[2023-03-15 08:55:06,628] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,629] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg2364e8e9-3345-4ed5-a42c-9998cf37cda4/dqc_reference
[2023-03-15 08:55:08,345] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,345] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,345] [INFO] Running command: cat /var/lib/cwl/stg805c2a9b-ff80-4273-89d6-c248c7aa801f/OceanDNA-b16120.fa | prodigal -d OceanDNA-b16120/cds.fna -a OceanDNA-b16120/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:26,494] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:26,495] [INFO] Task started: HMMsearch
[2023-03-15 08:55:26,495] [INFO] Running command: hmmsearch --tblout OceanDNA-b16120/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2364e8e9-3345-4ed5-a42c-9998cf37cda4/dqc_reference/reference_markers.hmm OceanDNA-b16120/protein.faa > /dev/null
[2023-03-15 08:55:26,781] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:26,782] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg805c2a9b-ff80-4273-89d6-c248c7aa801f/OceanDNA-b16120.fa]
[2023-03-15 08:55:26,807] [INFO] Query marker FASTA was written to OceanDNA-b16120/markers.fasta
[2023-03-15 08:55:26,807] [INFO] Task started: Blastn
[2023-03-15 08:55:26,807] [INFO] Running command: blastn -query OceanDNA-b16120/markers.fasta -db /var/lib/cwl/stg2364e8e9-3345-4ed5-a42c-9998cf37cda4/dqc_reference/reference_markers.fasta -out OceanDNA-b16120/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:27,249] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:27,249] [INFO] Selected 10 target genomes.
[2023-03-15 08:55:27,250] [INFO] Target genome list was writen to OceanDNA-b16120/target_genomes.txt
[2023-03-15 08:55:27,255] [INFO] Task started: fastANI
[2023-03-15 08:55:27,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg805c2a9b-ff80-4273-89d6-c248c7aa801f/OceanDNA-b16120.fa --refList OceanDNA-b16120/target_genomes.txt --output OceanDNA-b16120/fastani_result.tsv --threads 1
[2023-03-15 08:55:35,924] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:35,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2364e8e9-3345-4ed5-a42c-9998cf37cda4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:35,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2364e8e9-3345-4ed5-a42c-9998cf37cda4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:35,924] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:55:35,924] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:55:35,924] [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
--------------------------------------------------------------------------------
[2023-03-15 08:55:35,925] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16120/tc_result.tsv
[2023-03-15 08:55:35,925] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:35,925] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:35,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2364e8e9-3345-4ed5-a42c-9998cf37cda4/dqc_reference/checkm_data
[2023-03-15 08:55:35,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:35,933] [INFO] Task started: CheckM
[2023-03-15 08:55:35,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16120/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16120/checkm_input OceanDNA-b16120/checkm_result
[2023-03-15 08:56:23,720] [INFO] Task succeeded: CheckM
[2023-03-15 08:56:23,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.47%
Contamintation: 0.84%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 08:56:23,723] [INFO] ===== Completeness check finished =====
[2023-03-15 08:56:23,724] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:56:23,724] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16120/markers.fasta)
[2023-03-15 08:56:23,724] [INFO] Task started: Blastn
[2023-03-15 08:56:23,724] [INFO] Running command: blastn -query OceanDNA-b16120/markers.fasta -db /var/lib/cwl/stg2364e8e9-3345-4ed5-a42c-9998cf37cda4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16120/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:56:24,150] [INFO] Task succeeded: Blastn
[2023-03-15 08:56:24,151] [INFO] Selected 10 target genomes.
[2023-03-15 08:56:24,151] [INFO] Target genome list was writen to OceanDNA-b16120/target_genomes_gtdb.txt
[2023-03-15 08:56:24,178] [INFO] Task started: fastANI
[2023-03-15 08:56:24,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg805c2a9b-ff80-4273-89d6-c248c7aa801f/OceanDNA-b16120.fa --refList OceanDNA-b16120/target_genomes_gtdb.txt --output OceanDNA-b16120/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:56:32,285] [INFO] Task succeeded: fastANI
[2023-03-15 08:56:32,287] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:56:32,288] [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_010692635.1	s__SIO2C1 sp010692635	75.535	52	870	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__SIO2C1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:56:32,288] [INFO] GTDB search result was written to OceanDNA-b16120/result_gtdb.tsv
[2023-03-15 08:56:32,288] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:56:32,288] [INFO] DFAST_QC result json was written to OceanDNA-b16120/dqc_result.json
[2023-03-15 08:56:32,288] [INFO] DFAST_QC completed!
[2023-03-15 08:56:32,289] [INFO] Total running time: 0h1m26s