[2023-06-04 22:24:43,591] [INFO] DFAST_QC pipeline started.
[2023-06-04 22:24:43,600] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 22:24:43,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg02ee3cd8-1fed-474b-99d7-a53b55b85514/dqc_reference
[2023-06-04 22:24:45,190] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 22:24:45,190] [INFO] Task started: Prodigal
[2023-06-04 22:24:45,191] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d7a7388-cd73-4e40-8515-8df581463158/GCA_001776855.1_ASM177685v1_genomic.fna.gz | prodigal -d GCA_001776855.1_ASM177685v1_genomic.fna/cds.fna -a GCA_001776855.1_ASM177685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 22:24:47,148] [INFO] Task succeeded: Prodigal
[2023-06-04 22:24:47,149] [INFO] Task started: HMMsearch
[2023-06-04 22:24:47,149] [INFO] Running command: hmmsearch --tblout GCA_001776855.1_ASM177685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02ee3cd8-1fed-474b-99d7-a53b55b85514/dqc_reference/reference_markers.hmm GCA_001776855.1_ASM177685v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 22:24:47,365] [INFO] Task succeeded: HMMsearch
[2023-06-04 22:24:47,366] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7d7a7388-cd73-4e40-8515-8df581463158/GCA_001776855.1_ASM177685v1_genomic.fna.gz]
[2023-06-04 22:24:47,381] [INFO] Query marker FASTA was written to GCA_001776855.1_ASM177685v1_genomic.fna/markers.fasta
[2023-06-04 22:24:47,381] [INFO] Task started: Blastn
[2023-06-04 22:24:47,381] [INFO] Running command: blastn -query GCA_001776855.1_ASM177685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02ee3cd8-1fed-474b-99d7-a53b55b85514/dqc_reference/reference_markers.fasta -out GCA_001776855.1_ASM177685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:24:47,949] [INFO] Task succeeded: Blastn
[2023-06-04 22:24:47,954] [INFO] Selected 13 target genomes.
[2023-06-04 22:24:47,955] [INFO] Target genome list was writen to GCA_001776855.1_ASM177685v1_genomic.fna/target_genomes.txt
[2023-06-04 22:24:47,975] [INFO] Task started: fastANI
[2023-06-04 22:24:47,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d7a7388-cd73-4e40-8515-8df581463158/GCA_001776855.1_ASM177685v1_genomic.fna.gz --refList GCA_001776855.1_ASM177685v1_genomic.fna/target_genomes.txt --output GCA_001776855.1_ASM177685v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 22:24:53,424] [INFO] Task succeeded: fastANI
[2023-06-04 22:24:53,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02ee3cd8-1fed-474b-99d7-a53b55b85514/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 22:24:53,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02ee3cd8-1fed-474b-99d7-a53b55b85514/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 22:24:53,427] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 22:24:53,427] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 22:24:53,427] [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
--------------------------------------------------------------------------------
[2023-06-04 22:24:53,430] [INFO] DFAST Taxonomy check result was written to GCA_001776855.1_ASM177685v1_genomic.fna/tc_result.tsv
[2023-06-04 22:24:53,431] [INFO] ===== Taxonomy check completed =====
[2023-06-04 22:24:53,431] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 22:24:53,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02ee3cd8-1fed-474b-99d7-a53b55b85514/dqc_reference/checkm_data
[2023-06-04 22:24:53,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 22:24:53,449] [INFO] Task started: CheckM
[2023-06-04 22:24:53,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001776855.1_ASM177685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001776855.1_ASM177685v1_genomic.fna/checkm_input GCA_001776855.1_ASM177685v1_genomic.fna/checkm_result
[2023-06-04 22:25:08,184] [INFO] Task succeeded: CheckM
[2023-06-04 22:25:08,186] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 22:25:08,208] [INFO] ===== Completeness check finished =====
[2023-06-04 22:25:08,208] [INFO] ===== Start GTDB Search =====
[2023-06-04 22:25:08,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001776855.1_ASM177685v1_genomic.fna/markers.fasta)
[2023-06-04 22:25:08,209] [INFO] Task started: Blastn
[2023-06-04 22:25:08,209] [INFO] Running command: blastn -query GCA_001776855.1_ASM177685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02ee3cd8-1fed-474b-99d7-a53b55b85514/dqc_reference/reference_markers_gtdb.fasta -out GCA_001776855.1_ASM177685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:25:08,910] [INFO] Task succeeded: Blastn
[2023-06-04 22:25:08,915] [INFO] Selected 12 target genomes.
[2023-06-04 22:25:08,916] [INFO] Target genome list was writen to GCA_001776855.1_ASM177685v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 22:25:08,925] [INFO] Task started: fastANI
[2023-06-04 22:25:08,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d7a7388-cd73-4e40-8515-8df581463158/GCA_001776855.1_ASM177685v1_genomic.fna.gz --refList GCA_001776855.1_ASM177685v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001776855.1_ASM177685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 22:25:11,865] [INFO] Task succeeded: fastANI
[2023-06-04 22:25:11,869] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 22:25:11,869] [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_001777015.1	s__2-02-FULL-36-13 sp001777015	99.4614	163	174	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__Daviesbacterales;f__UBA10151;g__2-02-FULL-36-13	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-04 22:25:11,871] [INFO] GTDB search result was written to GCA_001776855.1_ASM177685v1_genomic.fna/result_gtdb.tsv
[2023-06-04 22:25:11,872] [INFO] ===== GTDB Search completed =====
[2023-06-04 22:25:11,874] [INFO] DFAST_QC result json was written to GCA_001776855.1_ASM177685v1_genomic.fna/dqc_result.json
[2023-06-04 22:25:11,874] [INFO] DFAST_QC completed!
[2023-06-04 22:25:11,875] [INFO] Total running time: 0h0m28s