[2023-06-13 11:30:03,003] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:30:03,007] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:30:03,007] [INFO] DQC Reference Directory: /var/lib/cwl/stgec440e66-b29d-4de2-9121-1beb2ea2f9bd/dqc_reference
[2023-06-13 11:30:04,426] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:30:04,427] [INFO] Task started: Prodigal
[2023-06-13 11:30:04,427] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d50effe-43c4-4eb8-8888-e5025bc0b9c2/GCA_947484335.1_RH-9nov16-7_genomic.fna.gz | prodigal -d GCA_947484335.1_RH-9nov16-7_genomic.fna/cds.fna -a GCA_947484335.1_RH-9nov16-7_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:30:06,836] [INFO] Task succeeded: Prodigal
[2023-06-13 11:30:06,837] [INFO] Task started: HMMsearch
[2023-06-13 11:30:06,837] [INFO] Running command: hmmsearch --tblout GCA_947484335.1_RH-9nov16-7_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec440e66-b29d-4de2-9121-1beb2ea2f9bd/dqc_reference/reference_markers.hmm GCA_947484335.1_RH-9nov16-7_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:30:07,090] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:30:07,091] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8d50effe-43c4-4eb8-8888-e5025bc0b9c2/GCA_947484335.1_RH-9nov16-7_genomic.fna.gz]
[2023-06-13 11:30:07,113] [INFO] Query marker FASTA was written to GCA_947484335.1_RH-9nov16-7_genomic.fna/markers.fasta
[2023-06-13 11:30:07,114] [INFO] Task started: Blastn
[2023-06-13 11:30:07,114] [INFO] Running command: blastn -query GCA_947484335.1_RH-9nov16-7_genomic.fna/markers.fasta -db /var/lib/cwl/stgec440e66-b29d-4de2-9121-1beb2ea2f9bd/dqc_reference/reference_markers.fasta -out GCA_947484335.1_RH-9nov16-7_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:30:07,714] [INFO] Task succeeded: Blastn
[2023-06-13 11:30:07,717] [INFO] Selected 30 target genomes.
[2023-06-13 11:30:07,718] [INFO] Target genome list was writen to GCA_947484335.1_RH-9nov16-7_genomic.fna/target_genomes.txt
[2023-06-13 11:30:07,726] [INFO] Task started: fastANI
[2023-06-13 11:30:07,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d50effe-43c4-4eb8-8888-e5025bc0b9c2/GCA_947484335.1_RH-9nov16-7_genomic.fna.gz --refList GCA_947484335.1_RH-9nov16-7_genomic.fna/target_genomes.txt --output GCA_947484335.1_RH-9nov16-7_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:30:28,873] [INFO] Task succeeded: fastANI
[2023-06-13 11:30:28,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec440e66-b29d-4de2-9121-1beb2ea2f9bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:30:28,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec440e66-b29d-4de2-9121-1beb2ea2f9bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:30:28,876] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:30:28,876] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 11:30:28,876] [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
--------------------------------------------------------------------------------
[2023-06-13 11:30:28,879] [INFO] DFAST Taxonomy check result was written to GCA_947484335.1_RH-9nov16-7_genomic.fna/tc_result.tsv
[2023-06-13 11:30:28,879] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:30:28,880] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:30:28,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec440e66-b29d-4de2-9121-1beb2ea2f9bd/dqc_reference/checkm_data
[2023-06-13 11:30:28,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:30:28,898] [INFO] Task started: CheckM
[2023-06-13 11:30:28,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947484335.1_RH-9nov16-7_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947484335.1_RH-9nov16-7_genomic.fna/checkm_input GCA_947484335.1_RH-9nov16-7_genomic.fna/checkm_result
[2023-06-13 11:30:44,536] [INFO] Task succeeded: CheckM
[2023-06-13 11:30:44,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:30:44,557] [INFO] ===== Completeness check finished =====
[2023-06-13 11:30:44,557] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:30:44,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947484335.1_RH-9nov16-7_genomic.fna/markers.fasta)
[2023-06-13 11:30:44,558] [INFO] Task started: Blastn
[2023-06-13 11:30:44,558] [INFO] Running command: blastn -query GCA_947484335.1_RH-9nov16-7_genomic.fna/markers.fasta -db /var/lib/cwl/stgec440e66-b29d-4de2-9121-1beb2ea2f9bd/dqc_reference/reference_markers_gtdb.fasta -out GCA_947484335.1_RH-9nov16-7_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:30:45,356] [INFO] Task succeeded: Blastn
[2023-06-13 11:30:45,360] [INFO] Selected 16 target genomes.
[2023-06-13 11:30:45,360] [INFO] Target genome list was writen to GCA_947484335.1_RH-9nov16-7_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:30:45,369] [INFO] Task started: fastANI
[2023-06-13 11:30:45,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d50effe-43c4-4eb8-8888-e5025bc0b9c2/GCA_947484335.1_RH-9nov16-7_genomic.fna.gz --refList GCA_947484335.1_RH-9nov16-7_genomic.fna/target_genomes_gtdb.txt --output GCA_947484335.1_RH-9nov16-7_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:30:52,730] [INFO] Task succeeded: fastANI
[2023-06-13 11:30:52,735] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 11:30:52,736] [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_903957805.1	s__VFJL01 sp903957805	87.1685	151	294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__VFJL01	95.0	98.18	96.38	0.74	0.70	5	-
GCA_013450215.1	s__VFJL01 sp013450215	86.966	232	294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__VFJL01	95.0	99.16	98.57	0.95	0.91	9	-
GCA_009886095.1	s__VFJL01 sp009886095	77.5708	106	294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__VFJL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 11:30:52,738] [INFO] GTDB search result was written to GCA_947484335.1_RH-9nov16-7_genomic.fna/result_gtdb.tsv
[2023-06-13 11:30:52,739] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:30:52,742] [INFO] DFAST_QC result json was written to GCA_947484335.1_RH-9nov16-7_genomic.fna/dqc_result.json
[2023-06-13 11:30:52,743] [INFO] DFAST_QC completed!
[2023-06-13 11:30:52,743] [INFO] Total running time: 0h0m50s