935] [INFO] Task succeeded: fastANI
[2023-06-18 12:30:33,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b9464d9-6aa1-4f7f-9c7c-2382c64418b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 12:30:33,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b9464d9-6aa1-4f7f-9c7c-2382c64418b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 12:30:33,937] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 12:30:33,937] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 12:30:33,938] [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
--------------------------------------------------------------------------------
[2023-06-18 12:30:33,941] [INFO] DFAST Taxonomy check result was written to GCA_018969185.1_ASM1896918v1_genomic.fna/tc_result.tsv
[2023-06-18 12:30:33,942] [INFO] ===== Taxonomy check completed =====
[2023-06-18 12:30:33,943] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 12:30:33,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b9464d9-6aa1-4f7f-9c7c-2382c64418b6/dqc_reference/checkm_data
[2023-06-18 12:30:33,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 12:30:33,968] [INFO] Task started: CheckM
[2023-06-18 12:30:33,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018969185.1_ASM1896918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018969185.1_ASM1896918v1_genomic.fna/checkm_input GCA_018969185.1_ASM1896918v1_genomic.fna/checkm_result
[2023-06-18 12:30:58,256] [INFO] Task succeeded: CheckM
[2023-06-18 12:30:58,257] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 12:30:58,291] [INFO] ===== Completeness check finished =====
[2023-06-18 12:30:58,291] [INFO] ===== Start GTDB Search =====
[2023-06-18 12:30:58,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018969185.1_ASM1896918v1_genomic.fna/markers.fasta)
[2023-06-18 12:30:58,292] [INFO] Task started: Blastn
[2023-06-18 12:30:58,292] [INFO] Running command: blastn -query GCA_018969185.1_ASM1896918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b9464d9-6aa1-4f7f-9c7c-2382c64418b6/dqc_reference/reference_markers_gtdb.fasta -out GCA_018969185.1_ASM1896918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:30:59,141] [INFO] Task succeeded: Blastn
[2023-06-18 12:30:59,147] [INFO] Selected 14 target genomes.
[2023-06-18 12:30:59,148] [INFO] Target genome list was writen to GCA_018969185.1_ASM1896918v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 12:30:59,176] [INFO] Task started: fastANI
[2023-06-18 12:30:59,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg921b8e50-541e-4bfd-96dd-53bb78afdca7/GCA_018969185.1_ASM1896918v1_genomic.fna.gz --refList GCA_018969185.1_ASM1896918v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018969185.1_ASM1896918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 12:31:03,034] [INFO] Task succeeded: fastANI
[2023-06-18 12:31:03,048] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 12:31:03,048] [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_018969185.1	s__UBA2645 sp018969185	100.0	488	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016882165.1	s__UBA2645 sp016882165	78.1078	132	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359655.1	s__UBA2645 sp002359655	78.0326	141	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	99.96	99.93	0.97	0.95	3	-
GCA_903937405.1	s__UBA2645 sp903937405	77.8637	152	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	99.33	98.10	0.93	0.79	16	-
GCA_014190355.1	s__CAILUF01 sp014190355	77.0353	74	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__CAILUF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903879805.1	s__UBA2645 sp903879805	76.908	107	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898475.1	s__UBA2645 sp903898475	76.5088	95	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	99.93	99.93	0.95	0.95	2	-
GCA_016778745.1	s__JADHOZ01 sp016778745	76.5059	57	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__JADHOZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693885.1	s__UBA2645 sp009693885	76.1644	58	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 12:31:03,050] [INFO] GTDB search result was written to GCA_018969185.1_ASM1896918v1_genomic.fna/result_gtdb.tsv
[2023-06-18 12:31:03,051] [INFO] ===== GTDB Search completed =====
[2023-06-18 12:31:03,054] [INFO] DFAST_QC result json was written to GCA_018969185.1_ASM1896918v1_genomic.fna/dqc_result.json
[2023-06-18 12:31:03,054] [INFO] DFAST_QC completed!
[2023-06-18 12:31:03,054] [INFO] Total running time: 0h0m45s