[2023-06-19 04:14:26,594] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:14:26,596] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:14:26,597] [INFO] DQC Reference Directory: /var/lib/cwl/stg3165d83b-ffc1-4cb1-81a2-852cb081ec84/dqc_reference
[2023-06-19 04:14:28,383] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:14:28,384] [INFO] Task started: Prodigal
[2023-06-19 04:14:28,384] [INFO] Running command: gunzip -c /var/lib/cwl/stg34a7a0f9-3515-4db3-813c-04576df89144/GCA_018675295.1_ASM1867529v1_genomic.fna.gz | prodigal -d GCA_018675295.1_ASM1867529v1_genomic.fna/cds.fna -a GCA_018675295.1_ASM1867529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:14:37,418] [INFO] Task succeeded: Prodigal
[2023-06-19 04:14:37,419] [INFO] Task started: HMMsearch
[2023-06-19 04:14:37,419] [INFO] Running command: hmmsearch --tblout GCA_018675295.1_ASM1867529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3165d83b-ffc1-4cb1-81a2-852cb081ec84/dqc_reference/reference_markers.hmm GCA_018675295.1_ASM1867529v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:14:37,647] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:14:37,648] [INFO] Found 6/6 markers.
[2023-06-19 04:14:37,682] [INFO] Query marker FASTA was written to GCA_018675295.1_ASM1867529v1_genomic.fna/markers.fasta
[2023-06-19 04:14:37,683] [INFO] Task started: Blastn
[2023-06-19 04:14:37,683] [INFO] Running command: blastn -query GCA_018675295.1_ASM1867529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3165d83b-ffc1-4cb1-81a2-852cb081ec84/dqc_reference/reference_markers.fasta -out GCA_018675295.1_ASM1867529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:14:38,412] [INFO] Task succeeded: Blastn
[2023-06-19 04:14:38,416] [INFO] Selected 31 target genomes.
[2023-06-19 04:14:38,417] [INFO] Target genome list was writen to GCA_018675295.1_ASM1867529v1_genomic.fna/target_genomes.txt
[2023-06-19 04:14:38,418] [INFO] Task started: fastANI
[2023-06-19 04:14:38,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg34a7a0f9-3515-4db3-813c-04576df89144/GCA_018675295.1_ASM1867529v1_genomic.fna.gz --refList GCA_018675295.1_ASM1867529v1_genomic.fna/target_genomes.txt --output GCA_018675295.1_ASM1867529v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:14:58,974] [INFO] Task succeeded: fastANI
[2023-06-19 04:14:58,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3165d83b-ffc1-4cb1-81a2-852cb081ec84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:14:58,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3165d83b-ffc1-4cb1-81a2-852cb081ec84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:14:58,977] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:14:58,977] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 04:14:58,977] [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
--------------------------------------------------------------------------------
[2023-06-19 04:14:58,979] [INFO] DFAST Taxonomy check result was written to GCA_018675295.1_ASM1867529v1_genomic.fna/tc_result.tsv
[2023-06-19 04:14:58,979] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:14:58,980] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:14:58,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3165d83b-ffc1-4cb1-81a2-852cb081ec84/dqc_reference/checkm_data
[2023-06-19 04:14:58,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:14:59,008] [INFO] Task started: CheckM
[2023-06-19 04:14:59,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018675295.1_ASM1867529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018675295.1_ASM1867529v1_genomic.fna/checkm_input GCA_018675295.1_ASM1867529v1_genomic.fna/checkm_result
[2023-06-19 04:15:29,990] [INFO] Task succeeded: CheckM
[2023-06-19 04:15:29,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 04:15:30,013] [INFO] ===== Completeness check finished =====
[2023-06-19 04:15:30,013] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:15:30,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018675295.1_ASM1867529v1_genomic.fna/markers.fasta)
[2023-06-19 04:15:30,014] [INFO] Task started: Blastn
[2023-06-19 04:15:30,014] [INFO] Running command: blastn -query GCA_018675295.1_ASM1867529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3165d83b-ffc1-4cb1-81a2-852cb081ec84/dqc_reference/reference_markers_gtdb.fasta -out GCA_018675295.1_ASM1867529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:15:30,832] [INFO] Task succeeded: Blastn
[2023-06-19 04:15:30,837] [INFO] Selected 25 target genomes.
[2023-06-19 04:15:30,838] [INFO] Target genome list was writen to GCA_018675295.1_ASM1867529v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:15:30,854] [INFO] Task started: fastANI
[2023-06-19 04:15:30,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg34a7a0f9-3515-4db3-813c-04576df89144/GCA_018675295.1_ASM1867529v1_genomic.fna.gz --refList GCA_018675295.1_ASM1867529v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018675295.1_ASM1867529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:15:41,263] [INFO] Task succeeded: fastANI
[2023-06-19 04:15:41,268] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:15:41,269] [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_009886755.1	s__UBA11891 sp009886755	99.6089	512	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA11891	95.0	99.16	98.70	0.90	0.89	3	conclusive
GCA_003533785.1	s__UBA11891 sp003533785	77.2187	132	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA11891	95.0	99.52	99.52	0.75	0.75	2	-
GCA_011524905.1	s__UBA11891 sp011524905	76.8046	110	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA11891	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:15:41,271] [INFO] GTDB search result was written to GCA_018675295.1_ASM1867529v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:15:41,271] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:15:41,280] [INFO] DFAST_QC result json was written to GCA_018675295.1_ASM1867529v1_genomic.fna/dqc_result.json
[2023-06-19 04:15:41,280] [INFO] DFAST_QC completed!
[2023-06-19 04:15:41,280] [INFO] Total running time: 0h1m15s