[2023-03-19 02:05:11,577] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:11,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:11,578] [INFO] DQC Reference Directory: /var/lib/cwl/stgbafdf9ce-b129-4415-94ef-3a93b5289057/dqc_reference
[2023-03-19 02:05:13,263] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:13,263] [INFO] Task started: Prodigal
[2023-03-19 02:05:13,263] [INFO] Running command: cat /var/lib/cwl/stgadb89e61-6322-4115-bf97-8652b0f6d796/OceanDNA-a611.fa | prodigal -d OceanDNA-a611/cds.fna -a OceanDNA-a611/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:14,548] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:14,548] [INFO] Task started: HMMsearch
[2023-03-19 02:05:14,548] [INFO] Running command: hmmsearch --tblout OceanDNA-a611/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbafdf9ce-b129-4415-94ef-3a93b5289057/dqc_reference/reference_markers.hmm OceanDNA-a611/protein.faa > /dev/null
[2023-03-19 02:05:14,720] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:14,721] [WARNING] Found 0/6 markers. [/var/lib/cwl/stgadb89e61-6322-4115-bf97-8652b0f6d796/OceanDNA-a611.fa]
[2023-03-19 02:05:14,726] [INFO] Query marker FASTA was written to OceanDNA-a611/markers.fasta
[2023-03-19 02:05:14,726] [ERROR] File is empty. [OceanDNA-a611/markers.fasta]
[2023-03-19 02:05:14,727] [ERROR] Taxonomy check failed. No marker genes found.
[2023-03-19 02:05:14,727] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:05:14,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbafdf9ce-b129-4415-94ef-3a93b5289057/dqc_reference/checkm_data
[2023-03-19 02:05:14,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:05:14,784] [INFO] Task started: CheckM
[2023-03-19 02:05:14,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a611/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a611/checkm_input OceanDNA-a611/checkm_result
[2023-03-19 02:05:30,603] [INFO] Task succeeded: CheckM
[2023-03-19 02:05:30,604] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.30%
Contamintation: 5.09%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:05:30,605] [INFO] ===== Completeness check finished =====
[2023-03-19 02:05:30,605] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:05:30,606] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a611/markers.fasta)
[2023-03-19 02:05:30,606] [ERROR] File is empty. [OceanDNA-a611/markers.fasta]
[2023-03-19 02:05:30,606] [ERROR] GTDB Search failed. No marker genes found.
[2023-03-19 02:05:30,606] [INFO] DFAST_QC result json was written to OceanDNA-a611/dqc_result.json
[2023-03-19 02:05:30,606] [INFO] DFAST_QC completed!
[2023-03-19 02:05:30,606] [INFO] Total running time: 0h0m19s