[2023-03-15 14:29:06,006] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:29:06,006] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:29:06,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg988509ef-f852-470a-a96b-181db344a8c5/dqc_reference
[2023-03-15 14:29:07,101] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:29:07,102] [INFO] Task started: Prodigal
[2023-03-15 14:29:07,102] [INFO] Running command: cat /var/lib/cwl/stg02f966dd-aa98-46d9-b69a-7a1b464e9a28/OceanDNA-b22925.fa | prodigal -d OceanDNA-b22925/cds.fna -a OceanDNA-b22925/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:29:18,438] [INFO] Task succeeded: Prodigal
[2023-03-15 14:29:18,438] [INFO] Task started: HMMsearch
[2023-03-15 14:29:18,438] [INFO] Running command: hmmsearch --tblout OceanDNA-b22925/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg988509ef-f852-470a-a96b-181db344a8c5/dqc_reference/reference_markers.hmm OceanDNA-b22925/protein.faa > /dev/null
[2023-03-15 14:29:18,612] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:29:18,612] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg02f966dd-aa98-46d9-b69a-7a1b464e9a28/OceanDNA-b22925.fa]
[2023-03-15 14:29:18,632] [INFO] Query marker FASTA was written to OceanDNA-b22925/markers.fasta
[2023-03-15 14:29:18,632] [INFO] Task started: Blastn
[2023-03-15 14:29:18,632] [INFO] Running command: blastn -query OceanDNA-b22925/markers.fasta -db /var/lib/cwl/stg988509ef-f852-470a-a96b-181db344a8c5/dqc_reference/reference_markers.fasta -out OceanDNA-b22925/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:29:19,130] [INFO] Task succeeded: Blastn
[2023-03-15 14:29:19,131] [INFO] Selected 17 target genomes.
[2023-03-15 14:29:19,131] [INFO] Target genome list was writen to OceanDNA-b22925/target_genomes.txt
[2023-03-15 14:29:19,140] [INFO] Task started: fastANI
[2023-03-15 14:29:19,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg02f966dd-aa98-46d9-b69a-7a1b464e9a28/OceanDNA-b22925.fa --refList OceanDNA-b22925/target_genomes.txt --output OceanDNA-b22925/fastani_result.tsv --threads 1
[2023-03-15 14:29:32,197] [INFO] Task succeeded: fastANI
[2023-03-15 14:29:32,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg988509ef-f852-470a-a96b-181db344a8c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:29:32,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg988509ef-f852-470a-a96b-181db344a8c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:29:32,198] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:29:32,198] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:29:32,198] [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 14:29:32,198] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22925/tc_result.tsv
[2023-03-15 14:29:32,198] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:29:32,199] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:29:32,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg988509ef-f852-470a-a96b-181db344a8c5/dqc_reference/checkm_data
[2023-03-15 14:29:32,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:29:32,206] [INFO] Task started: CheckM
[2023-03-15 14:29:32,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22925/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22925/checkm_input OceanDNA-b22925/checkm_result
[2023-03-15 14:30:05,087] [INFO] Task succeeded: CheckM
[2023-03-15 14:30:05,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.20%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:30:05,159] [INFO] ===== Completeness check finished =====
[2023-03-15 14:30:05,159] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:30:05,159] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22925/markers.fasta)
[2023-03-15 14:30:05,160] [INFO] Task started: Blastn
[2023-03-15 14:30:05,161] [INFO] Running command: blastn -query OceanDNA-b22925/markers.fasta -db /var/lib/cwl/stg988509ef-f852-470a-a96b-181db344a8c5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22925/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:30:05,874] [INFO] Task succeeded: Blastn
[2023-03-15 14:30:05,897] [INFO] Selected 20 target genomes.
[2023-03-15 14:30:05,898] [INFO] Target genome list was writen to OceanDNA-b22925/target_genomes_gtdb.txt
[2023-03-15 14:30:05,930] [INFO] Task started: fastANI
[2023-03-15 14:30:05,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg02f966dd-aa98-46d9-b69a-7a1b464e9a28/OceanDNA-b22925.fa --refList OceanDNA-b22925/target_genomes_gtdb.txt --output OceanDNA-b22925/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:30:24,887] [INFO] Task succeeded: fastANI
[2023-03-15 14:30:24,887] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:30:24,887] [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 14:30:24,894] [INFO] GTDB search result was written to OceanDNA-b22925/result_gtdb.tsv
[2023-03-15 14:30:24,894] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:30:24,900] [INFO] DFAST_QC result json was written to OceanDNA-b22925/dqc_result.json
[2023-03-15 14:30:24,900] [INFO] DFAST_QC completed!
[2023-03-15 14:30:24,900] [INFO] Total running time: 0h1m19s