[2023-06-05 18:01:55,797] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:01:55,800] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:01:55,800] [INFO] DQC Reference Directory: /var/lib/cwl/stg2af8b7cd-0b51-4b8c-9f45-523b2e6c58e3/dqc_reference
[2023-06-05 18:01:57,010] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:01:57,011] [INFO] Task started: Prodigal
[2023-06-05 18:01:57,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg805eea8c-662a-455a-9c67-3bd588c9ffa4/GCA_902602015.1_AG-457-C05_genomic.fna.gz | prodigal -d GCA_902602015.1_AG-457-C05_genomic.fna/cds.fna -a GCA_902602015.1_AG-457-C05_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:02:02,217] [INFO] Task succeeded: Prodigal
[2023-06-05 18:02:02,218] [INFO] Task started: HMMsearch
[2023-06-05 18:02:02,218] [INFO] Running command: hmmsearch --tblout GCA_902602015.1_AG-457-C05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2af8b7cd-0b51-4b8c-9f45-523b2e6c58e3/dqc_reference/reference_markers.hmm GCA_902602015.1_AG-457-C05_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:02:02,433] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:02:02,434] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg805eea8c-662a-455a-9c67-3bd588c9ffa4/GCA_902602015.1_AG-457-C05_genomic.fna.gz]
[2023-06-05 18:02:02,459] [INFO] Query marker FASTA was written to GCA_902602015.1_AG-457-C05_genomic.fna/markers.fasta
[2023-06-05 18:02:02,460] [INFO] Task started: Blastn
[2023-06-05 18:02:02,460] [INFO] Running command: blastn -query GCA_902602015.1_AG-457-C05_genomic.fna/markers.fasta -db /var/lib/cwl/stg2af8b7cd-0b51-4b8c-9f45-523b2e6c58e3/dqc_reference/reference_markers.fasta -out GCA_902602015.1_AG-457-C05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:02:03,068] [INFO] Task succeeded: Blastn
[2023-06-05 18:02:03,086] [INFO] Selected 15 target genomes.
[2023-06-05 18:02:03,087] [INFO] Target genome list was writen to GCA_902602015.1_AG-457-C05_genomic.fna/target_genomes.txt
[2023-06-05 18:02:03,094] [INFO] Task started: fastANI
[2023-06-05 18:02:03,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg805eea8c-662a-455a-9c67-3bd588c9ffa4/GCA_902602015.1_AG-457-C05_genomic.fna.gz --refList GCA_902602015.1_AG-457-C05_genomic.fna/target_genomes.txt --output GCA_902602015.1_AG-457-C05_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:02:16,416] [INFO] Task succeeded: fastANI
[2023-06-05 18:02:16,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2af8b7cd-0b51-4b8c-9f45-523b2e6c58e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:02:16,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2af8b7cd-0b51-4b8c-9f45-523b2e6c58e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:02:16,419] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:02:16,420] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:02:16,420] [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
--------------------------------------------------------------------------------
[2023-06-05 18:02:16,423] [INFO] DFAST Taxonomy check result was written to GCA_902602015.1_AG-457-C05_genomic.fna/tc_result.tsv
[2023-06-05 18:02:16,424] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:02:16,424] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:02:16,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2af8b7cd-0b51-4b8c-9f45-523b2e6c58e3/dqc_reference/checkm_data
[2023-06-05 18:02:16,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:02:16,453] [INFO] Task started: CheckM
[2023-06-05 18:02:16,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902602015.1_AG-457-C05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902602015.1_AG-457-C05_genomic.fna/checkm_input GCA_902602015.1_AG-457-C05_genomic.fna/checkm_result
[2023-06-05 18:02:38,756] [INFO] Task succeeded: CheckM
[2023-06-05 18:02:38,757] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 18:02:38,782] [INFO] ===== Completeness check finished =====
[2023-06-05 18:02:38,782] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:02:38,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902602015.1_AG-457-C05_genomic.fna/markers.fasta)
[2023-06-05 18:02:38,783] [INFO] Task started: Blastn
[2023-06-05 18:02:38,783] [INFO] Running command: blastn -query GCA_902602015.1_AG-457-C05_genomic.fna/markers.fasta -db /var/lib/cwl/stg2af8b7cd-0b51-4b8c-9f45-523b2e6c58e3/dqc_reference/reference_markers_gtdb.fasta -out GCA_902602015.1_AG-457-C05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:02:39,587] [INFO] Task succeeded: Blastn
[2023-06-05 18:02:39,592] [INFO] Selected 13 target genomes.
[2023-06-05 18:02:39,592] [INFO] Target genome list was writen to GCA_902602015.1_AG-457-C05_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:02:39,764] [INFO] Task started: fastANI
[2023-06-05 18:02:39,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg805eea8c-662a-455a-9c67-3bd588c9ffa4/GCA_902602015.1_AG-457-C05_genomic.fna.gz --refList GCA_902602015.1_AG-457-C05_genomic.fna/target_genomes_gtdb.txt --output GCA_902602015.1_AG-457-C05_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:02:48,632] [INFO] Task succeeded: fastANI
[2023-06-05 18:02:48,638] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:02:48,638] [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_002724555.1	s__UBA6544 sp002724555	87.0684	264	557	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002716125.1	s__UBA6544 sp002716125	77.0559	163	557	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:02:48,641] [INFO] GTDB search result was written to GCA_902602015.1_AG-457-C05_genomic.fna/result_gtdb.tsv
[2023-06-05 18:02:48,642] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:02:48,650] [INFO] DFAST_QC result json was written to GCA_902602015.1_AG-457-C05_genomic.fna/dqc_result.json
[2023-06-05 18:02:48,650] [INFO] DFAST_QC completed!
[2023-06-05 18:02:48,650] [INFO] Total running time: 0h0m53s