[2023-06-05 01:18:25,954] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:18:25,958] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:18:25,958] [INFO] DQC Reference Directory: /var/lib/cwl/stg98ecbde9-8495-47f0-bec5-049379622443/dqc_reference
[2023-06-05 01:18:29,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:18:29,402] [INFO] Task started: Prodigal
[2023-06-05 01:18:29,402] [INFO] Running command: gunzip -c /var/lib/cwl/stg3142bbaf-391e-4b0a-9b9f-70d15b712da4/GCA_902627475.1_AH-321-K06_genomic.fna.gz | prodigal -d GCA_902627475.1_AH-321-K06_genomic.fna/cds.fna -a GCA_902627475.1_AH-321-K06_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:18:30,114] [INFO] Task succeeded: Prodigal
[2023-06-05 01:18:30,115] [INFO] Task started: HMMsearch
[2023-06-05 01:18:30,115] [INFO] Running command: hmmsearch --tblout GCA_902627475.1_AH-321-K06_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98ecbde9-8495-47f0-bec5-049379622443/dqc_reference/reference_markers.hmm GCA_902627475.1_AH-321-K06_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:18:30,241] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:18:30,245] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg3142bbaf-391e-4b0a-9b9f-70d15b712da4/GCA_902627475.1_AH-321-K06_genomic.fna.gz]
[2023-06-05 01:18:30,259] [INFO] Query marker FASTA was written to GCA_902627475.1_AH-321-K06_genomic.fna/markers.fasta
[2023-06-05 01:18:30,259] [INFO] Task started: Blastn
[2023-06-05 01:18:30,260] [INFO] Running command: blastn -query GCA_902627475.1_AH-321-K06_genomic.fna/markers.fasta -db /var/lib/cwl/stg98ecbde9-8495-47f0-bec5-049379622443/dqc_reference/reference_markers.fasta -out GCA_902627475.1_AH-321-K06_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:18:33,275] [INFO] Task succeeded: Blastn
[2023-06-05 01:18:33,280] [INFO] Selected 5 target genomes.
[2023-06-05 01:18:33,281] [INFO] Target genome list was writen to GCA_902627475.1_AH-321-K06_genomic.fna/target_genomes.txt
[2023-06-05 01:18:33,286] [INFO] Task started: fastANI
[2023-06-05 01:18:33,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg3142bbaf-391e-4b0a-9b9f-70d15b712da4/GCA_902627475.1_AH-321-K06_genomic.fna.gz --refList GCA_902627475.1_AH-321-K06_genomic.fna/target_genomes.txt --output GCA_902627475.1_AH-321-K06_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:18:35,514] [INFO] Task succeeded: fastANI
[2023-06-05 01:18:35,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98ecbde9-8495-47f0-bec5-049379622443/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:18:35,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98ecbde9-8495-47f0-bec5-049379622443/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:18:35,518] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:18:35,518] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 01:18:35,518] [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 01:18:35,520] [INFO] DFAST Taxonomy check result was written to GCA_902627475.1_AH-321-K06_genomic.fna/tc_result.tsv
[2023-06-05 01:18:35,521] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:18:35,521] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:18:35,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98ecbde9-8495-47f0-bec5-049379622443/dqc_reference/checkm_data
[2023-06-05 01:18:35,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:18:35,533] [INFO] Task started: CheckM
[2023-06-05 01:18:35,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902627475.1_AH-321-K06_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902627475.1_AH-321-K06_genomic.fna/checkm_input GCA_902627475.1_AH-321-K06_genomic.fna/checkm_result
[2023-06-05 01:18:46,021] [INFO] Task succeeded: CheckM
[2023-06-05 01:18:46,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 4.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:18:46,041] [INFO] ===== Completeness check finished =====
[2023-06-05 01:18:46,041] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:18:46,041] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902627475.1_AH-321-K06_genomic.fna/markers.fasta)
[2023-06-05 01:18:46,042] [INFO] Task started: Blastn
[2023-06-05 01:18:46,042] [INFO] Running command: blastn -query GCA_902627475.1_AH-321-K06_genomic.fna/markers.fasta -db /var/lib/cwl/stg98ecbde9-8495-47f0-bec5-049379622443/dqc_reference/reference_markers_gtdb.fasta -out GCA_902627475.1_AH-321-K06_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:18:46,552] [INFO] Task succeeded: Blastn
[2023-06-05 01:18:46,556] [INFO] Selected 5 target genomes.
[2023-06-05 01:18:46,557] [INFO] Target genome list was writen to GCA_902627475.1_AH-321-K06_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:18:46,562] [INFO] Task started: fastANI
[2023-06-05 01:18:46,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg3142bbaf-391e-4b0a-9b9f-70d15b712da4/GCA_902627475.1_AH-321-K06_genomic.fna.gz --refList GCA_902627475.1_AH-321-K06_genomic.fna/target_genomes_gtdb.txt --output GCA_902627475.1_AH-321-K06_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:18:47,525] [INFO] Task succeeded: fastANI
[2023-06-05 01:18:47,528] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:18:47,529] [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_000218705.1	s__Prochlorococcus_A marinus_Q	95.2534	55	80	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	95.95	95.40	0.90	0.85	14	conclusive
--------------------------------------------------------------------------------
[2023-06-05 01:18:47,531] [INFO] GTDB search result was written to GCA_902627475.1_AH-321-K06_genomic.fna/result_gtdb.tsv
[2023-06-05 01:18:47,531] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:18:47,534] [INFO] DFAST_QC result json was written to GCA_902627475.1_AH-321-K06_genomic.fna/dqc_result.json
[2023-06-05 01:18:47,534] [INFO] DFAST_QC completed!
[2023-06-05 01:18:47,534] [INFO] Total running time: 0h0m22s