[2023-03-18 00:25:18,131] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:25:18,132] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:25:18,132] [INFO] DQC Reference Directory: /var/lib/cwl/stge5e8386a-354e-42e4-bc63-c24ae9bd5e4a/dqc_reference
[2023-03-18 00:25:19,205] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:25:19,205] [INFO] Task started: Prodigal
[2023-03-18 00:25:19,205] [INFO] Running command: cat /var/lib/cwl/stgc5ed4f13-17f7-4fb1-982a-103983e85adb/OceanDNA-a1805.fa | prodigal -d OceanDNA-a1805/cds.fna -a OceanDNA-a1805/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:25:27,123] [INFO] Task succeeded: Prodigal
[2023-03-18 00:25:27,123] [INFO] Task started: HMMsearch
[2023-03-18 00:25:27,123] [INFO] Running command: hmmsearch --tblout OceanDNA-a1805/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5e8386a-354e-42e4-bc63-c24ae9bd5e4a/dqc_reference/reference_markers.hmm OceanDNA-a1805/protein.faa > /dev/null
[2023-03-18 00:25:27,291] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:25:27,291] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc5ed4f13-17f7-4fb1-982a-103983e85adb/OceanDNA-a1805.fa]
[2023-03-18 00:25:27,303] [INFO] Query marker FASTA was written to OceanDNA-a1805/markers.fasta
[2023-03-18 00:25:27,304] [INFO] Task started: Blastn
[2023-03-18 00:25:27,304] [INFO] Running command: blastn -query OceanDNA-a1805/markers.fasta -db /var/lib/cwl/stge5e8386a-354e-42e4-bc63-c24ae9bd5e4a/dqc_reference/reference_markers.fasta -out OceanDNA-a1805/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:25:27,773] [INFO] Task succeeded: Blastn
[2023-03-18 00:25:27,774] [INFO] Selected 3 target genomes.
[2023-03-18 00:25:27,774] [INFO] Target genome list was writen to OceanDNA-a1805/target_genomes.txt
[2023-03-18 00:25:27,778] [INFO] Task started: fastANI
[2023-03-18 00:25:27,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5ed4f13-17f7-4fb1-982a-103983e85adb/OceanDNA-a1805.fa --refList OceanDNA-a1805/target_genomes.txt --output OceanDNA-a1805/fastani_result.tsv --threads 1
[2023-03-18 00:25:28,929] [INFO] Task succeeded: fastANI
[2023-03-18 00:25:28,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5e8386a-354e-42e4-bc63-c24ae9bd5e4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:25:28,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5e8386a-354e-42e4-bc63-c24ae9bd5e4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:25:28,929] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:25:28,929] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:25:28,929] [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
--------------------------------------------------------------------------------
[2023-03-18 00:25:28,930] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1805/tc_result.tsv
[2023-03-18 00:25:28,930] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:25:28,930] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:25:28,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5e8386a-354e-42e4-bc63-c24ae9bd5e4a/dqc_reference/checkm_data
[2023-03-18 00:25:28,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:25:29,289] [INFO] Task started: CheckM
[2023-03-18 00:25:29,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1805/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1805/checkm_input OceanDNA-a1805/checkm_result
[2023-03-18 00:25:54,504] [INFO] Task succeeded: CheckM
[2023-03-18 00:25:54,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:25:54,507] [INFO] ===== Completeness check finished =====
[2023-03-18 00:25:54,507] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:25:54,507] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1805/markers.fasta)
[2023-03-18 00:25:54,508] [INFO] Task started: Blastn
[2023-03-18 00:25:54,508] [INFO] Running command: blastn -query OceanDNA-a1805/markers.fasta -db /var/lib/cwl/stge5e8386a-354e-42e4-bc63-c24ae9bd5e4a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1805/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:25:54,921] [INFO] Task succeeded: Blastn
[2023-03-18 00:25:54,922] [INFO] Selected 10 target genomes.
[2023-03-18 00:25:54,922] [INFO] Target genome list was writen to OceanDNA-a1805/target_genomes_gtdb.txt
[2023-03-18 00:25:54,972] [INFO] Task started: fastANI
[2023-03-18 00:25:54,973] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5ed4f13-17f7-4fb1-982a-103983e85adb/OceanDNA-a1805.fa --refList OceanDNA-a1805/target_genomes_gtdb.txt --output OceanDNA-a1805/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:25:57,485] [INFO] Task succeeded: fastANI
[2023-03-18 00:25:57,485] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:25:57,486] [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
--------------------------------------------------------------------------------
[2023-03-18 00:25:57,486] [INFO] GTDB search result was written to OceanDNA-a1805/result_gtdb.tsv
[2023-03-18 00:25:57,486] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:25:57,486] [INFO] DFAST_QC result json was written to OceanDNA-a1805/dqc_result.json
[2023-03-18 00:25:57,486] [INFO] DFAST_QC completed!
[2023-03-18 00:25:57,486] [INFO] Total running time: 0h0m39s