[2023-03-16 10:20:34,808] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,808] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e2cdf92-3e28-47a4-8f23-c9caabc54180/dqc_reference
[2023-03-16 10:20:36,052] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:36,052] [INFO] Task started: Prodigal
[2023-03-16 10:20:36,052] [INFO] Running command: cat /var/lib/cwl/stgc1e3316b-e489-4f62-9657-f0d9adb448f7/OceanDNA-a857.fa | prodigal -d OceanDNA-a857/cds.fna -a OceanDNA-a857/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:20:39,018] [INFO] Task succeeded: Prodigal
[2023-03-16 10:20:39,019] [INFO] Task started: HMMsearch
[2023-03-16 10:20:39,019] [INFO] Running command: hmmsearch --tblout OceanDNA-a857/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e2cdf92-3e28-47a4-8f23-c9caabc54180/dqc_reference/reference_markers.hmm OceanDNA-a857/protein.faa > /dev/null
[2023-03-16 10:20:39,202] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:20:39,203] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc1e3316b-e489-4f62-9657-f0d9adb448f7/OceanDNA-a857.fa]
[2023-03-16 10:20:39,210] [INFO] Query marker FASTA was written to OceanDNA-a857/markers.fasta
[2023-03-16 10:20:39,210] [INFO] Task started: Blastn
[2023-03-16 10:20:39,210] [INFO] Running command: blastn -query OceanDNA-a857/markers.fasta -db /var/lib/cwl/stg8e2cdf92-3e28-47a4-8f23-c9caabc54180/dqc_reference/reference_markers.fasta -out OceanDNA-a857/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:20:39,738] [INFO] Task succeeded: Blastn
[2023-03-16 10:20:39,738] [INFO] Selected 0 target genomes.
[2023-03-16 10:20:39,738] [INFO] Target genome list was writen to OceanDNA-a857/target_genomes.txt
[2023-03-16 10:20:39,739] [ERROR] File is empty. [OceanDNA-a857/target_genomes.txt]
[2023-03-16 10:20:39,739] [ERROR] Task failed. No target genome found.
[2023-03-16 10:20:39,739] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:20:39,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e2cdf92-3e28-47a4-8f23-c9caabc54180/dqc_reference/checkm_data
[2023-03-16 10:20:39,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:20:39,804] [INFO] Task started: CheckM
[2023-03-16 10:20:39,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a857/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a857/checkm_input OceanDNA-a857/checkm_result
[2023-03-16 10:20:56,915] [INFO] Task succeeded: CheckM
[2023-03-16 10:20:56,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.97%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:20:56,917] [INFO] ===== Completeness check finished =====
[2023-03-16 10:20:56,917] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:20:56,917] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a857/markers.fasta)
[2023-03-16 10:20:56,917] [INFO] Task started: Blastn
[2023-03-16 10:20:56,917] [INFO] Running command: blastn -query OceanDNA-a857/markers.fasta -db /var/lib/cwl/stg8e2cdf92-3e28-47a4-8f23-c9caabc54180/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a857/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:20:57,721] [INFO] Task succeeded: Blastn
[2023-03-16 10:20:57,722] [INFO] Selected 5 target genomes.
[2023-03-16 10:20:57,722] [INFO] Target genome list was writen to OceanDNA-a857/target_genomes_gtdb.txt
[2023-03-16 10:20:57,727] [INFO] Task started: fastANI
[2023-03-16 10:20:57,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1e3316b-e489-4f62-9657-f0d9adb448f7/OceanDNA-a857.fa --refList OceanDNA-a857/target_genomes_gtdb.txt --output OceanDNA-a857/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:20:58,714] [INFO] Task succeeded: fastANI
[2023-03-16 10:20:58,715] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:20:58,715] [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
--------------------------------------------------------------------------------
[2023-03-16 10:20:58,715] [INFO] GTDB search result was written to OceanDNA-a857/result_gtdb.tsv
[2023-03-16 10:20:58,715] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:20:58,715] [INFO] DFAST_QC result json was written to OceanDNA-a857/dqc_result.json
[2023-03-16 10:20:58,715] [INFO] DFAST_QC completed!
[2023-03-16 10:20:58,716] [INFO] Total running time: 0h0m24s