[2023-07-01 03:04:23,123] [INFO] DFAST_QC pipeline started.
[2023-07-01 03:04:23,125] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 03:04:23,125] [INFO] DQC Reference Directory: /var/lib/cwl/stgc39eb078-9af8-4e61-85a4-54788fba6f28/dqc_reference
[2023-07-01 03:04:24,546] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 03:04:24,547] [INFO] Task started: Prodigal
[2023-07-01 03:04:24,547] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c843038-1307-4d8b-bee4-9407c4856f7c/GCA_024654045.1_ASM2465404v1_genomic.fna.gz | prodigal -d GCA_024654045.1_ASM2465404v1_genomic.fna/cds.fna -a GCA_024654045.1_ASM2465404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 03:04:29,939] [INFO] Task succeeded: Prodigal
[2023-07-01 03:04:29,939] [INFO] Task started: HMMsearch
[2023-07-01 03:04:29,940] [INFO] Running command: hmmsearch --tblout GCA_024654045.1_ASM2465404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc39eb078-9af8-4e61-85a4-54788fba6f28/dqc_reference/reference_markers.hmm GCA_024654045.1_ASM2465404v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 03:04:30,205] [INFO] Task succeeded: HMMsearch
[2023-07-01 03:04:30,207] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2c843038-1307-4d8b-bee4-9407c4856f7c/GCA_024654045.1_ASM2465404v1_genomic.fna.gz]
[2023-07-01 03:04:30,243] [INFO] Query marker FASTA was written to GCA_024654045.1_ASM2465404v1_genomic.fna/markers.fasta
[2023-07-01 03:04:30,244] [INFO] Task started: Blastn
[2023-07-01 03:04:30,244] [INFO] Running command: blastn -query GCA_024654045.1_ASM2465404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc39eb078-9af8-4e61-85a4-54788fba6f28/dqc_reference/reference_markers.fasta -out GCA_024654045.1_ASM2465404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:04:30,865] [INFO] Task succeeded: Blastn
[2023-07-01 03:04:30,868] [INFO] Selected 8 target genomes.
[2023-07-01 03:04:30,869] [INFO] Target genome list was writen to GCA_024654045.1_ASM2465404v1_genomic.fna/target_genomes.txt
[2023-07-01 03:04:30,871] [INFO] Task started: fastANI
[2023-07-01 03:04:30,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c843038-1307-4d8b-bee4-9407c4856f7c/GCA_024654045.1_ASM2465404v1_genomic.fna.gz --refList GCA_024654045.1_ASM2465404v1_genomic.fna/target_genomes.txt --output GCA_024654045.1_ASM2465404v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 03:04:35,774] [INFO] Task succeeded: fastANI
[2023-07-01 03:04:35,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc39eb078-9af8-4e61-85a4-54788fba6f28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 03:04:35,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc39eb078-9af8-4e61-85a4-54788fba6f28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 03:04:35,777] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 03:04:35,777] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 03:04:35,777] [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
--------------------------------------------------------------------------------
[2023-07-01 03:04:35,779] [INFO] DFAST Taxonomy check result was written to GCA_024654045.1_ASM2465404v1_genomic.fna/tc_result.tsv
[2023-07-01 03:04:35,779] [INFO] ===== Taxonomy check completed =====
[2023-07-01 03:04:35,779] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 03:04:35,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc39eb078-9af8-4e61-85a4-54788fba6f28/dqc_reference/checkm_data
[2023-07-01 03:04:35,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 03:04:35,817] [INFO] Task started: CheckM
[2023-07-01 03:04:35,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024654045.1_ASM2465404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024654045.1_ASM2465404v1_genomic.fna/checkm_input GCA_024654045.1_ASM2465404v1_genomic.fna/checkm_result
[2023-07-01 03:04:59,567] [INFO] Task succeeded: CheckM
[2023-07-01 03:04:59,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 03:04:59,592] [INFO] ===== Completeness check finished =====
[2023-07-01 03:04:59,593] [INFO] ===== Start GTDB Search =====
[2023-07-01 03:04:59,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024654045.1_ASM2465404v1_genomic.fna/markers.fasta)
[2023-07-01 03:04:59,594] [INFO] Task started: Blastn
[2023-07-01 03:04:59,594] [INFO] Running command: blastn -query GCA_024654045.1_ASM2465404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc39eb078-9af8-4e61-85a4-54788fba6f28/dqc_reference/reference_markers_gtdb.fasta -out GCA_024654045.1_ASM2465404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:05:00,328] [INFO] Task succeeded: Blastn
[2023-07-01 03:05:00,334] [INFO] Selected 19 target genomes.
[2023-07-01 03:05:00,334] [INFO] Target genome list was writen to GCA_024654045.1_ASM2465404v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 03:05:00,344] [INFO] Task started: fastANI
[2023-07-01 03:05:00,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c843038-1307-4d8b-bee4-9407c4856f7c/GCA_024654045.1_ASM2465404v1_genomic.fna.gz --refList GCA_024654045.1_ASM2465404v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024654045.1_ASM2465404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 03:05:09,539] [INFO] Task succeeded: fastANI
[2023-07-01 03:05:09,549] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 03:05:09,550] [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_900232105.1	s__Kuenenia stuttgartiensis	93.6241	488	557	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Kuenenia	95.0	99.22	98.74	0.94	0.87	9	-
GCA_016873165.1	s__Kuenenia sp016873165	79.8747	337	557	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Kuenenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017347445.1	s__Brocadia pituitae	77.652	57	557	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Brocadia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873155.1	s__XYD2-FULL-41-16 sp016873155	77.2462	61	557	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__XYD2-FULL-41-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360945.1	s__Brocadia sp013360945	76.8167	58	557	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Brocadia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 03:05:09,580] [INFO] GTDB search result was written to GCA_024654045.1_ASM2465404v1_genomic.fna/result_gtdb.tsv
[2023-07-01 03:05:09,581] [INFO] ===== GTDB Search completed =====
[2023-07-01 03:05:09,584] [INFO] DFAST_QC result json was written to GCA_024654045.1_ASM2465404v1_genomic.fna/dqc_result.json
[2023-07-01 03:05:09,584] [INFO] DFAST_QC completed!
[2023-07-01 03:05:09,585] [INFO] Total running time: 0h0m46s