[2023-03-15 06:28:21,414] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:28:21,414] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:28:21,414] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7098549-f56e-4829-9113-6488ec854442/dqc_reference
[2023-03-15 06:28:22,539] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:28:22,540] [INFO] Task started: Prodigal
[2023-03-15 06:28:22,540] [INFO] Running command: cat /var/lib/cwl/stg740a376e-5a94-4a6d-a2eb-22be5b3194a8/OceanDNA-b22387.fa | prodigal -d OceanDNA-b22387/cds.fna -a OceanDNA-b22387/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:28:38,432] [INFO] Task succeeded: Prodigal
[2023-03-15 06:28:38,432] [INFO] Task started: HMMsearch
[2023-03-15 06:28:38,432] [INFO] Running command: hmmsearch --tblout OceanDNA-b22387/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7098549-f56e-4829-9113-6488ec854442/dqc_reference/reference_markers.hmm OceanDNA-b22387/protein.faa > /dev/null
[2023-03-15 06:28:38,645] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:28:38,646] [INFO] Found 6/6 markers.
[2023-03-15 06:28:38,688] [INFO] Query marker FASTA was written to OceanDNA-b22387/markers.fasta
[2023-03-15 06:28:38,690] [INFO] Task started: Blastn
[2023-03-15 06:28:38,690] [INFO] Running command: blastn -query OceanDNA-b22387/markers.fasta -db /var/lib/cwl/stgb7098549-f56e-4829-9113-6488ec854442/dqc_reference/reference_markers.fasta -out OceanDNA-b22387/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:28:39,205] [INFO] Task succeeded: Blastn
[2023-03-15 06:28:39,206] [INFO] Selected 19 target genomes.
[2023-03-15 06:28:39,207] [INFO] Target genome list was writen to OceanDNA-b22387/target_genomes.txt
[2023-03-15 06:28:39,217] [INFO] Task started: fastANI
[2023-03-15 06:28:39,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg740a376e-5a94-4a6d-a2eb-22be5b3194a8/OceanDNA-b22387.fa --refList OceanDNA-b22387/target_genomes.txt --output OceanDNA-b22387/fastani_result.tsv --threads 1
[2023-03-15 06:28:52,515] [INFO] Task succeeded: fastANI
[2023-03-15 06:28:52,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7098549-f56e-4829-9113-6488ec854442/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:28:52,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7098549-f56e-4829-9113-6488ec854442/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:28:52,515] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:28:52,516] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 06:28:52,516] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-15 06:28:52,516] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22387/tc_result.tsv
[2023-03-15 06:28:52,516] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:28:52,516] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:28:52,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7098549-f56e-4829-9113-6488ec854442/dqc_reference/checkm_data
[2023-03-15 06:28:52,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:28:52,540] [INFO] Task started: CheckM
[2023-03-15 06:28:52,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22387/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22387/checkm_input OceanDNA-b22387/checkm_result
[2023-03-15 06:29:35,944] [INFO] Task succeeded: CheckM
[2023-03-15 06:29:35,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:29:35,961] [INFO] ===== Completeness check finished =====
[2023-03-15 06:29:35,961] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:29:35,962] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22387/markers.fasta)
[2023-03-15 06:29:35,963] [INFO] Task started: Blastn
[2023-03-15 06:29:35,963] [INFO] Running command: blastn -query OceanDNA-b22387/markers.fasta -db /var/lib/cwl/stgb7098549-f56e-4829-9113-6488ec854442/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22387/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:29:36,691] [INFO] Task succeeded: Blastn
[2023-03-15 06:29:36,692] [INFO] Selected 25 target genomes.
[2023-03-15 06:29:36,692] [INFO] Target genome list was writen to OceanDNA-b22387/target_genomes_gtdb.txt
[2023-03-15 06:29:36,710] [INFO] Task started: fastANI
[2023-03-15 06:29:36,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg740a376e-5a94-4a6d-a2eb-22be5b3194a8/OceanDNA-b22387.fa --refList OceanDNA-b22387/target_genomes_gtdb.txt --output OceanDNA-b22387/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:29:52,158] [INFO] Task succeeded: fastANI
[2023-03-15 06:29:52,158] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:29:52,158] [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 06:29:52,158] [INFO] GTDB search result was written to OceanDNA-b22387/result_gtdb.tsv
[2023-03-15 06:29:52,159] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:29:52,159] [INFO] DFAST_QC result json was written to OceanDNA-b22387/dqc_result.json
[2023-03-15 06:29:52,159] [INFO] DFAST_QC completed!
[2023-03-15 06:29:52,159] [INFO] Total running time: 0h1m31s