[2023-06-27 01:14:38,982] [INFO] DFAST_QC pipeline started.
[2023-06-27 01:14:38,984] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 01:14:38,984] [INFO] DQC Reference Directory: /var/lib/cwl/stg67c9ce72-3379-4dd3-9f0c-2342b992509d/dqc_reference
[2023-06-27 01:14:40,238] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 01:14:40,239] [INFO] Task started: Prodigal
[2023-06-27 01:14:40,239] [INFO] Running command: gunzip -c /var/lib/cwl/stg97b18212-9282-4a2e-a3e1-453f729abc0c/GCA_026396175.1_ASM2639617v1_genomic.fna.gz | prodigal -d GCA_026396175.1_ASM2639617v1_genomic.fna/cds.fna -a GCA_026396175.1_ASM2639617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 01:14:45,099] [INFO] Task succeeded: Prodigal
[2023-06-27 01:14:45,100] [INFO] Task started: HMMsearch
[2023-06-27 01:14:45,100] [INFO] Running command: hmmsearch --tblout GCA_026396175.1_ASM2639617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67c9ce72-3379-4dd3-9f0c-2342b992509d/dqc_reference/reference_markers.hmm GCA_026396175.1_ASM2639617v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 01:14:45,341] [INFO] Task succeeded: HMMsearch
[2023-06-27 01:14:45,343] [INFO] Found 6/6 markers.
[2023-06-27 01:14:45,556] [INFO] Query marker FASTA was written to GCA_026396175.1_ASM2639617v1_genomic.fna/markers.fasta
[2023-06-27 01:14:45,556] [INFO] Task started: Blastn
[2023-06-27 01:14:45,556] [INFO] Running command: blastn -query GCA_026396175.1_ASM2639617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67c9ce72-3379-4dd3-9f0c-2342b992509d/dqc_reference/reference_markers.fasta -out GCA_026396175.1_ASM2639617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:14:46,142] [INFO] Task succeeded: Blastn
[2023-06-27 01:14:46,146] [INFO] Selected 16 target genomes.
[2023-06-27 01:14:46,146] [INFO] Target genome list was writen to GCA_026396175.1_ASM2639617v1_genomic.fna/target_genomes.txt
[2023-06-27 01:14:46,150] [INFO] Task started: fastANI
[2023-06-27 01:14:46,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg97b18212-9282-4a2e-a3e1-453f729abc0c/GCA_026396175.1_ASM2639617v1_genomic.fna.gz --refList GCA_026396175.1_ASM2639617v1_genomic.fna/target_genomes.txt --output GCA_026396175.1_ASM2639617v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 01:14:58,969] [INFO] Task succeeded: fastANI
[2023-06-27 01:14:58,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67c9ce72-3379-4dd3-9f0c-2342b992509d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 01:14:58,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67c9ce72-3379-4dd3-9f0c-2342b992509d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 01:14:58,972] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 01:14:58,972] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 01:14:58,972] [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
--------------------------------------------------------------------------------
[2023-06-27 01:14:58,974] [INFO] DFAST Taxonomy check result was written to GCA_026396175.1_ASM2639617v1_genomic.fna/tc_result.tsv
[2023-06-27 01:14:58,975] [INFO] ===== Taxonomy check completed =====
[2023-06-27 01:14:58,975] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 01:14:58,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67c9ce72-3379-4dd3-9f0c-2342b992509d/dqc_reference/checkm_data
[2023-06-27 01:14:58,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 01:14:58,995] [INFO] Task started: CheckM
[2023-06-27 01:14:58,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026396175.1_ASM2639617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026396175.1_ASM2639617v1_genomic.fna/checkm_input GCA_026396175.1_ASM2639617v1_genomic.fna/checkm_result
[2023-06-27 01:15:20,499] [INFO] Task succeeded: CheckM
[2023-06-27 01:15:20,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 01:15:20,521] [INFO] ===== Completeness check finished =====
[2023-06-27 01:15:20,522] [INFO] ===== Start GTDB Search =====
[2023-06-27 01:15:20,522] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026396175.1_ASM2639617v1_genomic.fna/markers.fasta)
[2023-06-27 01:15:20,523] [INFO] Task started: Blastn
[2023-06-27 01:15:20,523] [INFO] Running command: blastn -query GCA_026396175.1_ASM2639617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67c9ce72-3379-4dd3-9f0c-2342b992509d/dqc_reference/reference_markers_gtdb.fasta -out GCA_026396175.1_ASM2639617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:15:21,364] [INFO] Task succeeded: Blastn
[2023-06-27 01:15:21,369] [INFO] Selected 19 target genomes.
[2023-06-27 01:15:21,369] [INFO] Target genome list was writen to GCA_026396175.1_ASM2639617v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 01:15:21,382] [INFO] Task started: fastANI
[2023-06-27 01:15:21,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg97b18212-9282-4a2e-a3e1-453f729abc0c/GCA_026396175.1_ASM2639617v1_genomic.fna.gz --refList GCA_026396175.1_ASM2639617v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026396175.1_ASM2639617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 01:15:26,474] [INFO] Task succeeded: fastANI
[2023-06-27 01:15:26,482] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 01:15:26,482] [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_903937035.1	s__UBA9630 sp903937035	79.5666	137	319	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__UBA2206;g__UBA9630	95.0	99.97	99.93	0.97	0.97	4	-
GCA_903842445.1	s__UBA9630 sp903842445	78.2814	110	319	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__UBA2206;g__UBA9630	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003482885.1	s__UBA9630 sp003482885	77.2988	65	319	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__UBA2206;g__UBA9630	95.0	99.85	99.85	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-27 01:15:26,484] [INFO] GTDB search result was written to GCA_026396175.1_ASM2639617v1_genomic.fna/result_gtdb.tsv
[2023-06-27 01:15:26,485] [INFO] ===== GTDB Search completed =====
[2023-06-27 01:15:26,488] [INFO] DFAST_QC result json was written to GCA_026396175.1_ASM2639617v1_genomic.fna/dqc_result.json
[2023-06-27 01:15:26,489] [INFO] DFAST_QC completed!
[2023-06-27 01:15:26,489] [INFO] Total running time: 0h0m48s