[2023-03-17 11:08:00,438] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,438] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg40fdc114-9c84-49da-b9e2-231846afa29f/dqc_reference
[2023-03-17 11:08:01,563] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,563] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,564] [INFO] Running command: cat /var/lib/cwl/stg5f1bc5dd-f456-499b-8a79-d188c2735e5a/OceanDNA-b15912.fa | prodigal -d OceanDNA-b15912/cds.fna -a OceanDNA-b15912/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:10,790] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:10,790] [INFO] Task started: HMMsearch
[2023-03-17 11:08:10,790] [INFO] Running command: hmmsearch --tblout OceanDNA-b15912/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40fdc114-9c84-49da-b9e2-231846afa29f/dqc_reference/reference_markers.hmm OceanDNA-b15912/protein.faa > /dev/null
[2023-03-17 11:08:10,943] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:10,944] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5f1bc5dd-f456-499b-8a79-d188c2735e5a/OceanDNA-b15912.fa]
[2023-03-17 11:08:10,955] [INFO] Query marker FASTA was written to OceanDNA-b15912/markers.fasta
[2023-03-17 11:08:10,955] [INFO] Task started: Blastn
[2023-03-17 11:08:10,955] [INFO] Running command: blastn -query OceanDNA-b15912/markers.fasta -db /var/lib/cwl/stg40fdc114-9c84-49da-b9e2-231846afa29f/dqc_reference/reference_markers.fasta -out OceanDNA-b15912/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:11,493] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:11,494] [INFO] Selected 0 target genomes.
[2023-03-17 11:08:11,494] [INFO] Target genome list was writen to OceanDNA-b15912/target_genomes.txt
[2023-03-17 11:08:11,494] [ERROR] File is empty. [OceanDNA-b15912/target_genomes.txt]
[2023-03-17 11:08:11,494] [ERROR] Task failed. No target genome found.
[2023-03-17 11:08:11,494] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:11,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40fdc114-9c84-49da-b9e2-231846afa29f/dqc_reference/checkm_data
[2023-03-17 11:08:11,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:11,501] [INFO] Task started: CheckM
[2023-03-17 11:08:11,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15912/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15912/checkm_input OceanDNA-b15912/checkm_result
[2023-03-17 11:08:39,149] [INFO] Task succeeded: CheckM
[2023-03-17 11:08:39,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:08:39,151] [INFO] ===== Completeness check finished =====
[2023-03-17 11:08:39,151] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:08:39,151] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15912/markers.fasta)
[2023-03-17 11:08:39,151] [INFO] Task started: Blastn
[2023-03-17 11:08:39,151] [INFO] Running command: blastn -query OceanDNA-b15912/markers.fasta -db /var/lib/cwl/stg40fdc114-9c84-49da-b9e2-231846afa29f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15912/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:39,854] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:39,855] [INFO] Selected 11 target genomes.
[2023-03-17 11:08:39,855] [INFO] Target genome list was writen to OceanDNA-b15912/target_genomes_gtdb.txt
[2023-03-17 11:08:40,026] [INFO] Task started: fastANI
[2023-03-17 11:08:40,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f1bc5dd-f456-499b-8a79-d188c2735e5a/OceanDNA-b15912.fa --refList OceanDNA-b15912/target_genomes_gtdb.txt --output OceanDNA-b15912/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:08:45,930] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:45,931] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:08:45,931] [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
--------------------------------------------------------------------------------
[2023-03-17 11:08:45,931] [INFO] GTDB search result was written to OceanDNA-b15912/result_gtdb.tsv
[2023-03-17 11:08:45,931] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:08:45,932] [INFO] DFAST_QC result json was written to OceanDNA-b15912/dqc_result.json
[2023-03-17 11:08:45,932] [INFO] DFAST_QC completed!
[2023-03-17 11:08:45,932] [INFO] Total running time: 0h0m45s