[2023-03-18 09:15:00,470] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:15:00,471] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:15:00,471] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f73fd44-24a8-476a-a384-0e8693229223/dqc_reference
[2023-03-18 09:15:02,030] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:15:02,030] [INFO] Task started: Prodigal
[2023-03-18 09:15:02,030] [INFO] Running command: cat /var/lib/cwl/stg44b76d27-b5dd-4a20-a891-bb5ef431ac6c/OceanDNA-a5195.fa | prodigal -d OceanDNA-a5195/cds.fna -a OceanDNA-a5195/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:15:09,594] [INFO] Task succeeded: Prodigal
[2023-03-18 09:15:09,595] [INFO] Task started: HMMsearch
[2023-03-18 09:15:09,595] [INFO] Running command: hmmsearch --tblout OceanDNA-a5195/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f73fd44-24a8-476a-a384-0e8693229223/dqc_reference/reference_markers.hmm OceanDNA-a5195/protein.faa > /dev/null
[2023-03-18 09:15:09,753] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:15:09,754] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg44b76d27-b5dd-4a20-a891-bb5ef431ac6c/OceanDNA-a5195.fa]
[2023-03-18 09:15:09,768] [INFO] Query marker FASTA was written to OceanDNA-a5195/markers.fasta
[2023-03-18 09:15:09,768] [INFO] Task started: Blastn
[2023-03-18 09:15:09,768] [INFO] Running command: blastn -query OceanDNA-a5195/markers.fasta -db /var/lib/cwl/stg8f73fd44-24a8-476a-a384-0e8693229223/dqc_reference/reference_markers.fasta -out OceanDNA-a5195/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:10,234] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:10,239] [INFO] Selected 0 target genomes.
[2023-03-18 09:15:10,239] [INFO] Target genome list was writen to OceanDNA-a5195/target_genomes.txt
[2023-03-18 09:15:10,239] [ERROR] File is empty. [OceanDNA-a5195/target_genomes.txt]
[2023-03-18 09:15:10,239] [ERROR] Task failed. No target genome found.
[2023-03-18 09:15:10,239] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:15:10,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f73fd44-24a8-476a-a384-0e8693229223/dqc_reference/checkm_data
[2023-03-18 09:15:10,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:15:10,247] [INFO] Task started: CheckM
[2023-03-18 09:15:10,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a5195/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a5195/checkm_input OceanDNA-a5195/checkm_result
[2023-03-18 09:15:36,198] [INFO] Task succeeded: CheckM
[2023-03-18 09:15:36,198] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.01%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:15:36,200] [INFO] ===== Completeness check finished =====
[2023-03-18 09:15:36,200] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:15:36,200] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a5195/markers.fasta)
[2023-03-18 09:15:36,201] [INFO] Task started: Blastn
[2023-03-18 09:15:36,202] [INFO] Running command: blastn -query OceanDNA-a5195/markers.fasta -db /var/lib/cwl/stg8f73fd44-24a8-476a-a384-0e8693229223/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a5195/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:36,812] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:36,813] [INFO] Selected 7 target genomes.
[2023-03-18 09:15:36,813] [INFO] Target genome list was writen to OceanDNA-a5195/target_genomes_gtdb.txt
[2023-03-18 09:15:36,821] [INFO] Task started: fastANI
[2023-03-18 09:15:36,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg44b76d27-b5dd-4a20-a891-bb5ef431ac6c/OceanDNA-a5195.fa --refList OceanDNA-a5195/target_genomes_gtdb.txt --output OceanDNA-a5195/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:15:39,494] [INFO] Task succeeded: fastANI
[2023-03-18 09:15:39,495] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:15:39,495] [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
--------------------------------------------------------------------------------
[2023-03-18 09:15:39,495] [INFO] GTDB search result was written to OceanDNA-a5195/result_gtdb.tsv
[2023-03-18 09:15:39,495] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:15:39,496] [INFO] DFAST_QC result json was written to OceanDNA-a5195/dqc_result.json
[2023-03-18 09:15:39,496] [INFO] DFAST_QC completed!
[2023-03-18 09:15:39,496] [INFO] Total running time: 0h0m39s