[2023-06-08 17:09:11,207] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:09:11,210] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:09:11,211] [INFO] DQC Reference Directory: /var/lib/cwl/stga4dc337d-a28d-4385-9e01-5a26a4964b04/dqc_reference
[2023-06-08 17:09:12,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:09:12,403] [INFO] Task started: Prodigal
[2023-06-08 17:09:12,404] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c0772e2-6e0d-40c0-90dd-a1028741500d/GCA_947445795.1_CH-Oct18-101_genomic.fna.gz | prodigal -d GCA_947445795.1_CH-Oct18-101_genomic.fna/cds.fna -a GCA_947445795.1_CH-Oct18-101_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:09:14,801] [INFO] Task succeeded: Prodigal
[2023-06-08 17:09:14,802] [INFO] Task started: HMMsearch
[2023-06-08 17:09:14,802] [INFO] Running command: hmmsearch --tblout GCA_947445795.1_CH-Oct18-101_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4dc337d-a28d-4385-9e01-5a26a4964b04/dqc_reference/reference_markers.hmm GCA_947445795.1_CH-Oct18-101_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:09:14,988] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:09:14,989] [INFO] Found 6/6 markers.
[2023-06-08 17:09:15,009] [INFO] Query marker FASTA was written to GCA_947445795.1_CH-Oct18-101_genomic.fna/markers.fasta
[2023-06-08 17:09:15,010] [INFO] Task started: Blastn
[2023-06-08 17:09:15,010] [INFO] Running command: blastn -query GCA_947445795.1_CH-Oct18-101_genomic.fna/markers.fasta -db /var/lib/cwl/stga4dc337d-a28d-4385-9e01-5a26a4964b04/dqc_reference/reference_markers.fasta -out GCA_947445795.1_CH-Oct18-101_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:15,592] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:15,599] [INFO] Selected 25 target genomes.
[2023-06-08 17:09:15,600] [INFO] Target genome list was writen to GCA_947445795.1_CH-Oct18-101_genomic.fna/target_genomes.txt
[2023-06-08 17:09:15,602] [INFO] Task started: fastANI
[2023-06-08 17:09:15,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c0772e2-6e0d-40c0-90dd-a1028741500d/GCA_947445795.1_CH-Oct18-101_genomic.fna.gz --refList GCA_947445795.1_CH-Oct18-101_genomic.fna/target_genomes.txt --output GCA_947445795.1_CH-Oct18-101_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:09:29,326] [INFO] Task succeeded: fastANI
[2023-06-08 17:09:29,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4dc337d-a28d-4385-9e01-5a26a4964b04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:09:29,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4dc337d-a28d-4385-9e01-5a26a4964b04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:09:29,329] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:09:29,330] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 17:09:29,330] [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
--------------------------------------------------------------------------------
[2023-06-08 17:09:29,333] [INFO] DFAST Taxonomy check result was written to GCA_947445795.1_CH-Oct18-101_genomic.fna/tc_result.tsv
[2023-06-08 17:09:29,333] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:09:29,334] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:09:29,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4dc337d-a28d-4385-9e01-5a26a4964b04/dqc_reference/checkm_data
[2023-06-08 17:09:29,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:09:29,354] [INFO] Task started: CheckM
[2023-06-08 17:09:29,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947445795.1_CH-Oct18-101_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947445795.1_CH-Oct18-101_genomic.fna/checkm_input GCA_947445795.1_CH-Oct18-101_genomic.fna/checkm_result
[2023-06-08 17:09:45,370] [INFO] Task succeeded: CheckM
[2023-06-08 17:09:45,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:09:45,394] [INFO] ===== Completeness check finished =====
[2023-06-08 17:09:45,394] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:09:45,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947445795.1_CH-Oct18-101_genomic.fna/markers.fasta)
[2023-06-08 17:09:45,395] [INFO] Task started: Blastn
[2023-06-08 17:09:45,395] [INFO] Running command: blastn -query GCA_947445795.1_CH-Oct18-101_genomic.fna/markers.fasta -db /var/lib/cwl/stga4dc337d-a28d-4385-9e01-5a26a4964b04/dqc_reference/reference_markers_gtdb.fasta -out GCA_947445795.1_CH-Oct18-101_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:46,267] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:46,277] [INFO] Selected 24 target genomes.
[2023-06-08 17:09:46,278] [INFO] Target genome list was writen to GCA_947445795.1_CH-Oct18-101_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:09:46,289] [INFO] Task started: fastANI
[2023-06-08 17:09:46,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c0772e2-6e0d-40c0-90dd-a1028741500d/GCA_947445795.1_CH-Oct18-101_genomic.fna.gz --refList GCA_947445795.1_CH-Oct18-101_genomic.fna/target_genomes_gtdb.txt --output GCA_947445795.1_CH-Oct18-101_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:09:56,148] [INFO] Task succeeded: fastANI
[2023-06-08 17:09:56,157] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:09:56,158] [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_014190895.1	s__BJGV01 sp014190895	98.9001	371	382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__BJGV01	95.0	99.33	98.77	0.94	0.93	9	conclusive
GCA_004525885.1	s__GCA-2721545 sp004525885	76.3706	56	382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__GCA-2721545	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356775.1	s__GCA-2721545 sp004356775	76.3321	57	382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__GCA-2721545	95.0	99.38	99.38	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-08 17:09:56,160] [INFO] GTDB search result was written to GCA_947445795.1_CH-Oct18-101_genomic.fna/result_gtdb.tsv
[2023-06-08 17:09:56,161] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:09:56,165] [INFO] DFAST_QC result json was written to GCA_947445795.1_CH-Oct18-101_genomic.fna/dqc_result.json
[2023-06-08 17:09:56,166] [INFO] DFAST_QC completed!
[2023-06-08 17:09:56,166] [INFO] Total running time: 0h0m45s