[2023-03-15 08:21:23,536] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:21:23,538] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:21:23,539] [INFO] DQC Reference Directory: /var/lib/cwl/stg036ffb58-e3c3-4411-9fec-e60689f65f95/dqc_reference
[2023-03-15 08:21:24,621] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:21:24,622] [INFO] Task started: Prodigal
[2023-03-15 08:21:24,622] [INFO] Running command: cat /var/lib/cwl/stg5962a8b4-acef-47b1-8407-fb8c2c8e288c/OceanDNA-a4091.fa | prodigal -d OceanDNA-a4091/cds.fna -a OceanDNA-a4091/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:21:30,332] [INFO] Task succeeded: Prodigal
[2023-03-15 08:21:30,333] [INFO] Task started: HMMsearch
[2023-03-15 08:21:30,333] [INFO] Running command: hmmsearch --tblout OceanDNA-a4091/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg036ffb58-e3c3-4411-9fec-e60689f65f95/dqc_reference/reference_markers.hmm OceanDNA-a4091/protein.faa > /dev/null
[2023-03-15 08:21:30,486] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:21:30,487] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg5962a8b4-acef-47b1-8407-fb8c2c8e288c/OceanDNA-a4091.fa]
[2023-03-15 08:21:30,519] [INFO] Query marker FASTA was written to OceanDNA-a4091/markers.fasta
[2023-03-15 08:21:30,519] [INFO] Task started: Blastn
[2023-03-15 08:21:30,519] [INFO] Running command: blastn -query OceanDNA-a4091/markers.fasta -db /var/lib/cwl/stg036ffb58-e3c3-4411-9fec-e60689f65f95/dqc_reference/reference_markers.fasta -out OceanDNA-a4091/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:21:30,949] [INFO] Task succeeded: Blastn
[2023-03-15 08:21:30,956] [INFO] Selected 0 target genomes.
[2023-03-15 08:21:30,956] [INFO] Target genome list was writen to OceanDNA-a4091/target_genomes.txt
[2023-03-15 08:21:30,956] [ERROR] File is empty. [OceanDNA-a4091/target_genomes.txt]
[2023-03-15 08:21:30,956] [ERROR] Task failed. No target genome found.
[2023-03-15 08:21:30,957] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:21:30,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg036ffb58-e3c3-4411-9fec-e60689f65f95/dqc_reference/checkm_data
[2023-03-15 08:21:30,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:21:30,963] [INFO] Task started: CheckM
[2023-03-15 08:21:30,963] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4091/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4091/checkm_input OceanDNA-a4091/checkm_result
[2023-03-15 08:21:48,846] [INFO] Task succeeded: CheckM
[2023-03-15 08:21:48,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.34%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:21:48,893] [INFO] ===== Completeness check finished =====
[2023-03-15 08:21:48,894] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:21:48,894] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4091/markers.fasta)
[2023-03-15 08:21:48,895] [INFO] Task started: Blastn
[2023-03-15 08:21:48,896] [INFO] Running command: blastn -query OceanDNA-a4091/markers.fasta -db /var/lib/cwl/stg036ffb58-e3c3-4411-9fec-e60689f65f95/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4091/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:21:49,572] [INFO] Task succeeded: Blastn
[2023-03-15 08:21:49,573] [INFO] Selected 5 target genomes.
[2023-03-15 08:21:49,573] [INFO] Target genome list was writen to OceanDNA-a4091/target_genomes_gtdb.txt
[2023-03-15 08:21:49,589] [INFO] Task started: fastANI
[2023-03-15 08:21:49,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg5962a8b4-acef-47b1-8407-fb8c2c8e288c/OceanDNA-a4091.fa --refList OceanDNA-a4091/target_genomes_gtdb.txt --output OceanDNA-a4091/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:21:50,718] [INFO] Task succeeded: fastANI
[2023-03-15 08:21:50,719] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:21:50,719] [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
--------------------------------------------------------------------------------
[2023-03-15 08:21:50,720] [INFO] GTDB search result was written to OceanDNA-a4091/result_gtdb.tsv
[2023-03-15 08:21:50,721] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:21:50,723] [INFO] DFAST_QC result json was written to OceanDNA-a4091/dqc_result.json
[2023-03-15 08:21:50,723] [INFO] DFAST_QC completed!
[2023-03-15 08:21:50,723] [INFO] Total running time: 0h0m27s