[2023-03-14 12:33:23,745] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:33:23,745] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:33:23,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg50751d26-1186-4b60-af53-ab734a043b33/dqc_reference
[2023-03-14 12:33:24,809] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:33:24,809] [INFO] Task started: Prodigal
[2023-03-14 12:33:24,809] [INFO] Running command: cat /var/lib/cwl/stg1ec07e29-e441-4b46-8420-3cb555d17bd6/OceanDNA-b42426.fa | prodigal -d OceanDNA-b42426/cds.fna -a OceanDNA-b42426/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:33:29,682] [INFO] Task succeeded: Prodigal
[2023-03-14 12:33:29,683] [INFO] Task started: HMMsearch
[2023-03-14 12:33:29,683] [INFO] Running command: hmmsearch --tblout OceanDNA-b42426/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50751d26-1186-4b60-af53-ab734a043b33/dqc_reference/reference_markers.hmm OceanDNA-b42426/protein.faa > /dev/null
[2023-03-14 12:33:29,821] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:33:29,822] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1ec07e29-e441-4b46-8420-3cb555d17bd6/OceanDNA-b42426.fa]
[2023-03-14 12:33:29,832] [INFO] Query marker FASTA was written to OceanDNA-b42426/markers.fasta
[2023-03-14 12:33:29,833] [INFO] Task started: Blastn
[2023-03-14 12:33:29,833] [INFO] Running command: blastn -query OceanDNA-b42426/markers.fasta -db /var/lib/cwl/stg50751d26-1186-4b60-af53-ab734a043b33/dqc_reference/reference_markers.fasta -out OceanDNA-b42426/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:33:30,334] [INFO] Task succeeded: Blastn
[2023-03-14 12:33:30,335] [INFO] Selected 17 target genomes.
[2023-03-14 12:33:30,335] [INFO] Target genome list was writen to OceanDNA-b42426/target_genomes.txt
[2023-03-14 12:33:30,347] [INFO] Task started: fastANI
[2023-03-14 12:33:30,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ec07e29-e441-4b46-8420-3cb555d17bd6/OceanDNA-b42426.fa --refList OceanDNA-b42426/target_genomes.txt --output OceanDNA-b42426/fastani_result.tsv --threads 1
[2023-03-14 12:33:37,964] [INFO] Task succeeded: fastANI
[2023-03-14 12:33:37,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50751d26-1186-4b60-af53-ab734a043b33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:33:37,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50751d26-1186-4b60-af53-ab734a043b33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:33:37,965] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:33:37,965] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:33:37,965] [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
--------------------------------------------------------------------------------
[2023-03-14 12:33:37,966] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42426/tc_result.tsv
[2023-03-14 12:33:37,966] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:33:37,966] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:33:37,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50751d26-1186-4b60-af53-ab734a043b33/dqc_reference/checkm_data
[2023-03-14 12:33:37,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:33:37,973] [INFO] Task started: CheckM
[2023-03-14 12:33:37,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42426/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42426/checkm_input OceanDNA-b42426/checkm_result
[2023-03-14 12:33:55,514] [INFO] Task succeeded: CheckM
[2023-03-14 12:33:55,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.18%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:33:55,517] [INFO] ===== Completeness check finished =====
[2023-03-14 12:33:55,517] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:33:55,517] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42426/markers.fasta)
[2023-03-14 12:33:55,518] [INFO] Task started: Blastn
[2023-03-14 12:33:55,519] [INFO] Running command: blastn -query OceanDNA-b42426/markers.fasta -db /var/lib/cwl/stg50751d26-1186-4b60-af53-ab734a043b33/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42426/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:33:56,203] [INFO] Task succeeded: Blastn
[2023-03-14 12:33:56,204] [INFO] Selected 20 target genomes.
[2023-03-14 12:33:56,204] [INFO] Target genome list was writen to OceanDNA-b42426/target_genomes_gtdb.txt
[2023-03-14 12:33:56,220] [INFO] Task started: fastANI
[2023-03-14 12:33:56,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ec07e29-e441-4b46-8420-3cb555d17bd6/OceanDNA-b42426.fa --refList OceanDNA-b42426/target_genomes_gtdb.txt --output OceanDNA-b42426/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:34:00,553] [INFO] Task succeeded: fastANI
[2023-03-14 12:34:00,553] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:34:00,553] [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
--------------------------------------------------------------------------------
[2023-03-14 12:34:00,554] [INFO] GTDB search result was written to OceanDNA-b42426/result_gtdb.tsv
[2023-03-14 12:34:00,554] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:34:00,555] [INFO] DFAST_QC result json was written to OceanDNA-b42426/dqc_result.json
[2023-03-14 12:34:00,556] [INFO] DFAST_QC completed!
[2023-03-14 12:34:00,556] [INFO] Total running time: 0h0m37s